title: Brucella-infected Brain 5

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

data_processing:
OnestopRNASeq
FastQC and MultiQC were used for raw reads quality control and QoRTs for post-alignment quality control
Reads were aligned to the reference genome assembly mm10 with star_2.7.5a and annotated with gencode.vM25.
Aligned exon reads were counted toward gene expression with featureCounts_2.0.0 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited excel file include TPM  values for each Sample

source_name: whole brain

extract_protocol:
RNA was harvested using Trizol reagent and further purifed on an Rneasy column.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: whole brain

value: B. melitensis

tag: time

value: Day 54


title: Homeostasis CD45+ replicate 2

status: Public on Mar 17 2023

type: SRA

city: Denver

first: William

last: Janssen

state: CO

address: 1400 Jackson St

country: USA

institute: National Jewish Health

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped, tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Mice were euthanized and anti-CD45 antibody was instilled into the trachea. After 4 minutes, anti-CD45 solution was aspirated and bronchoalveolar lavage (BAL) was performed. Lungs were perfused by injecting 10 mL of PBS through the right ventricle during which lungs visibly blanched. Lung tissue was finely chopped with a razor blade and then incubated at 37C in 1 mL of 0.4 mg/mL Liberase TM for 25 min. Following incubation, tissue was pipetted rapidly up and down to further disaggregate, then filtered through 100 μm filters. Lung cells were pelleted and resuspended in then filter through 70 μm filters then resuspended HBSS containing 0.3% BSA and 0.3 mM EDTA. Cells were sorted using FACS into 3 bins: 1) CD45+ cells (live, CD45+), 2) resident IMs (live, CD45+, CD64+, CD88+, IT CD45-, tdT+), or 3) recruited IM (live, CD45+, CD64+, CD88+, IT CD45-, tdT-). Cells were manually counted using a hemocytometer and resuspended at 1x 10^6 cells/ml in 0.06% BSA in PBS solution.
Library was contructed according to manufacturer's instructions. Single cells were captured using a Chromium Box (10x Genomics, Pleasanton, CA, USA). Libraries were sequenced using the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA).  Sequencing was targeted to 5,000 cells in the CD45+ library, 3,000 cells in each of the IM sorts with sequencing depth of 100,000 reads per cell.

treatment_protocol:
Intraperitoneal Tampoxifen (0.25 mg/g) every 3 days for 1 week at age 10-12 weeks, 4 weeks prior to:
Intratracheal E. coli O111:B4 LPS (20 μg)

tag: strain

value: CX3CR1-ERT2 x R26-stopfl/fl-TdTomato (C57BL6/J background)

tag: tissue

value: lung

tag: Sex

value: male

tag: flow sorting

tag: days after_lps


title: ag49+52VT_E13.5_MS263_156

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: ag49+52 AG-VT+

library_source: transcriptomic

data_processing:
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.).
Read counts per genes were calculated using HTseq v0.11.0.
For allelic expression analysis, read data were re-mapped using masked MacFas5.0 reference, as described above.
Mapped BAM files were processed with SNPsplit and masked MacFas5.0 reference to split into paternal and maternal allele
Read counts per genes were calculated using HTseq for both BAM, separately.
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample

molecule: polyA RNA

organism: Macaca fascicularis

extract_protocol:
Total RNA extraction from 5000-20000 cells were carried out using Nucleospin RNA XS extraction kit (Takara, 740902).
cDNA synthesis was performed as described previously (Nakamura et al, 2015). Briefly, 0.2ng/µL of V1(dT)24 sequence was annealed to the 3’ end of the 1ng of total RNA by incubation at 70ºC for 90 seconds. Reverse transcription was performed by adding 133U/µL of SuperScript III (Invitrogen, 1089075) and serial incubation at 50ºC for 5 min and at 70ºC for 10 min. The residual primers were excised by treating with 0.5U/µL of Exonuclease I (Takara, 2650A) at 37ºC for 30 min followed by 80ºC for 25 min. Poly-A was added to the 3’ end of the cDNA by incubating at 37ºC 15 min and 70ºC for 10 min in the presence of 3mM dATPs (GE Healthcare, 28-4065-01) and 0.75U/µL terminal nucleotidyl transferase (TdT, Invitrogen, 10533-065). For cDNA amplification, the cDNA was applied to thermal cycling in the presence of 0.62 µM of V3(dT)24 and V1(dT)24, 0.05U/µL Ex Taq HS (Takara, RR006).

tag: cell line

tag: cell type

value: PGCLC

tag: tag

value: TFAP2C-EGFP, DDX4-tdTomato

tag: genotype

value: wildtype

tag: treatment

value: aggregate culture with mouse ovarian somatic cells at E13.5


title: Brucella-infected Brain 4

value: Day 40


title: Homeostasis recruited IM replicate 2

description: 10x Genomics

value: IMrec


title: run5_ESC_AgW_iX29

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description:
counts_run5.csv.gz
meta_run5.csv

data_processing:
We used the MARS-seq2.0 pipeline, the reads structure is as follow : R1 : 5I.4P.66M (ignore 5 first bases, followed by 4 nt of plate barcode and finally the 66 nt of the insert), R2 : 7W.8R.1I (7 nt of well barcodes, 8nt of UMIs and 1 nt ignore)
Genome_build: mm10
Supplementary_files_format_and_content: raw counts tables and metadata files (including FACS output)

growth_protocol: Serum+Lif (D1,D3,D8,D10). N2B27 + Lif (D18, ESC_N2B27Lif, Gastruloid_AgW, ESC_AgW, Gastruloid_F2, Gastruloid_F5, ELS_M7)

extract_protocol:
Cells were sorted into 384-well cell capture plates using a BD FACSAria III Cell Sorter (BD Biosciences) to collect live cells and sort only singlets. Plates were snap frozen on dry ice and stored at -80°C until further processing. All single cell libraries were prepared with the same conditions and reagents using the MARS-seq protocol as previously described (Jaitin et al, Science, 2014).
All single cell libraries were prepared with the same conditions and reagents using the MARS-seq protocol as previously described (Jaitin et al, Science, 2014). Briefly, a Bravo Automated Liquid Handling Platform (Agilent) was used to reverse transcribe (Invitrogen #18080085) mRNA into cDNA with an oligonucleotide containing both the unique molecule identifiers (UMIs) and cell barcodes. Unused oligonucleotides were removed by Exonuclease I (New England Biolabs #M0293S) treatment. cDNAs were pooled (each pool containing half of a 384-well plate) for second strand synthesis (New England Biolabs #E6111S) and in vitro transcription amplification (New England Biolabs #E2040S). DNA template was removed (Invitrogen #AM2238) before fragmenting (Invitrogen #AM8740) and ligating (New England Biolabs #M0204S) resulting RNA to an oligo containing the pool barcode and Illumina sequences. Finally, RNA was reverse transcribed (Agilent Technologies #600107) and libraries were amplified (Roche #7958935001). Libraries were quantified with a Qubit 2.0 (Invitrogen) and their size distribution was determined by a 4200 TapeStation System (Agilent Technologies). Finally, libraries were pooled at equimolar concentration and sequenced on an Illumina NextSeq500, in 8 sequencing runs, using high-output 75 cycles v2.5 kits (Illumina #20024906).
ScRNA-seq (MARS-seq)

treatment_protocol: We used ML-792, a highly selective inhibitor of the SUMO E1 enzyme, to decrease the global level of SUMOylation in mouse ESCs, with two rounds of 48 h treatments (2.5mM) between D1 and D3, D8 and D10

value: control

value: ES cell


title: run5_ESC_AgW_iX25

description:
counts_run5.csv.gz
meta_run5.csv


title: ag77AGVT_MS257_022

description: a77 AG+VT+

value: aggregate culture with mouse ovarian somatic cells at E12.5


title: Brucella-infected Brain 3


title: run5_ESC_AgW_iX26

description:
counts_run5.csv.gz
meta_run5.csv


title: ag49AGVT_1_MS257_021

description: ag49 AG+VT+


title: Brucella-infected Brain 1

value: Day 39


title: ag35AGVT_2_MS330_141

description: ag35 AG+VT+


title: Brucella-infected Brain 2


title: run5_empty_iX16

description:
counts_run5.csv.gz
meta_run5.csv


title: Mock-infected Brain 5

value: PBS


title: ag49+52VT_E15.5_MS257_024

description: ag49+52 AG-VT+

value: aggregate culture with mouse ovarian somatic cells at E15.5


title: ag49+52VT_E14.5_MS277_002

description: ag49+52 AG-VT+

value: aggregate culture with mouse ovarian somatic cells at E14.5


title: ag35AGVT_1_MS257_019

description: ag35 AG+VT+


title: Mock-infected Brain 4

value: whole brain

value: Day 54


title: run5_empty_iX02

description:
counts_run5.csv.gz
meta_run5.csv


title: Mock-infected Brain 3


title: Mock-infected Brain 2


title: ag35AG_2_MS330_140

description: ag35 AG+VT-


title: run4_D1_iX04

description:
counts_run4.csv.gz
meta_run4.csv


title: Mock-infected Brain 1


title: ag35AG_1_MS257_020

description: ag35 AG+VT-


title: ag21AG_2_MS263_154

description: ag21 AG+VT-


title: Colon adenocarcinoma, STING-N153S, 477_GEX

city: München

first: Jürgen

last: Ruland

address: Einsteinstraße 25

country: Germany

institute: Technical University of Munich

description: filtered_feature_bc_matrix_sample_477.h5ad

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Assembly: mm10
Supplementary files format and content: Anndata h5ad object

source_name: Colon adenocarcinoma

extract_protocol:
CD45+/CD45- cells were pooled 1:1
Sorted cells were washed with PBS + 2% FCS
Libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics, PN-1000269) and the 3’ Feature Barcode Kit (10X Genomics, PN-1000262)
All libraries from gene expression and feature barcoding were pooled and sequenced according to 10X Genomics’ recommendations on an Illumina NovaSeq6000 system with a target read depth of 50000 reads/cell gene expression libraries and 5000 reads/cell for feature barcoding libraries

value: Colon adenocarcinoma

tag: library type

value: mRNA

tag: antibodies/tags


title: Colon adenocarcinoma, STING-N153S, 477_CS

library_source: other

molecule: protein

value: ADT

value: TotalSeqB (see barcodes_citeseq.csv)


title: run4_ESC_N2B27Lif_iX27

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3, ID 328

city: San Francisco

first: Karl

middle: Mark

last: Ansel

state: CA

address: 500 Parnassus Ave

department: Microbiology

institute: University of California, San Francisco

data_processing:
Reads were aligned to the mouse genome GRCm38 and quantified using the STAR aligner software version 2.7.2b. Read normalization and differential expression analysis was performed in the R computing environment version 3.6.1 using the software DESeq2 version 1.26.
Genes that contained less than 100 Mean Normalized Counts were excluded from downstream analyses.
Assembly: GRCm38
Supplementary files format and content: Processed_Wheeler_Ansel.csv contains summary data where each row represents a RefSeq annotated gene in the mouse genome. A variety of summary data is provided in the columns for each gene including but not limited to: raw read counts for each sample, normalized read counts for each sample, expression comparsions between experimental groups as fold change and FDR values, categorical assignments to gene lists, and descriptve infomation for the gene.

source_name: Spleen

growth_protocol: CD8+ T cells were isolated from spleens using negative selection from the EasySep Mouse CD8+ T Cell Isolation Kit (cat# 19853). Cells were counted using trypan blue staining and the nexelcom cellometer spectrum. Cells were plated in Kool AID complete media (DMEM high glucose media supplemented with 10% FCS, pyruvate, nonessential amino acids, MEM vitamins, L-arginine, L-asparagine, L-glutamine, folic acid, beta mercaptoethanol, penicillin, and streptomycin) and spun at 450 r.c.f. for 5 minutes at 25°C to begin stimulation. Cells were harvested 24 hours after stimulation for mRNA-seq.

extract_protocol:
1*10^6 CD8+ T cells were harvested 24 hours after αCD3 ± αCD28 stimulation as described above. Cells were pelleted at 450 r.c.f. for 5 minutes at 4°C. Cell pellet was resuspended in 700 uL Trizol reagent (ambion ref #15596018) and kept at -80°C. RNA was was isolated using using the Direct-zol-96 RNA Kit (zymogen Cat #R2054).
The integrity of total RNA was checked on Fragment Analyzer (Agilent, Cat. No. DNF-472), only RNA with RQN number of above 7 was used for library construction. The starting quantity of 100ng of total RNA was used according to vendor instructions with Universal plus mRNA with Nu Quant (TECAN, Cat. No. 0520), final library PCR amplification was 17 cycles. After library completion, individual libraries were pooled equally by volume, and quantified on Fragment Analyzer (Agilent, Cat. No. DNF-474). Quantified library pool was diluted to 1nM and further diluted as per protocol and sequenced on Illumina MiniSeq (Illumina, Cat. No. FC-420-1001) to check for quality of reads. Finally, individual libraries were normalized according to MiniSeq output reads, specifically by % protein coding genes and were sequenced on one lane of NovaSeq6000 S4 PE100 (Illumina, Cat. No. 20028313).

treatment_protocol: Cultures were started via stimulation with plate bound αCD3 (1 μg/mL, clone 2C11) alone or incombination with αCD28 (1 μg/mL, clone 37.51); plates coated overnight in PBS with Ca++ & Mg++ at 4°C.

value: Spleen

value: CD8+ T cells

value: WT


title: ag21AG_1_MS263_153

description: ag21 AG+VT-

value: PGCLC

value: TFAP2C-EGFP, DDX4-tdTomato

value: wildtype


title: run4_D1_iX01

description:
counts_run4.csv.gz
meta_run4.csv

value: control

value: ES cell


title: CD8 T cells, WT, anti-CD3, ID 325


title: Colon adenocarcinoma, WT, 476_CS

description: filtered_feature_bc_matrix_sample_476.h5ad


title: run4_ESC_N2B27Lif_iX26

description:
counts_run4.csv.gz
meta_run4.csv


title: run4_ESC_N2B27Lif_iX28

description:
counts_run4.csv.gz
meta_run4.csv


title: ag7AG_1_MS263_151

description: ag7 AG+VT-

value: aggregate culture with mouse ovarian somatic cells at E12.5


title: CD8 T cells, WT, anti-CD3, ID 329


title: Colon adenocarcinoma, WT, 476_GEX


title: d8_2_MS257_018

description: PGCLC day 8


title: ag7AG_2_MS263_152

description: ag7 AG+VT-

value: aggregate culture with mouse ovarian somatic cells at E15.5


title: CD8 T cells, WT, anti-CD3, ID 57


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 329

value: Anti-CD3 and anti-CD28


title: run4_ESC_N2B27Lif_iX25

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3, ID 53


title: run4_empty_iX32

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3, ID 55


title: d8_1_MS257_017

description: PGCLC day 8


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 57


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 325


title: run4_empty_iX31

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 55


title: run4_empty_iX03

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 53


title: CD8 T cells, Malat1-scr, anti-CD3, ID 333


title: cyESC_2_MS330_139

description: Cynomolgus ES cells


title: cyESC_1_MS257_015

description: Cynomolgus ES cells


title: run4_empty_iX02

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, Malat1-scr, anti-CD3, ID 331


title: CEF_2_MS330_144

source_name: Embryonic fibroblasts

value: Embryonic fibroblasts


title: CEF_1_MS330_143


title: CD8 T cells, Malat1-scr, anti-CD3, ID 324


title: CD8 T cells, Malat1-scr, anti-CD3, ID 330


title: CD8 T cells, Malat1-scr, anti-CD3, ID 322


title: run4_D8_iX12

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, Malat1-scr, anti-CD3, ID 323


title: run4_D8_iX11

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, WT, anti-CD3 and anti-CD28, ID 328


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 332


title: run4_D8_iX09

description:
counts_run4.csv.gz
meta_run4.csv


title: run4_D8_iX10

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 331


title: AGVT7_d8_MS235_007

data_processing:
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.)
Expression levels as RPKM (Reads per kilobase of exon per million reads mapped) were calculated using cufflinks v2.2.1.
Assembly: macFas5.0
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

extract_protocol:
Total RNA was extracted by using RNeasy Mini Kit (QIAGEN, 74104) according to manufacturer’s instructions.
library was prepared by using NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765).


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 333


title: CD8 T cells, Malat1-scr, anti-CD3, ID 332


title: AGVT7_ESC_MS235_006

value: ESC


title: Homeostasis recruited IM replicate 1

description: 10x Genomics

value: CX3CR1-ERT2 x R26-stopfl/fl-TdTomato (C57BL6/J background)

value: lung

value: male

value: IMrec


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 330

value: Spleen


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 324

value: CD8+ T cells


title: run4_D3_iX08

description:
counts_run4.csv.gz
meta_run4.csv


title: 22XRi_ESC_MS235_005


title: run4_D3_iX06

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 320


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 316


title: 656-BTAG_ESC_MS260_001

value: Blimp1-tdTomato, TFAP2C-EGFP


title: run4_D3_iX05

description:
counts_run4.csv.gz
meta_run4.csv


title: 18XRi_ESC_MS235_003


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 309


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 305


title: 15XRi_ESC_MS235_002


title: run4_D18_iX24

description:
counts_run4.csv.gz
meta_run4.csv


title: 3XRi_ESC_MS235_001


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 320


title: run4_D18_iX23

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 323


title: run4_D3_iX07

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 315


title: CD8 T cells, Malat1-scr, anti-CD3 and anti-CD28, ID 322


title: run4_D18_iX22

description:
counts_run4.csv.gz
meta_run4.csv


title: CEF_1

library_source: genomic

data_processing:
All reads were processed with Trim_galore v0.6.3 with default setting to remove adapter and low-quality sequences.
Processed reads were mapped on cynomolgus macFas5.0 or human GRCh38.p12 genome, using Bismark v0.22.1 and bowtie2 v2.3.4.1 with "-X 2000" option. Resulting BAM files were, then, processed with deduplicate_bismark to remove PCR duplicate, and methylation levels per CpG were calculated using bismark_methylation_extractor script, included in Biskmark package.
For allelic methylation analysis, EM-seq data were re-mapped on SNP masked macFas5.0 or GRCh38.p12 genome as described above.
BAM files after PCR duplicate removal were processed with SNPsplit v0.3.2 with "--paired" and "--bisulfite" options and masked macFas5.0 or GRCh38.p12 reference to split mapped reads into paternal and maternal alleles.
Resulting BAM files were processed with bismark_methylation_extractor script with "-p" and "--comprehensive" options
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: biskark report text

molecule: genomic DNA

extract_protocol:
Genomic DNAs were purified from 10,000 - 20,000 cells by using Nucleospin Tissue XS (Macherey-Nagel, 740901) and eluted in 10µL Elution buffer. DNA concentration was quantitated by using Qubit dsDNA HS assay kit (ThermoFisher Scientific) and 20-140 ng of gDNA were mixed with 1pg of pUP19 DNA and 20pg of unmethylated lambda DNA in 50µL total volume.
Genomic DNAs were fragmented by sonication using Covaris focused-sonicator E220 (peak incident power 140W, Duty factor 10%, Cycles per burst 200 and Treatment time 130 msec). The fragmented DNA samples were purified by two-rounds of Axygen beads purification (0.7×, then 0.9× volumes). Then, all fragments were applied to library construction using NEBNext Enzymatic Methy-seq Kit (New England Biolabs, E7120) according to manufacturer’s instructions. Library concentration and fragment size were evaluated with KAPA Library quantification kits (Nippon Genetics, KK4828) and Labchip GX Touch HT (Perkin Elmer).
Enzymatic Methyl-seq (EMseq)


title: run4_D18_iX21

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 309


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 302


title: 19XRi_ESC_MS235_004


title: CEF_2


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 302


title: Oogonia_2

source_name: Oogonia from 8 wpf embryonic ovary

value: Oogonia from 8 wpf embryonic ovary


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 312

value: miR-15/16 delta/delta


title: CD8 T cells, miR-15/16 FL, anti-CD3, ID 315


title: run4_D10_iX16

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 310


title: Oogonia_1

value: wildtype


title: run4_D10_iX15

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 307


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 306


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 304


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 316


title: CD8 T cells, miR-15/16 KO, anti-CD3, ID 303


title: ag49AGVT

description: ag49 AG+VT+

value: Oogonia

value: TFAP2C-EGFP, DDX4-tdTomato


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 312


title: CD8 T cells, miR-15/16 FL, anti-CD3 and anti-CD28, ID 305


title: run3_D1_iX03

description:
counts_run3.csv.gz
meta_run3.csv

value: control

value: ES cell


title: run4_D10_iX13

description:
counts_run4.csv.gz
meta_run4.csv


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 307

value: Anti-CD3 and anti-CD28


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 310


title: run3_D1_iX02

description:
counts_run3.csv.gz
meta_run3.csv


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 304


title: ag21AG

description: ag21 AG+VT-

value: PGCLC

value: aggregate culture with mouse ovarian somatic cells at E12.5


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 306


title: ag35AG

description: ag35 AG+VT-


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, LPS injection

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

description: 10x Genomics 3' scRNA-Seq

data_processing:
Demultiplexing, barcode processing (cell calling) and gene counting were carried out using the Cell Ranger pipeline (version 3.0.2; 10x Genomics) and the 10x Genomics mm10 reference transcriptome package (version 3.0.0).
Assembly: mm10
Supplementary files format and content: Tab-separated files and matrix files from the filtered_feature_bc_matrix folder of Cell Ranger count pipeline output

source_name: aorta

extract_protocol:
Mice were sacrificed and perfused by cardiac puncture with 10 ml of ice-cold PBS supplemented with 20 U/ml heparin and placed on ice for dissection. The entire thoracic aorta (i.e., the ascending aorta, the aortic arch and the descending aorta up to the diaphragm) was extracted and used in scRNA-Seq sample preparation. The adventitia was mechanically removed under a dissection microscope and discarded. Each thoracic aorta minced with a scalpel and enzymatically dissociated into single-cell suspension in 0.8 ml of Multi Tissue Dissociation Kit 1 (Miltenyi Biotec #130-110-201) enzymatic mixture reconstituted in RPMI 1640 medium supplemented with 0.5% bovine serum albumin (BSA) and 20 mM HEPES buffer, pH = 7.2. The mixture was incubated at 37 °C with end-over-end rotation. After 20, 40 and 60 minutes of incubation time, tissue pieces were left to settle for 10 seconds and 0.8 ml of cell suspension supernatant was collected from the tube and placed on ice. To continue the digestion, 0.8 ml of fresh enzymatic digestion mixture was added. The collected cell suspension was filtered through a 30 μm cell strainer, centrifuged at 400 g for 8 min at 4 °C, resuspended in PBS supplemented with 1% BSA and placed on ice. The three cell suspension fractions for each aorta were subsequently pooled together and red blood cell lysis was carried out by adding 9 volumes of ice-cold 1X RBC Lysis Buffer, Multi-species (eBioscience #00-4300-54) and incubating on ice for 3 min. Subsequently, PBS was added to normalize the buffer and the cells were collected by centrifugation (400 g for 8 min at 4 °C). Magnetic removal of dead cells was carried out using the Dead Cell Removal Kit (Miltenyi Biotec #130-090-101) with Miltenyi MS magnetic columns following the manufacturer’s instructions. Cells were resuspended in PBS containing 0.04% BSA and counted by hemocytometry with Trypan Blue staining. In each experiment group, aortic cell isolation was carried out separately from 3 male mice and subsequently the cells were pooled in equal proportions into one lane of the Chromium Controller microfluidics chip (10x Genomics).
The Chromium Single Cell 3’ Kit (v2 Chemistry; 10x Genomics) was used to prepare scRNA-Seq libraries.

value: aorta

tag: diet

value: 1 month high-fat diet

value: LPS injection (100ng, one time, intraperitoneal, 2 weeks before sacrifice)


title: ag7AG

description: ag7 AG+VT-


title: ag35AGVT

description: ag35 AG+VT+


title: run3_D1_iX01

description:
counts_run3.csv.gz
meta_run3.csv


title: CD8 T cells, miR-15/16 KO, anti-CD3 and anti-CD28, ID 303


title: run4_D10_iX14

description:
counts_run4.csv.gz
meta_run4.csv


title: aorta, LDLR-/- ApoB100/100, chow diet

description: 10x Genomics 3' scRNA-Seq

value: chow

value: male


title: ag49AGVT_2_MS263_155

description: ag49 AG+VT+


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet

description: 10x Genomics 3' scRNA-Seq


title: run3_ESC_N2B27Lif_iX28

description:
counts_run3.csv.gz
meta_run3.csv


title: run3_ESC_N2B27Lif_iX27

description:
counts_run3.csv.gz
meta_run3.csv


title: ag49+52VT

description: ag49+52 AG-VT+

value: Early oocyte

value: aggregate culture with mouse ovarian somatic cells at E15.5


title: MM, 1821, PBIC, PC

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Read count extraction was performed using Salmon v1.5.2 with Gencode vM29 gene models
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw abundance values for each Sample

source_name: Multiple myeloma plasma cells

extract_protocol:
RNA was harvested from samples maintained in TRIzol (Invitrogen )
RNA libraries for RNA-seq were prepared using TruSeq mRNA Library Prep Kit following manufacturer's protocols.

value: Multiple myeloma plasma cells

tag: disease model


title: cyESC

description: Cynomolgus ES cells


title: run3_ESC_N2B27Lif_iX26

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6719, MMSetBIC, PC


title: ag49+52VT (E15.5)_MS245_B08

data_processing:
Read data were processed with 'cellranger mkfastq' and 'cellranger count' with default setting and transcript reference, macFass5 Annotation Release 101.
Assembly: macFas5.0
Supplementary files format and content: tab-delimited text files include FPKM for each Sample
Supplementary files format and content: Cell Ranger output, h5 files

extract_protocol: Single-cell library was prepared using the 10X Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics) according to the manufacturer’s instructions. Briefly, xrOvary at ag49+52 was trypsinized and applied to flow cytometry (BD, FACS Aria III). CyESC-derived germ cells were collected as FSC-W high/DRAQ7-negative/AG and/or VT-positive cells, on the other hand, mouse gonadal somatic cells were obtained as FSC-W low/DRAQ7-negative/AG-VT- population. Cy germ cells and mouse cells were mixed and the cell concentration was adjusted to 1000 cells/µL and applied to Chromium 10X Single Cell System (10X Genomics) to generate the Gel-Bead in Emulsions (GEMs). cDNA libraries were prepared using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) following the manufacturer’s instructions.

value: Early oogonia


title: run3_ESC_N2B27Lif_iX25

description:
counts_run3.csv.gz
meta_run3.csv


title: aorta, LDLR-/- ApoB100/100, 3 months high-fat diet

description: 10x Genomics 3' scRNA-Seq

value: 3 months high-fat diet


title: MM, 6556, MMSetBIC, PC


title: ag49+52VT (E14.5)_MS245_B11

value: wildtype

value: aggregate culture with mouse ovarian somatic cells at E14.5


title: run3_empty_iX06

description:
counts_run3.csv.gz
meta_run3.csv

value: control


title: MM, 6844, CyD1BIC, PC


title: ag49+52VT (E13.5)_MS245_B10

value: TFAP2C-EGFP, DDX4-tdTomato

value: aggregate culture with mouse ovarian somatic cells at E13.5


title: MM, 6553, MMSetBIC, PC


title: d8

description: day 8 PGCLC

value: PGCLC


title: MM, 5278, CyD1BIC, PC


title: aorta, wild type, chow diet

description: 10x Genomics 3' scRNA-Seq

value: wild type


title: MM, 6575, CyD1BIC, PC


title: run3_empty_iX04

description:
counts_run3.csv.gz
meta_run3.csv

value: ES cell


title: MM, 6392, PBIC, PC


title: run3_D8_iX12

description:
counts_run3.csv.gz
meta_run3.csv


title: run3_D8_iX10

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 1978, PBIC, PC


title: MM, 6916, KBIC, PC


title: MM, 6128, PBIC, PC


title: MM, 1697, BIC, PC


title: run3_D8_iX11

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6723, MMSetBIC, PC


title: MM, 6921, BIC, PC


title: MM, 6577, CyD1BIC, PC


title: sample_154

type: RNA

city: Minneapolis

first: Andrew

middle: C

last: Nelson

state: Minnesota

address: 420 Delaware St SE

institute: University of Minnesota

hyb_protocol: Prepared RNA was hybridized to the nCounter custom CodeSet per manufacturer's instructions (MAN-10056, Nanostring) and loaded onto the nCounter prep station for purification and immobilization in a sample cartridge (MAN-C0035)

scan_protocol: Sample scanning was performed on the nCounter MAX/FLEX digital analyzer for scanning at high resolution per manufacturer's protocol (MAN-C0035)

data_processing: RCC files were processed using Nanostring nSolver software for both positive control and codeset content normalization (using ACTB, MRPL19, PSMC4, PUM1, and SF3A1) using default geometric mean parameters (MAN-C0019). Raw gene expression counts were analyzed within R (ver 3.6.1, R Core Team, 2019) using the NanoStringQCPro package (ver 1.18.0). Flagged outliers (26 cases out of 120 cases) were removed for downstream analysis. After normalization, each gene was median-centered and scaled (root mean square) based on expression levels across all 94 high-quality samples.

label: NanoString nCounter  CodeSet

organism: Homo sapiens

source_name: Patient tumor tissue

label_protocol: RNA was quantified fluorometrically and normalized to 25 ng/uL for a total input of 100 ng in RNase free water for hybridization with Nanostring codeset (see next). RNA amplification was not performed.

extract_protocol: 10 unstained 10-micron thick FFPE sections were used for extraction. Tumor areas were macroenriched based on annotation of a serial H&E stained slide to achieve a minimum of 30% tumor cellularity if necessary. Extraction was performed with the Qiagen  RNeasy FFPE Kit per manufacturer's instructions.

tag: procedure

value: mast

tag: er

value: pos

tag: pr

tag: dcis

value: int

value: neg

tag: Stage

value: LumA


title: sample_152

value: lump

value: high

value: LumB


title: sample_149

value: Basal


title: MM, 1389, BIC, PC

value: Multiple myeloma plasma cells


title: MM, 1278, BIC, PC


title: run3_D8_iX09

description:
counts_run3.csv.gz
meta_run3.csv


title: run3_D3_iX08

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, MIC112, PC


title: MM, MIC124, PC


title: sample_142


title: sample_143


title: MGUS, MIC122, PC


title: run3_D3_iX07

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6577, CyD1BIC, BM

source_name: Bone marrow bulk

value: Bone marrow


title: sample_140

value: CNB


title: run3_D3_iX05

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6726, MMSetBIC, BM


title: sample_139


title: MM, 1162, PBIC, BM


title: MM, 6723, MMSetBIC, BM


title: MM, 6553, MMSetBIC, BM


title: run3_D18_iX24

description:
counts_run3.csv.gz
meta_run3.csv

value: control


title: sample_138


title: run3_D18_iX23

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6556, MMSetBIC, BM


title: MM, 5983, MMSetBIC, BM


title: MM, 6719, MMSetBIC, BM


title: sample_137

value: low


title: run3_D18_iX22

description:
counts_run3.csv.gz
meta_run3.csv


title: run3_D18_iX21

description:
counts_run3.csv.gz
meta_run3.csv


title: MM, 6844, CyD1BIC, BM


title: sample_136


title: MUT_K14J29

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Mus musculus GRCm38.p3
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Ensembl Mus musculus GRCm38.p3
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and raw count number

source_name: Lower molars - left and right, from K14:cre; Jagged1 fl/fl embryos, E18.5

extract_protocol:
Cells were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: genotype/variation

value: Mutant

tag: tissue

value: Lower molars - left and right


title: MM, 5278, CyD1BIC, BM


title: sample_133


title: sample_135

value: Normal


title: MM, 6575, CyD1BIC, BM


title: MUT_K14J28


title: MUT_K14J26


title: run3_D10_iX16

description:
counts_run3.csv.gz
meta_run3.csv

tag: cell line

value: ES cell


title: sample_132

value: mast

value: pos


title: MM, 6392, PBIC, BM

tag: cell type


title: run3_D10_iX14

description:
counts_run3.csv.gz
meta_run3.csv


title: CTRL_J7

source_name: Lower molars - left and right, from Jagged1 fl/fl embryos, E18.5

value: Control


title: MM, 6128, PBIC, BM


title: sample_130

value: neg


title: run3_D10_iX13

description:
counts_run3.csv.gz
meta_run3.csv


title: sample_128


title: MUT_K14J30


title: run2_empty_iX31

description:
counts_run2.csv.gz
meta_run2.csv


title: CTRL_J5


title: run2_empty_iX32

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_127

value: lump


title: CTRL_J3


title: MM, 1821, PBIC, BM


title: MM, 1826, PBIC, BM


title: CCR6high_day7-P_D2_AB3074

type: genomic

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 B1 using standard Illumina protocol

scan_protocol: Illumina HiSeq using standard protoocol

data_processing:
Genome Studio 2011.1
Average Beta (normalized using Genome Studio 2011.1)

label: biotin

source_name: Healthy Donor PBMC

label_protocol: Bisulfite conversion of genomic DNA (500 ng) was performed using the Zymo Research EZ DNA Methylation kit (Zymo Research) according to the manufacturer’s recommendations for the Illumina Infinium assay. The bisulfite conversion incubation was processed using alternative thermocycler settings as outlined in the “Alternative Incubation Conditions When Using the Illumina Infinium® Methylation” section of the Zymo instruction manual appendix.

growth_protocol: CD4+ T cells were isolated from elutriated lymphocytes by negative selection using RosetteSep CD4+ T cell enrichment cocktail (StemCell Technologies) followed by Ficoll/Hypaque (Amersham Biosciences) density centrifugation according to the protocol from StemCell Technologies. If necessary, red blood cells were removed using Pharm Lyse (BD Biosciences) according to the manufacturer’s protocol. For staining cells were suspended in 250 μl of Hanks Balanced Salt Solution (HBSS, Mediatech) containing 4% fetal bovine serum (FBS, GeminiBio) and incubated with following antibodies: anti-CD4, anti-CD45RO, and anti-CCR6 for 30 min at room temperature. In some experiments, in addition to these antibodies, cells were incubated with anti-CD25 and anti-CD62L, anti-CXCR5, anti-CXCR3 and anti-CCR4 antibodies. All antibodies were against human antigens. Cells were washed and resuspended in HBSS plus 4% FBS. CD4+ T cells were sorted into CD45RO- (naïve), and CD45RO+ subsets, and the CD45RO+ subset was further separated into CCR6neg, CCR6pos, and, within the CCR6pos cells, into CCR6low, CCR6int and CCR6high subsets. For in vitro polarization experiments, cells were sorted into naïve (CD4+CD45RO-CD25-CXCR5-CCR4-CXCR3-), CCR6neg (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6- or CD4+CD45RO+CD25-CXCR5- CCR4-CCR6- or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6-), CCR6low (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6low or CD4+CD45RO+CD25-CXCR5-CCR4-CCR6low or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6low), and CCR6high (CD4+CD45RO+CD25-CXCR5-CXCR3-CCR6high or CD4+CD45RO+CD25-CXCR5-CCR4-CCR6high or CD4+CD45RO+CD25-CXCR5-CXCR3-CCR4-CCR6high). All cell sorting was done using a FACSAria Cell Sorter (BD Biosciences).  By post-sort analysis, the purity of populations was 95-99%. Cells were used for experiments immediately after sorting.

extract_protocol: DNeasy kit (Qiagen).

treatment_protocol: In some experiments, after purification by cell sorting, a portion of cells were used as starting cells (day 0) and the remaining cells were labeled with CFSE, activated with soluble anti-CD3 (100 ng/ml, eBiosciences) and cultured with the homeostatic cytokines IL-7 and IL-15 (10 ng/ml each, R and D Systems ), for 7 days. Cells from the different subgroups were again sorted, based on CFSE dilution, into non-proliferated and proliferated cells

tag: disease state

value: Healthy

value: PBMC

tag: biosample

tag: donor

tag: cell culture

tag: t-cell subset


title: run3_D10_iX15

description:
counts_run3.csv.gz
meta_run3.csv

tag: treatment


title: sample_125

value: high


title: run2_empty_iX29

description:
counts_run2.csv.gz
meta_run2.csv


title: run2_empty_iX30

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_124

value: int

value: LumA


title: MM, 6918, KBIC, BM

value: Bone marrow

tag: disease model


title: sample_122

tag: procedure


title: MM, 6921, BIC, BM


title: sample_123

tag: er

value: LumB


title: MM, 1697, BIC, BM


title: CTRL_J6


title: sample_121

tag: pr

value: Basal


title: MM, 1978, PBIC, BM


title: MM, 1686, BIC, BM


title: CCR6neg_day7-P_D2_AB3071


title: CCR6low_day7-P_D2_AB3072


title: Naive_day7-P_D2_AB3070

value: Naive


title: MM, 1389, BIC, BM


title: sample_120

tag: dcis


title: sample_119

tag: Stage


title: CCR6int_day7-P_D2_AB3073


title: run2_D8_iX12

description:
counts_run2.csv.gz
meta_run2.csv

value: control


title: MM, 1278, BIC, BM


title: run2_empty_iX28

description:
counts_run2.csv.gz
meta_run2.csv


title: Naive_day0_D2_AB3060


title: MM, MIC124, BM


title: CCR6high_day7-P_D1_AB3059


title: run2_empty_iX05

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_117


title: CCR6int_day7-P_D1_AB3058


title: run2_D8_iX10

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_118


title: run2_empty_iX26

description:
counts_run2.csv.gz
meta_run2.csv


title: run2_D8_iX11

description:
counts_run2.csv.gz
meta_run2.csv


title: run2_empty_iX27

description:
counts_run2.csv.gz
meta_run2.csv


title: CCR6low_day7-P_D1_AB3057


title: run2_D8_iX09

description:
counts_run2.csv.gz
meta_run2.csv


title: MM, MIC114, BM


title: sample_115


title: sample_116

value: Normal


title: MM, MIC120, BM


title: run2_D3_iX08

description:
counts_run2.csv.gz
meta_run2.csv

value: ES cell


title: CCR6high_day7-NP_D2_AB3069


title: CCR6neg_day7-P_D1_AB3056


title: sample_114


title: MM, MIC113, BM


title: MM, 1315, BIC, BM


title: run2_D3_iX07

description:
counts_run2.csv.gz
meta_run2.csv


title: run2_D3_iX06

description:
counts_run2.csv.gz
meta_run2.csv


title: CCR6high_day7-NP_D1_AB3092


title: sample_111


title: MM, MIC112, BM


title: sample_113


title: CCR6int_day7-NP_D1_AB3053


title: run2_D1_iX04

description:
counts_run2.csv.gz
meta_run2.csv


title: MGUS, 1950, KBIC, BM


title: MGUS, 6907, KBIC, BM


title: sample_110

value: mast


title: run2_D1_iX03

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_109

value: pos


title: MGUS, 1830, BIC, BM


title: sample_106


title: MGUS, 1949, KBIC, BM


title: CCR6low_day7-NP_D1_AB3052


title: run2_D1_iX02

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_105

value: low


title: CCR6neg_day7-NP_D1_AB3051


title: run2_D1_iX01

description:
counts_run2.csv.gz
meta_run2.csv


title: Naive_day7-NP_D1_AB3050


title: run2_D18_iX19

description:
counts_run2.csv.gz
meta_run2.csv


title: MGUS, MIC126, BM


title: run2_D18_iX18

description:
counts_run2.csv.gz
meta_run2.csv


title: CCR6high_day0_D1_AB3049


title: CCR6low_day0_D1_AB3047


title: Naive_day7-P_D1_AB3093


title: MGUS, MIC122, BM


title: sample_102

value: neg


title: CCR6neg_day0_D1_AB3046


title: YC92, CONTROL, BM

value: Control


title: CCR6int_day0_D1_AB3048

value: Healthy


title: run2_D18_iX17

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_99

value: CNB


title: Naive_day0_D1_AB3045

value: PBMC


title: YFP61, CONTROL, BM


title: Heart_CharmeKO2_PN [PN_KO_2_S5]

city: Rome

first: Monica

last: Ballarino

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
counts.tsv
fpkm_table.tsv

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using a combination of Trimmatic and Cutadapt softwares (see methods for further details).
Trimmed sequence reads were mapped to mm10 using  STAR aligner (parameters: --outSAMstrandField intronMotif --outSAMattrIHstart 0  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --peOverlapNbasesMin 35)
Gene counts were obtained with STAR software (parameter: --quantMode GeneCounts) using  Ensembl gene annotation (release 87)
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: Heart

extract_protocol:
RNA was harvested using Direct-zolTM RNA MiniPrep (Zymo Research). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep following manufacturer's protocols.

tag: strain

value: Heart

tag: genotype

value: KO

tag: developmental stage


title: sample_97

value: lump

value: high


title: run2_D18_iX20

description:
counts_run2.csv.gz
meta_run2.csv

tag: cell line


title: Heart_CharmeWT3_PN [PN_WT_3_S3]

description:
counts.tsv
fpkm_table.tsv

tag: tissue

value: WT


title: sample_95

value: LumB


title: YC90, CONTROL, BM

tag: cell type

value: Bone marrow


title: CCR6int_day7-NP_D2_AB3068

tag: disease state

tag: biosample


title: run2_D10_iX16

description:
counts_run2.csv.gz
meta_run2.csv


title: run2_D10_iX15

description:
counts_run2.csv.gz
meta_run2.csv


title: sample_96


title: sample_94

value: int

value: LumA


title: sample_92


title: run1_empty_iX32

description:
counts_run1.csv.gz
meta_run1.csv

value: control

value: ES cell


title: sample_91

value: pos


title: sample_88

value: neg


title: sample_93

value: mast


title: CCR6neg_day7-NP_D2_AB3066

value: Healthy

tag: donor

tag: cell culture


title: CCR6low_day7-NP_D2_AB3067

tag: t-cell subset


title: Naive_day7-NP_D2_AB3065

value: Naive


title: CCR6int_day0_D2_AB3063

value: PBMC


title: run2_D10_iX13

description:
counts_run2.csv.gz
meta_run2.csv

tag: treatment


title: run2_D10_iX14

description:
counts_run2.csv.gz
meta_run2.csv


title: Heart_CharmeWT2_PN [PN_WT_2_S2]

description:
counts.tsv
fpkm_table.tsv

value: Heart


title: Heart_CharmeWT1_PN [PN_WT_1_S1]

description:
counts.tsv
fpkm_table.tsv


title: run1_empty_iX31

description:
counts_run1.csv.gz
meta_run1.csv


title: CCR6high_day0_D2_AB3064


title: CCR6low_day0_D2_AB3062


title: E15_Heart_MATR3_IgG

data_processing:
Reads were trimmed for adaptor sequence/low-quality sequence using a combination of Trimmatic and Cutadapt software (see methods for further details).
Trimmed reads were mapped to mm10 using STAR aligner (2.7.7a)
PCR duplicates were removed using MarkDuplicates tool included in the Picard suite version 2.24.1
Peaks were called using Piranha version 1.2.1 with parameters –x -s –u 0. See Methods for a complete description of peaks processing steps.
bigWig files were generated using the bamCoverage function from deepTools. Score represents the normalized reads coverage at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, bed

extract_protocol: CLIP-seq libraries were prepared accordiing to Trio RNA-Seq protocol (Tecan Genomics, Redwood City, CA)

treatment_protocol: Embryonic hearts were pestled 2 min in PBST. The homogenate was then filtered in 70 μm strainer to purify the cardiac cells. Cells were UV-crosslinked at 4,000 mJ

tag: clip antibody

value: Rabbit IgG (Immunoreagents Inc. Rb-003-N)


title: sample_87

tag: procedure

value: lump

tag: er


title: Heart_CharmeKO1_PN [PN_KO_1_S4]

description:
counts.tsv
fpkm_table.tsv

value: KO


title: run1_empty_iX30

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_80

tag: pr

tag: dcis


title: run1_empty_iX29

description:
counts_run1.csv.gz
meta_run1.csv


title: run1_empty_iX27

description:
counts_run1.csv.gz
meta_run1.csv


title: E15_Heart_MATR3_WT1

tag: strain

value: MATR3 (Bethyl cat#A300-591A)


title: sample_81

tag: Stage


title: E15_Heart_MATR3_WT2


title: sample_85

value: low


title: run1_empty_iX25

description:
counts_run1.csv.gz
meta_run1.csv


title: run1_empty_iX28

description:
counts_run1.csv.gz
meta_run1.csv


title: CCR6neg_day0_D2_AB3061


title: run1_D8_iX11

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_74


title: E15_Heart_INP


title: sample_79


title: RUBELLA-IFB-IFL-2 SID14611_fpkm

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

data_processing:
After mapping of sequencing reads, RNA expression data was analyzed as FPKM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample and fold changes

source_name: HUVEC

extract_protocol:
RNA was isolated using the miRNeasy mini kit (#217004, Qiagen) or the ReliaPrep RNA cell miniprep system (#Z6010, Promega).
Illumina stranded Total RNA Prep Kit

value: HUVEC

value: endothelial cells

tag: genotype

value: WT

value: IFN-β (300-02BC, Peprotech) and IFN-λ1 (1598-IL-025, RD Systems) on UV inactivated Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)

tag: time

value: 24 hours past infection


title: RUBELLA-IFB-IFL-4 SID14621_fpkm

tag: cell line


title: RUBELLA-IFB-IFL-1 SID14606_fpkm

tag: cell type


title: run1_empty_iX26

description:
counts_run1.csv.gz
meta_run1.csv

value: control

value: ES cell


title: RUBELLA-IFL-3 SID14615_fpkm

value: IFN-λ1 (1598-IL-025, RD Systems) on UV inactivated Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)


title: RUBELLA-IFB-IFL-3 SID14616_fpkm


title: run1_D8_iX10

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_77

value: CNB

value: pos

value: high

value: LumB


title: run1_D8_iX09

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_76

value: mast

value: neg

value: int


title: RUBELLA-IFL-2 SID14610_fpkm


title: run1_D8_iX12

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_72

value: Basal


title: sample_70


title: run1_D3_iX08

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_68


title: RUBELLA-IFL-1 SID14605_fpkm


title: run1_D3_iX07

description:
counts_run1.csv.gz
meta_run1.csv


title: RUBELLA-IFB-4 SID14619_fpkm

value: IFN-β (300-02BC, Peprotech) on UV inactivated Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)


title: sample_67

value: lump

value: LumA


title: run1_D3_iX06

description:
counts_run1.csv.gz
meta_run1.csv


title: RUBELLA-IFB-3 SID14614_fpkm

value: HUVEC

value: endothelial cells

value: WT


title: sample_66


title: RUBELLA-IFL-4 SID14620_fpkm

value: 24 hours past infection


title: run1_D3_iX05

description:
counts_run1.csv.gz
meta_run1.csv

value: ES cell


title: run1_D1_iX04

description:
counts_run1.csv.gz
meta_run1.csv

value: control


title: sample_64


title: RUBELLA-UV-3 SID14612_fpkm

value: UV inactivated Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)


title: RUBELLA-UV-4 SID14617_fpkm


title: run1_D1_iX02

description:
counts_run1.csv.gz
meta_run1.csv


title: RUBELLA-IFB-1 SID14604_fpkm


title: RUBELLA-IFB-2 SID14609_fpkm


title: sample_63

value: pos


title: run1_D1_iX01

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_65


title: sample_60


title: sample_61


title: run1_D18_iX20

description:
counts_run1.csv.gz
meta_run1.csv


title: RUBELLA-UV-1 SID14602_fpkm


title: run1_D18_iX19

description:
counts_run1.csv.gz
meta_run1.csv


title: RUBELLA-UV-2 SID14607_fpkm


title: run1_D18_iX18

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_58

value: high


title: sample_59


title: RUBELLA-1 SID14603_fpkm

value: Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)


title: run1_D1_iX03

description:
counts_run1.csv.gz
meta_run1.csv


title: iPSC_EMseq

value: iPS cell

tag: tag

value: DDX4-tdTomato, TFAP2C-EGFP

value: wildtype


title: run1_D10_iX16

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_57

value: neg

value: het

value: Basal


title: sample_55

value: lump

value: int

value: LumA


title: run1_D10_iX15

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_54


title: run1_D10_iX14

description:
counts_run1.csv.gz
meta_run1.csv


title: sample_51

value: CNB


title: BF_rep3

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

data_processing:
The sequence quality and read coverage were checked using FastQC V0.11.7.
The RNA sequences were mapped onto the reference genome using BBMap V37.66.
The SAMtools package V2.0.3 was used to generate, sort and index BAM files.
Subsequent RNAseq data processing was performed in R V3.6.0.
Mapped reads were quantified per each Borrelia burgdorferi open reading frame using the R rsamtools package V2.0.3.
Raw counts for open reading frames were retrieved using the GenomicAlignments R package V1.20.1.
Assembly: Borrelia burgdorferi B31 NCBI genome aaccession: ASM868v2, RefSeq assembly accession: GCF_000008685.2.
Supplementary files format and content: The processed data file contains a matrix of raw count values for each replicate and each mapped gene.

organism: Borreliella burgdorferi

source_name: biofilm

growth_protocol: Spirochete culture was gained by raising B. burgdorferi in BSK-H medium containing 6% rabbit serum in conical tubes with a tightly closed lids. Inoculations of spirochete culture were added to 3 different culturing media to gain round body, bleb and biofilm rich cultures. Cultures rich with round bodies were raised by incubating spirochetes in molecular-biology grade water for 10-30 minutes. Blebs were gained by incubating spirochetes in conical tubes with a vented lid. Biofilms were induced by cultivation of spirochetes in tissue-culture dishes. All cultures, were raised at 37°C.

extract_protocol:
The samples for RNA-extraction were processed with the Direct-zolTM RNA Minprep Plus Kit (Zymo Research) according to the manufacturer’s instructions. An on-column DNA digest was performed with the RNase-free DNase set (Qiagen) directly after loading of the samples. The RNA was eluted in RNAse free water and stored in two aliquots at -80°C. The RNA-quantity was measured spectroscopically and the integrity was assessed by agarose-gel electrophoresis.
The library was constructed according to the standard RNAseq library procotol at the EMBL Genomics Core Facility (Heidelberg, Germany).

tag: pleomorphic variant

value: biofilm

tag: culturing conditions

value: cultivation in tissue-culture dishes


title: RUBELLA-4 SID14618_fpkm

value: HUVEC

value: endothelial cells

value: WT

value: 24 hours past infection


title: sample_50

value: mast

value: pos


title: RUBELLA-2 SID14608_fpkm

value: Rubella infection (RVi/Wuerzburg.DEU/47.11 [Wb12], genotype 2B)


title: run1_D18_iX17

description:
counts_run1.csv.gz
meta_run1.csv

value: control

value: ES cell


title: Patient M140

first: Rafael

middle: Mena

last: Osuna

state: ile de France

address: 26 Rue D'ulm

department: Unit 932

institute: Institut Curie

hyb_protocol: Hybridization was performed in a PCR for 20 hours at 65°C

scan_protocol: Scanned with NanoString Digital analyser with 555 FOV

data_processing: Data analysis was performed by using nSolver software 4.0  to manage the raw expression data generated for each gene and for normalization

label: Nanostring bar coding

source_name: Colorectal adenocarcinoma

label_protocol: RNA species were identified and counted using the NanoString PanCancer Immune Profiling Panel.

extract_protocol: Total RNA was extracted from tumor tissue using the commercial RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. Then, total RNA was quantified using the NanoDropTM 1000 spectrophotometer (NanoDrop® ND-1000 UV- Vis Spectrophotometer, NanoDrop Technology), and RNA integrity Number (RIN) was measured using the Agilent 2200 TapeStation equipment.

tag: individual

tag: disease state

value: Colorectal adenocarcinoma

tag: tissue

value: CRC tumor

tag: age

tag: Sex

value: Male

value: Stage III


title: Patient M130

value: Female


title: sample_48

tag: procedure

value: lump

tag: er

value: high

value: neg

value: Basal


title: BF_rep1

value: biofilm

value: cultivation in tissue-culture dishes


title: BF_rep2


title: sample_46

tag: pr

tag: dcis


title: Patient M135

tag: Stage


title: Patient M127 bis

value: M127 bis


title: BL_rep2

source_name: bleb

tag: strain

value: bleb

value: BSK-H medium containing 6% rabbit serum in conical tubes with a vented lid


title: Patient M127


title: BL_rep1


title: sample_53

value: mast

value: pos

value: LumA


title: RB_rep2

source_name: round body

value: round body

value: exposure to molecular-biology grade water


title: Patient M126

value: Colorectal adenocarcinoma

value: CRC tumor


title: run1_D10_iX13

description:
counts_run1.csv.gz
meta_run1.csv

tag: treatment

value: ES cell


title: sample_52

value: Normal


title: sample_44

value: high


title: sample_43

value: neg

value: LumB


title: sample_42

value: CNB


title: Patient M118

value: Female

value: Stage III


title: RB_rep1


title: Patient M116

value: Male

value: Stage II


title: Patient M131


title: sample_40

value: lump

value: int


title: SP_rep3

source_name: spirochete

value: spirochete

value: BSK-H medium containing 6% rabbit serum in conical tubes with a tightly closed lid


title: Patient M111

value: Stage IV


title: sample_38

value: pos


title: SP_rep2


title: sample_45


title: RB_rep3

value: round body

value: exposure to molecular-biology grade water


title: Patient M108

value: Colorectal adenocarcinoma

value: CRC tumor


title: SP_rep1


title: Patient M110


title: Patient M90


title: sample_37

value: neg

value: high


title: Patient M91


title: sample_36

value: mast


title: sample_33

value: low

value: Normal


title: C6-45 Post1

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description: single-cell RNA-seq of C6-45 after 1 month from DNKI treatment

data_processing:
The Cell Ranger 3.1.0 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq X run.
This pipeline performed de-multiplexing, alignment (GRCh38/STAR), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Sparse matrix table with raw gene counts for every gene and every cell in Matrix Market Exchange Format

source_name: peripheral blood mononuclear cell

extract_protocol:
Cryopreserved PBMCs of the AML patients were quickly thawed and carefully transferred to the 35ml of pre-warmed α-MEM media (22 °C). Cells were pelleted by centrifugation at 300xg for 5 min at 22 °C, and then washed with 30ml of 0.04% BSA in PBS (22 °C). Live cells were collected by sorting with FACS after staining with CD45 and PI.
RNA libraries were prepared for sequencing using Single Cell 3' Reagent Kit v3 (10x genomics).

value: blood

tag: patient diagnosis

value: acute myeloid leukemia (AML)

tag: subject id

tag: time point


title: Patient M117

value: Female

value: Stage II


title: sample_32

value: CNB

value: int

value: LumB


title: sample_30

value: lump

value: pos


title: C6-29 Post3

description: single-cell RNA-seq of C6-29 after 3 month from DNKI treatment


title: Patient M83


title: Patient M78

value: Male


title: sample_29

value: Basal


title: C6-29 Post1

description: single-cell RNA-seq of C6-29 after 1 month from DNKI treatment


title: sample_26


title: C6-29 Pre

description: single-cell RNA-seq of C6-29 before DNKI treatment

value: Pre


title: C6-45 Post3

description: single-cell RNA-seq of C6-45 after 3 month from DNKI treatment


title: C6-24 Post3

description: single-cell RNA-seq of C6-24 after 3 month from DNKI treatment


title: C6-45 Pre

description: single-cell RNA-seq of C6-45 before DNKI treatment


title: Patient M63

value: Colorectal adenocarcinoma

value: CRC tumor


title: C6-24 Post1

description: single-cell RNA-seq of C6-24 after 1 month from DNKI treatment


title: Patient M77

value: Stage I


title: sample_23

value: mast

value: neg

value: LumA


title: C6-24 Pre

description: single-cell RNA-seq of C6-24 before DNKI treatment

value: blood

value: acute myeloid leukemia (AML)


title: sample_22

value: high


title: C6-3 Post1

description: single-cell RNA-seq of C6-3 after 1 month from DNKI treatment


title: 187R, WT, biol rep 2

city: Shanghai

first: Dengyong

last: Lan

address: Yangpu district

country: China

institute: Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Oryza. Sativa L. spp. Japonica
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oryza sativa Japonica Group

source_name: panicle

extract_protocol:
RNA was harvested using the FastPure® Plant Total RNA Isolation Kit (Vazyme, Nanjing, China). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: panicle

tag: genotype

value: natural


title: 187R, mutant, biol rep 1


title: C6-3 Pre

description: single-cell RNA-seq of C6-3 before DNKI treatment


title: Patient M87

value: Female

value: Stage IV


title: 187R, WT, biol rep 3


title: PDSG420 rep3

status: Public on Mar 16 2023

city: Paterna (Valencia)

first: Carolina

last: Ropero-Pérez

state: Comunidad Valenciana

address: Carrer del Catedràtic Agustín Escardino Benlloch, 7

department: Biotechnology

country: Spain

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

data_processing:
Adapters were eliminated and low-quality reads were filtered (average Q < 20, read length < 20 bp) using Cutadapt
Filtered reads were mapped onto the P. digitatum CECT 20796 genome (NCBI, WGS AKCT01) with TopHat2 (v.2.0.10)
Gene count analysis and DEGs identification was carried out with the OmicsBox suite the OmicsBox suite (OmicsBox 2.1). The number of reads that overlap with gene features (gene_id) were counted based on HT-Seq 0.9.0.
Genes for which Count Per Millions (CPM) < 0.5 in a minimum of three samples were removed and library sizes were normalized using the Trimmed Mean of M-values (TMM) method. Differentially expressed genes (DEGs) were identified using |log2(Fold change)| > 1 and false discovery rate (FDR) < 0.05.
Count data output was used for pairwise differential expression analysis with edgeR.
Assembly: GCA_000315665.1
Supplementary files format and content: tab-delimited text file include raw counts of sequencing reads in gene_id features (htseq-count output). Each row is a gene and each column is a sample

organism: Penicillium digitatum

source_name: mycelia

growth_protocol: 1x10^6 conidia/mL were inoculated in 1 L Erlenmeyer flasks containing 200 mL Potato Dextrose Broth (PDB) 25 % for 48 h at 25 ºC and 180 rpm

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, United States) following manufacturer’s instruction
Complementary DNA (cDNA) libraries were prepared with the TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Treatment 1: PHI26 grown without PdAfpB (control) during 48 h, 2: P. digitatum mycelia treated with 1 μg/mL AfpB for 1 h after 48h growth; 3: P. digitatum mycelia treated with 1 μg/mL AfpB for 3 h after 48h growth; 4: P. digitatum mycelia grown for 48 h in the presence of 0.03 μg/mL AfpB; 5: PDSG420 strain grown during 48 h

value: mycelia

value: Growth in PDB 25%


title: PHI26, 0.03 ug/ml, rep3

value: Growth in PDB 25% + 0.03 µg/mL PdAfpB


title: 187R, WT, biol rep 1


title: sample_18

value: pos

value: int

value: Basal


title: sample_20

value: lump

value: low


title: PHI26, 3h 1 ug/ml, rep3


title: C6-3 Post3

description: single-cell RNA-seq of C6-3 after 3 month from DNKI treatment


title: Stromal cells LI replicate 02

city: Lyngby

first: Line

last: Wulff

address: Kemitorvet, Building 204

department: Health Technology

country: Denmark

institute: Technical University of Denmark

description: single cell RNA sequencing analysis of intestinal adult stroma cells at homeostasis

data_processing:
Demultipexing and alignment of reads with CellRanger v3.0.2 for replicates 01 and v3.1.0 for replicates 02.
Cells with very low counts of reads and genes (2-300) dependent on individual sample distribution, and mitonchondiral gene load > 10 % were discarded.
Contaminating cell types were removed from the merged replicates before merging all samples all done w. Seurat v3.
Genome_build: mm10 (replicates 01) and mm10-2.1.0 (replicates 02)
Supplementary_files_format_and_content: tsv.gz & mtx.gz

source_name: Intestinal sorted stromal cells

extract_protocol:
Two independent experiments with three female mice/experiment. Muscularis externa was removed from small and large intestine prior to single cell suspensions and sorting (Live, CD45-, Ter119-, CD31-, BP3-, EpCAM-, L1CAM-, Itgb1+) of mesenchymal stromal cells for scRNA-seq.
Single cell RNA-seqg libraries were prepared according to the manufacturer’s instructions using Chromium Single Cell 3' Library & Gel Bead Kit v3 (10x Genomics, PN-1000092) or 5' kit Chromium Single Cell 5′ Library & Gel Bead Kit (10x Genomics, PN-1000006), and Chromium Chip B Single Cell Kit (PN-1000074) with the Chromium Controller & Next GEM Accessory Kit (10x Genomics, PN-120223).

treatment_protocol: Adult mice were untreated and 8-10 week old

value: Colonic lamina propria

tag: cell type

value: Mesenchymal stromal cells


title: 187R, mutant, biol rep 3


title: Stromal cells SI replicate 02

value: Small intestinal lamina propria


title: PDSG420 rep2


title: sample_27

value: mast

value: neg

value: LumB


title: sample_21

value: LumA


title: 187R, mutant, biol rep 2

value: panicle

value: natural


title: PHI26, 1h 1 ug/ml, rep1

value: mycelia


title: PHI26, control, rep3

value: Growth in PDB 25%


title: sample_19

value: high

value: Normal


title: PHI26, control, rep2


title: PHI26, rep4

data_processing:
RNA-Seq analysis were performed though the OmicsBox suite (OmicsBox 2.1). Raw data were firstly trimmed (3' trimming if Q < 20), and low-quality reads (average Q < 20, read length < 25 bp) were filtered using Trimmomatic 0.38
Filtered reads were mapped onto the P. digitatum CECT 20796 genome (NCBI, WGS AKCT01) with STAR (v.2.7.8a) using parameters: Overhang 74, 2-pass Mapping: false, Max. Intron Length: 1000,  Max. # of Multiple Alignments: 20, Max. # of Mismatches: 2
The number of reads that overlap with gene features (gene_id) were counted based on HT-Seq 0.9.0.
Genes for which Count Per Millions (CPM) < 0.6 in a minimum of four samples were removed and library sizes were normalized using the Trimmed Mean of M-values (TMM) method. Differentially expressed genes (DEGs) were identified using |log2(Fold change)| > 1 and false discovery rate (FDR) < 0.05.
Count data output was used for pairwise differential expression analysis with edgeR.
Assembly: GCA_000315665.1
Supplementary files format and content: tab-delimited text file include raw counts of sequencing reads in gene_id features (htseq-count output)


title: PHI26, control, rep1


title: PHI26, 0.03 ug/ml, rep1

value: Growth in PDB 25% + 0.03 µg/mL PdAfpB


title: PHI26, rep1


title: PHI26, 3h 1 ug/ml, rep2


title: PDSG420 rep1


title: PHI26, 3h 1 ug/ml, rep1


title: PHI26, 0.03 ug/ml, rep2


title: PHI26, rep3


title: PHI26, 1h 1 ug/ml, rep2


title: PHI26, rep2


title: PDMG122, rep3


title: PHI26, 1h 1 ug/ml, rep3


title: PDMG122, rep2


title: SuRE49

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500, or Illumina HiSeq-X10.
For polyA-RNA samples the barcode sequence was extracted from the read (using cutadapt and custom scripts) and counted.
For gDNA samples the barcode and the gDNA was extracted from the paired-end reads (using cutadapt and custom scripts). gDNA was then aligned to the reference genome (using bowtie2). Barcodes were then associated with genomic regions.
gDNA barcode, locations and counts were associated with polyA-RNA counts using barcode
counts for barcodes with same start and end location were summed up
Assembly: hg19
Supplementary files format and content: Tabular text file containing location on hg19, gDNA counts, and polyA-RNA counts for 2 biological replicates

source_name: collection of 4 BACs: CTD-3252A18, CTD-3156P24, CTD-2153L18, CTD-3075C4

growth_protocol: K562 (ATCC® CCL-243™) and HepG2 ((#HB 8065; ATCC) were cultured according to supplier's protocol.

extract_protocol:
To find out which barcodes were associated with which genomic fragments, we digested 4 µg SuRE library with I-CeuI (#R0699S; NEB), followed by magnetic bead purification (1:1 ratio beads:DNA solution). Of this, 2 µg was self-ligated overnight at 16 °C in a total volume of 2 ml (#10799009001 Roche), and purified using phenol-chloroform extraction and isopropanol precipitation. This material was treated with 25 units of Plasmid-Safe™ ATP-Dependent DNase for 1 hour and purified again with phenol-chloroform and isopropanol precipitation. To facilitate PCR, the resulting mini-circles were linearized by digesting with I-SceI (#R0694S; NEB) in a volume of 25 µl. Finally, 8 cycles of PCR (1¢ at 98°C, 10x(15¢ at 98°,15¢ at 60°, 20¢ at 72°)) with KAPA high-fidelity DNA Polymerase (#KE2502; KAPA biosystems) were performed on 1/10th of the I-SceI digested material using primers 151AR (containing the S1 and p5 adapter) and (index variants of) 117JvA (containing the S2, index and p7 adapter). The PCR product was bead purified and subjected to high-throughput paired-end sequencing on the Illumina HiseqX10 platform.
PolyA RNA was divided into 10 µl reactions containing 500 ng RNA and DNase treated with 10 units for 30 minutes (#04716728001; Roche) and DNAse was inactivated by addition of 1µl of 25mM EDTA and incubation at 70ºC for 10 minutes. Next, cDNA was produced by first adding 1 µl of 10 mM gene specific primer targeting the GFP ORF (247JvA) and 1 µl dNTP (10mM each) and incubating for 5 minutes at 65°C. Then 4 µl of RT buffer, 20 units RNAse inhibitor (#EO0381; ThermoFisher Scientific), 200 units of Maxima reverse transcriptase (#EP0743; ThermoFisher Scientific) and 2.5 µl water was added and the reaction was incubated for 30 minutes at 50°C followed by heat-inactivation at 85° for 5 minutes. Per biological replicate, 20-30 reactions were done in parallel. Each 20 µl reaction was then PCR amplified (1’ 96 °C, 20x(15’’ 96 °C, 15’’ 60 °C, 15’’ 72 °C)) in a 100 µl reaction with MyTaq™ Red Mix and primers 151AR (containing the S1 and p5 adapter) and (index variants of) 211JvA (containing the S2, index and p7 adapter) for 21 cycles. Reactions were then pooled and 500 µl was purified using CleanPCR beads (#CPCR-0050; GC biotech) and subjected to single read 50 bp high throughput sequencing on an Illumina HiSeq2000 or HiSeq2500.

value: collection of 4 BACs:CTD-3252A18, CTD-3156P24, CTD-2153L18, CTD-3075C4


title: PDMG122, rep1


title: ANGPTL2 (A2)

city: shanghai

first: wenqian

last: yang

address: 280 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

data_processing:
The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads for subsequent analysis with SOAPnuke1.3.0. The steps of sequencing data filtering: 1) removing reads containing adapter; 2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%; 3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read); All the downstream analyses were based on clean data with high quality.
Mapping to the reference genome:The reference genome and gene model annotation files were downloaded directly from the  genome website. The reference genome index was built using hisat2-build, and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Transcriptome assembly: The mapped reads of each sample were assembled using Stringtie (v1.3.3) with a reference-based approach. This method employed spliced reads to determine exon connectivity.
Quantification of gene expression levels: Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample. Gene FPKMs were computed by summing the FPKMs of the transcripts in each gene group. FPKM stands for  “fragments per kilobase of exon per million fragments mapped”, and it is calculated based on the  length of the fragments and the reads count mapped to each fragment.
Differential expression analysis,Gene Ontology (GO) and KEGG enrichment analysis.
Genome_build: HG38
Supplementary_files_format_and_content: FPKM

source_name: cord blood

extract_protocol:
Cells were lysed by TRIzol reagent for extraction of RNA. RNA was prepared using RNasey Mini Kit(Qiagen p/n 74104) according to the manufacturer's recommendations. After clean-up, RNA purity was detected by NanoDrop® spectrophotometers (Thermo Fihser, MA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumia, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X Ten platform and 150bp pired-end module.

value: HSCs treated with ANGPTL2 for 24 hours

value: hematopoietic stem/progenitor cells

value: cord blood


title: Ctrl

value: untreated HSCs


title: PDMG122, rep4


title: 64 NRCWE-062

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Healthy Environments and Consumer Safety Branch

country: Canada

institute: Health Canada

hyb_protocol: Each cRNA sample and cRNA reference was mixed at an equimolar amount of 300 ng to be hybridized to Agilent 8X60K Sure Print G3 Mouse gene expression microarray for 17 h at 65°C, rotation speed of 10 rpm.

scan_protocol: Slides were washed and scanned on an Agilent Scanner G2505B.

data_processing: Expression data were extracted using Agilent Feature Extraction Software version 11.0.1.1

source_name: Lung tissue of female mice

label_protocol: The Low Input Quick Amp Labeling Kit (#5190-2331, Agilent Technologies) was used to generate double-stranded cDNA and fluorescent cRNA. cRNA was purified using RNAeasy MiniKit according to the protocol provided by the manufacturer (#74106, Qiagen).

growth_protocol: Female mice were acclimatized and housed in polypropylene cages with access to food and tap water ad libitum. Temperature (21 ± 1°C), humidity (50% ± 10%) and 12 hours light/dark period.

extract_protocol: RNA extraction was performed using TrizolTM reagent (#15596-026) and stainless-steel beads for homogenization with Retsch Mixer Mill NM400 (25.0 Hz for 2 minutes). RNA was purified using Direct-zol RNA Miniprep Kits (#R2052, Zymo Research). The RNA concentration and purity were determined through 260/280 and 260/230 absorbances using NanoDrop Spectrophotometer 2000. RNA quality and integrity were determined using the Agilent TapeStation System (Agilent). Samples showed ratios of ~2.0 and RNA integrity numbers were above 5.

treatment_protocol: Mice were exposed to CNTs by single intratracheal instillation of 6, 18 or 54 μg/mouse. The control group was instilled with NanoPure water with 2% serum. After 24 h of exposure, mice were sacrificed and the lung lobes were frozen and stored at -80°C for RNA extraction. n=8 per control group, n=5 per experimental group.

value: C57BL/6J BomTac

value: NRCWE-062 (Pristine MWCNTs)

tag: dose

value: 6 μg/mouse

value: 24 hours

value: lung

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines

tag: sample type

value: Universal Mouse Reference RNA


title: 12 NM411

value: NM411 CNT (Pristine SWCNTs)

value: 18 μg/mouse


title: 7 NRCWE-064

value: NRCWE-064 (Carboxylated MWCNTs)

tag: tissue


title: 623 NRCWE-063

value: NRCWE-063 (Hydroxylated MWCNTs)


title: 582 NRCWE-061

value: NRCWE-061 (Aminated MWCNTs)

value: 54 μg/mouse


title: 624 NRCWE-063


title: 77 NRCWE-062


title: 565 NRCWE-061


title: 8 NRCWE-064


title: 192 NRCWE-064

value: 0 μg/mouse


title: 16 NRCWE-064


title: 575 NRCWE-061


title: 569 NRCWE-061


title: 574 NRCWE-061


title: 630 NRCWE-063


title: 637 NRCWE-063


title: 568 NRCWE-061


title: 193 NRCWE-064


title: 629 NRCWE-063


title: 618 NRCWE-063


title: 622 NRCWE-063


title: 76 NRCWE-062


title: 63 NRCWE-062


title: 71 NRCWE-062


title: 62 NRCWE-062


title: 631 NRCWE-063


title: 21 NRCWE-064


title: 636 NRCWE-063


title: sample_25

source_name: Patient tumor tissue

value: CNB

value: neg

value: pos


title: 58 NRCWE-062

value: C57BL/6J BomTac


title: 617 NRCWE-063


title: 12 NRCWE-064


title: 5 NCRCWE-064


title: 570 NRCWE-061


title: 61 NRCWE-062

value: NRCWE-062 (Pristine MWCNTs)


title: 632 NRCWE-063


title: 583 NRCWE-061


title: 573 NRCWE-061


title: 69 NRCWE-062


title: 20 NRCWE-064


title: 13 NRCWE-064


title: 621 NRCWE-063

value: 6 μg/mouse


title: 19 NRCWE-064

value: 24 hours


title: 584 NRCWE-061

value: lung


title: 638 NRCWE-063

value: 11 mouse cell lines


title: 572 NRCWE-061

value: Universal Mouse Reference RNA


title: 72 NRCWE-062


title: 78 NRCWE-062


title: 581 NRCWE-061


title: 562 NRCWE-061


title: 6 NRCWE-064


title: 635 NRCWE-063


title: 57 NRCWE-062


title: 11 NRCWE-064


title: 620 NRCWE-063


title: 634 NRCWE-063


title: 4 NRCWE-064


title: 18 NRCWE-064


title: 578 NRCWE-061


title: 23 NRCWE-064


title: 571 NRCWE-061


title: 564 NRCWE-061


title: 60 NRCWE-062


title: 627 NRCWE-063


title: 68 NRCWE-062


title: 561 NRCWE-061


title: 74 NRCWE-062


title: 289 NRCWE-053

value: NRCWE-053 (Hydroxylated SWCNTs)


title: 352 NRCWE-054

value: NRCWE-054 (Carboxylated SWCNTs)

value: 18 μg/mouse


title: 299 NRCWE-053


title: 183 NRCWE-051

value: NRCWE-051 (Pristine SWCNTS)


title: 345 NRCWE-054


title: 343 NRCWE-054


title: 176 NRCWE-051


title: 182 NRCWE-051


title: 294 NRCWE-053


title: 339 NRCWE-054


title: 175 NRCWE-051


title: 233 NRCWE-052

value: NRCWE-052 (Pristine SWCNTs)


title: 357 NRCWE-054

value: NRCWE-054 (Hydroxylated SWCNTs)

value: 54 μg/mouse


title: 301 NRCWE-053


title: 287 NRCWE-053


title: 351 NRCWE-054


title: 189 NRCWE-051


title: 230 NRCWE-052


title: 283 NRCWE-053

value: 0 μg/mouse


title: 70 NRCWE-062


title: 245 NRCWE-052


title: 237 NRCWE-052


title: 293 NRCWE-053


title: 295 NRCWE-053


title: 356 NRCWE-054


title: 286 NRCWE-053


title: 231 NRCWE-052


title: 300 NRCWE-053


title: 181 NRCWE-051


title: 281 NRCWE-053


title: 227 NRCWE-052


title: 244 NRCWE-052


title: 174 NRCWE-051


title: 338 NRCWE-054


title: 188 NRCWE-051


title: 342 NRCWE-054


title: 229 NRCWE-052


title: 243 NRCWE-052


title: 173 NRCWE-051

value: 1 day


title: 240 NRCWE-052


title: 285 NRCWE-053


title: 337 NRCWE-054


title: 302-NRCWE-053


title: 355 NRCWE-054


title: 238 NRCWE-052


title: 341 NRCWE-054


title: 246 NRCWE-052


title: 187 NRCWE-051


title: 348 NRCWE-054


title: 347 NRCWE-054


title: 282 NRCWE-053


title: 298 NRCWE-053


title: 349 NRCWE-054


title: 292 NRCWE-053


title: 354 NRCWE-054


title: 291 NRCWE-053


title: 284 NRCWE-053


title: 186 NRCWE-051


title: 228 NRCWE-052

value: NRCWE-052 (Pristine SWCNTS)


title: 190 NRCWE-051

value: C57BL/6J BomTac


title: 340 NRCWE-054


title: 235 NRCWE-052


title: 359 NRCWE-054


title: 179 NRCWE-051


title: 172 NRCWE-051


title: 242 NRCWE-052


title: 225 NRCWE-052


title: 463 NRCWE-056

value: NRCWE-056 (Hydroxylated SWCNTs)


title: 14 NM411

value: NM411 CNT (Pristine SWCNTs)


title: 394 NRCWE-055

value: NRCWE-055 CNT (Pristine SWCNTs)

value: 24 hours


title: 470 NRCWE-056

value: lung

value: 11 mouse cell lines


title: 518 NRCWE-057

value: NRCWE-057 CNT (Carboxylated SWCNTs)

value: Universal Mouse Reference RNA


title: 414 NRCWE-055


title: 412 NRCWE-055


title: 511 NRCWE-057

value: 6 μg/mouse


title: 450 NRCWE-056


title: 406 NRCWE-055

value: 18 μg/mouse


title: 527 NRCWE-057


title: 526 NRCWE-057


title: 462 NRCWE-056


title: 507 NRCWE-057


title: 519 NRCWE-057


title: 400 NRCWE-055


title: 512 NRCWE-057


title: 468 NRCWE-056


title: 510 NRCWE-057


title: 15 NM411


title: 455 NRCWE-056


title: 405 NRCWE-055


title: 524 NRCWE-057


title: 467 NRCWE-056


title: 7 NM411


title: 21 NM411


title: 456 NRCWE-056


title: 399 NRCWE-055


title: 16 NM411


title: 404 NRCWE-055


title: 20 NM411


title: 517 NRCWE-057


title: 461 NRCWE-056


title: 5 NM411


title: 2 NM411


title: 8 NM411


title: 236 NRCWE-052

value: NRCWE-052 (Pristine SWCNTs)


title: 460 NRCWE-056


title: 516 NRCWE-057


title: 454 NRCWE-056


title: 401 NRCWE-055


title: 449 NRCWE-056


title: 505 NRCWE-057


title: 23 NM411


title: 509 NRCWE-057


title: 411 NRCWE-055


title: 522 NRCWE-057


title: 453 NRCWE-056


title: 459 NRCWE-056


title: 471 NRCWE-056


title: 408 NRCWE-055


title: 466 NRCWE-056


title: 410 NRCWE-055


title: 1 NM411


title: 4 NM411


title: 508 NRCWE-057


title: 452 NRCWE-056

value: NRCWE-056 (Hydroxylated CNTs)


title: 515 NRCWE-057


title: 18 NM411

value: 54 μg/mouse


title: 393 NRCWE-055

value: 0 μg/mouse


title: SSM3 cells, rep3

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v 2.17.1.14), low quality (Q < 30) reads removed, and trimmed at the 5’ and 3’ ends using cutadapt (v 2.1) to remove adapter sequences and poly-A-tail derived reads respectively
Sequencing reads were mapped to the mouse reference genome (mm10) using HISAT2 (v 2.0.4).
Reads were counted using the featureCounts command of the Subread package (v 2.0.0).
Read normalization and differential gene expression analysis was performed in R (v 4.1.0) using R packages limma (v 3.48.3) and EdgeR (v 3.34.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing the raw counts output from featurecounts

source_name: Mammary cancer

extract_protocol:
RNA was extracted using Trizol lysis following the manufacturer’s instructions (Invitrogen) and then phenol, chloroform extraction. RNA was precipitated using isopropanol, cleaned with ethanol and then solubilized in RNase-free water.
RNA libraries were prepared using the QuantSeq 3´ mRNA-seq Library Prep Kit for Illumina (Lexogen 015), according to the manufacturer’s instructions

value: Mammary cancer

tag: cell line


title: J110 cells, rep3


title: 396 NRCWE-055

value: 1 day


title: J110 cells, rep2


title: 11 NM411

value: C57BL/6J BomTac


title: 397 NRCWE-055


title: J110 cells, rep1


title: SSM3 cells, rep2


title: P5_4n

city: Odense M

first: Ditte

middle: Caroline

last: Andersen

address: Campusvej 55

department: Clinical Research

institute: University of Southern Denmark

description:
Background.txt
MarkersbetweenE165andP5_all_G2M_wo2n.txt

data_processing:
For demultiplexing, barcode processing, and sc 3´counting, the software Cell Ranger (10xGenomics) was used. In order to generate gene-barcode matrices, cDNA reads were aligned to the mm10 reference genome. Single cell gene counts matrices were generated using the cellranger count command. During this step, FASTQ files generated by the cellranger mkfastq step, were aligned to the Mus musculus genome (mm10/GRCm38) using the splice-aware aligner STAR
STAR used the Mus musculus transcriptome reference (GRCm38.84) to segregate the mapped reads into exonic, intronic and intergenic regions and for assessment of how confidently the reads have been mapped to these regions. Only non-duplicated reads which were confidently mapped to the transcriptome and which had barcodes and unique molecular identifiers (UMIs) were used for UMI counting. The expression matrices were generated by counting the number of strand-specific UMI for each cell mapping to either the exonic or intronic regions of each gene.
Using Seurat v 2.3.0 and 3.1.5  a Seurat object was created, and the cells filtered based on whether they expressed a combination of the CM-specific markers Tnni3, Tnnt2, Actc1 and Tnnc1.
Each sample was then log-normalized, variable genes were identified, and the data was scaled using nUMI for vars.to.regress.
Using the R package Seurat18 performs dimensionality reduction by principal component  analysis (PCA) was performed; subsequently, , and then use the PCA data analysis was used as input for visualization by t-Distributed Stochastic Neighbor Embedding (t-SNE) clustering.
Genome_build: mm10
Supplementary_files_format_and_content: Background genes for online transcription factor analysis
Supplementary_files_format_and_content: List of marker genes with p-value and avg_logFC when comparing subsets of E16.5 and P5 cells

source_name: Tetraploid (4n) cardiomyocytes originating from the left heart ventricle of mice at P5

growth_protocol: Animals were housed with a 12/12 hours light/dark cycle at the Biomedical Laboratory (University of Southern Denmark, Odense) and fed ad libitum.

extract_protocol:
Cells from the left heart ventricle of mice at E16.5, P1 and P5 were dissociated by enzymatic dissociation and stained with a fixable viability stain prior to methanol fixation followed by rehydration. Fixed cardiac cells were stained with the cardiomyocyte marker MYH1 and the DNA marker Hoechst and diploid and tetraploid cardiomyocytes were isolated by FACS.   Sorted diploid and tetraploid cardiomyocytes were subjected to single cell RNA sequencing using the 10x Genomics platform. Single Cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 (10x Genomics).
NGS libraries were  constructed by adapter ligation and PCR mediated sample indexing (No. of cycles: 13).

value: Cardiomyocytes

tag: age

value: Post natal day 5


title: E16.5_2n

source_name: Diploid (2n) cardiomyocytes originating from the left heart ventricle of mice at embryonic day 16.5

value: Embryonic day 16.5


title: P1_4n

source_name: Tetraploid (4n) cardiomyocytes originating from the left heart ventricle of mice at P1

value: Post natal day 1


title: P1_2n

source_name: Diploid (2n) cardiomyocytes originating from the left heart ventricle of mice at P1


title: SSM3 cells, rep1


title: Mouse.631727.3L

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

institute: University Hospital Basel

data_processing:
Mapping and transposon integration site identification: The expected transposon-derived sequence (5’-TAGGGTTAA-3’) was removed from the beginning of the first read (read pairs with non-matching first reads were discarded) using the preprocessReads function from the QuasR Bioconductor package (version 1.12.0). Read pairs were aligned to the mouse genome (BSgenome. Mmusculus.UCSC.mm10) using the QuasR qAlign function with the parameters alignmentParameter = “-m 1 --best --strata --maxins 1000”; this will report only uniquely mapping pairs with up to 1000 bp between-pair distance. Mapping rates were recorded, and non-mapped read pairs were further aligned against the non-mobilized transposon sequence to estimate the probable fraction of read pairs that originate from non-mobilized copies of the transposon. For each aligned read pair, the piggyBac insertion coordinate was identified as the coordinate of the first (most 5’) base of the first read.
Identification of enriched unique integration sites: For each unique integration site, the number of distinct supporting alignments (distinct read pairs, referred to as “diversity”), and the genomic sequence from the four base pairs on the same strand as the first read directly upstream of the insertion site were recorded. These diversity values were normalized by dividing trough the total alignments in a sample and then multiplied by 10^5 (normalized diversity values “divN”). Only integration sites with the expected upstream TTAA sequence were used for the downstream analysis.
Association of integration sites with genes: Coordinates of known genes (exons/introns, 5’-untranslated region [UTR], coding sequence [CDS], 3’UTR) were obtained from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package (version 3.2.2). Promoter regions were defined as regions 2000 bp upstream of known transcript start sites. Integration sites were matched against these genomic regions to identify overlaps on any strand and orientation, selecting the first overlap in the case of multiple overlaps. Integration sites were classified hierarchically as follows: sites without overlaps to any transcript were labelled as promoter sites (in the case of an overlap with a promoter region) or intergenic sites. All other sites were labelled with the first region type that they overlapped, in the following order: 5’UTR, CDS, 3’UTR, intron or ncRNA (defined as an overlap with a transcript without annotated CDS). Sites were further labelled according to their orientation with respect to the associated gene (same or opposite). Finally, sites were grouped according to the gene they overlapped (including promoter sites) or, for intergenic sites, according to the pair of flanking genes.
Identification of enriched unique integration sites: For each insert the normalized diversity values were calculated as described above. The normalized diversity values of all unique insertions sites in a gene were summed over one category of samples (divNsum). We identified a total of 61’241 insertions in the resistant samples and 98’373 insertions in the untreated controls corresponding to a total of 24’032 affected genes. We excluded 2 genes that were found in all analyzed resistance samples as a potential PCR contamination. To find putative resistance genes we focused on the genes with a higher number of unique transposon integrations in the BYL treated samples compared to the untreated samples.
Assembly: UCSC version mm10
Supplementary files format and content: PiggyBacBYLResistanceScreen_integration_sites.csv; big table that contains: insertion coordinate: is the first base downstream of the transposon sequence (first 9 bases of R1); cnt (coverage): the number of alignments starting at the insertion coordinate; cnt2 (coverage): the number of alignments of the most frequent fragment starting at the insertion coordinate (only for paired-end data); div (diversity): the number of distinct alignment-pairs starting at the insertion coordinate (only available for paired-end data); cntN, cnt2N, divN: the normalized values of cont, cnt2, div; context.5p: are the 4 genomic bases on the same strand and directly upstream of the insertion site; context.3p: are the 4 genomic bases on the same strand and directly downstream of the insertion site (including the insertion site coordinate)
Supplementary files format and content: combined_table_BYLResWAPtg-inVivoTumorWAPtg.csv; table contains: gCIS.signedNegativeLog10Pvalue: the gene centered common insertion sites  -log10 Pvalue; nInsertions.total: total number of inserteions in a gene; information on the strand where the insertion was observed; percentSamplesWithInsertionInGene: indicating the percent of samples with insertions in a given gene; divNsum: the normalized diversity values of all unique insertions sites in a gene were summed over one category of samples; all those values are given for the untreated samples and the BYL resistant samples seperatly.

source_name: MFP tumor

growth_protocol: Experimental mice were mated to trigger WAP expression during late pregnancy in the mammary gland resulting in the expression the PIK3CA-H1047R mutation and the PB-transposase simultaneously specifically in the mammary gland (Rad 2010, Meyer 2011).

extract_protocol:
gDNA of 94 untreated tumors and 51 resistant tumors (from a total of 53 mice) was isolated with a DNeasy Blood and Tissue Kit (Qiagen #69504) and fragmented by sonication (Covaris sonicator) to a size of 250 bp.
DNA fragments were end repaired, A-tailed, purified and then ligated to the splikerette adaptor (annealed 5’-gttcccatggtactactcatataatacgactcactataggtgacagcgagcgct-3’ with 5’-gcgctcgctgtcacctatagtgagtcgtattataatttttttttcaaaaaaa-3’). Transposon containing DNA fragments were enriched by PCR using a primer specific for the 5’-transposon arm (5’-gacggattcgcgctatttagaaagagag-3’) and the common splinkerette primer (5’-gttcccatggtactactcata-3’). An additional PCR was performed for barcoding the individual samples by using a primer specific for the 5’ arm of the transposon (5’- aatgatacggcgaccaccgagatctacacatgcgtcaattttacgcagactatc-3’) and another primer specific tor the splinkerette side (5’-caagcagaagacggcatacgagatcggtXXXXXXXXtaatacgactcactatagg-3’; Xs standing for the eight-base barcode). Purified libraries were assembled in four pools and sequenced on Illumina HiSeq 2500 (Paired-End, 2 × 100 bp, rapid run, 200 cycles).

treatment_protocol: Once tumors reached 250 mm3, animals were treated daily with 30 mg/kg BYL719. Tumors that increased in their volume over at least 3 consecutive measurements (in a total of 3 weeks) in their volume while being treated were classified as resistant. Such resistant tumors and tumors from an untreated control group were isolated once the total tumor volume of a mouse reached the allowed maximal tumor size.

tag: sample group

value: BYLResWAPtg

value: MFP tumor


title: Mouse.6460872.3L


title: Mouse.646087.4L


title: Mouse.648067.2.3R


title: Mouse.650650.2.3L


title: Mouse.634370.2.3L


title: P5_2n

source_name: Diploid (2n) cardiomyocytes originating from the left heart ventricle of mice at P5


title: E16.5_4n

source_name: Tetraploid (4n) cardiomyocytes originating from the left heart ventricle of mice at embryonic day 16.6

value: Embryonic day 16.6


title: 413 NRCWE-055

value: NRCWE-055 CNT (Pristine SWCNTs)

value: 24 hours

value: lung

value: 11 mouse cell lines

value: Universal Mouse Reference RNA


title: Mouse.619999.2.3R


title: Mouse.602172.2.3R


title: Mouse.602170.1R


title: Mouse.648067.5R


title: Mouse.619999.5R


title: Mouse.628194.2.3R


title: Tgtumor_627064.1L


title: Mouse.608856.5L


title: Tgtumor_628196.2.3L


title: Tgtumor_619999.2.3L


title: Tgtumor_627443.2.3L


title: Tgtumor_627443.2.3R


title: Tgtumor_628196.2.3R


title: Tgtumor_627060.5L


title: Tgtumor_628194.5L


title: Tgtumor_627061.2.3R


title: Mouse.628194.2.3L


title: Tgtumor_627060.2.3R


title: Mouse.602172.5R


title: Tgtumor_608856.2.3L


title: Tgtumor_610096.2.3L


title: Tgtumor_624220.2.3L


title: Tgtumor_603938.1L


title: Tgtumor_603938.4L


title: Tgtumor_627443.5L


title: Tgtumor_602169.4R


title: Tgtumor_602170.3R


title: Tgtumor_610093.2.3R


title: Tgtumor_602170.3L


title: Tgtumor_618614.2.3L


title: Tgtumor_611364.2.3L


title: Tgtumor_610093.2.3L


title: Tgtumor_627060.4L


title: Tgtumor_602169.2.3L


title: Tgtumor_602169.2.3R


title: Tgtumor_610101.2.3R


title: 523 NRCWE-057

value: NRCWE-057 CNT (Carboxylated SWCNTs)

value: 54 μg/mouse


title: Tgtumor_610101.2.3L


title: Tgtumor_608671.2.3R


title: Tgtumor_597307.5


title: Tgtumor_610096.2.3R


title: Tgtumor_597307.1L


title: Tgtumor_608671.5L


title: tgTum_598496.5R

value: inVivoTumorWAPtg

value: untreated


title: Tgtumor_597307.2.3R


title: Tgtumor_602170.2R


title: tgTum_591167.5R


title: tgTum_594972.1R


title: tgTum_594972.1L


title: TgTum_587659.3R_R2


title: tgTum_591170.2.3L


title: tgTum_583687.2.3L


title: tgTum_591170.4R


title: tgTum_600405.4R


title: tgTum_594973.2.3L


title: tgTum_600405.5R.L


title: tgTum_600405.1L


title: tgTum_583687.1L


title: tgTum_591170.4L


title: tgTum_600405.1R


title: tgTum_597909.2.3R


title: tgTum_583687.5


title: tgTum_583687.4L


title: tgTum_594972.4R


title: tgTum_583687.1R


title: tgTum_591167.2.3R


title: tgTum_591167.2.3L


title: tgTum_583687.2.3R


title: tgTum_594973.4L


title: tgTum_591167.4.5L


title: tgTum_591167.4R


title: tgTum_594972.2.3R


title: tgTum_591170.1L


title: tgTum_594972.5R


title: tgTum_594973.2.3R


title: tgTum_594972.2.3L


title: tgTum_597909.4.5L


title: tgTum_591170.2.3R


title: TgTum_591686.4L


title: TgTum_591686.2L


title: TgTum_587659.2L


title: TgTum_587659.4R


title: TgTum_586251.4R


title: TgTum_586251.3L


title: TgTum_586251.1L


title: TgTum_586251.1R


title: TgTum_586251.5L


title: tgTum_594972.4.5L


title: TgTum_586249.1L


title: TgTum_586249.4L


title: TgTum_586249.2L


title: TgTum_586249.4R