title: Tconv EAE CNS 4

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

description:
DJK60_CNS_GFP_neg
Tconv cells in CNS of mice at peak of EAE.

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturer's instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.

data_processing: In DRFZ with GeneChip Operating System (GCOS, Affymetrix) generated CHP and CEL files were analyzed at INRAE, France (Luc Jouneau). Only chips, which fulfilled all chip and hybridization quality criteria, were selected for analysis. Normalization has been performed using R package GCRMA. To detect which probe sets were expressed in a given sample and to get Present/Marginal/Absent calls, mas5calls function of affy R package was used. Differential expression was detected using limma R package.

source_name: CD4+FOXP3- T cells from the CNS of EAE mice

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

treatment_protocol: For EAE induction, each mouse received 100 μg of MOG(35–55) peptide emulsified in CFA containing 50 μg of heat-killed Mycobacterium tuberculosis H37Ra (Sigma-Aldrich) at a final volume of 100 μl injected s.c. into the hind legs. In addition, 200 ng of pertussis toxin (European Cell and Culture Collection, Dorset, U.K.) was given in 0.5 ml of PBS i.p. on the same day and 2 days later. Spleens were processed to obtain single cell suspensions, followed by red blood cells lysis. To isolate CNS cells, mice were sacrificed by CO2 asphyxiation and perfused with cold PBS. Brains were harvested. Spinal cords were removed by intrathecal hydrostatic pressure. Cords and brains were cut into small pieces and digested with 2.5 mg/ml collagenase (Worthington Biochemical) and 1 mg/ml deoxyribonuclease (Sigma-Aldrich) for 25 min at 37°C followed by mechanical disaggregation. Single cell suspensions were washed in tissue culture and resuspended in medium containing 30% percoll (Invitrogen Life Technologies). Mononuclear cells were prepared from the interface of a 30:70% discontinuous percoll gradient after centrifugation for 20 min at 2000 × g. Cells were then stained for CD4 and CD11b. Tregs and Tcons were then isolated by flow cytometry. Cells were then pelleted for RNA extraction.

tag: gender

value: Male

value: CNS

tag: cell type

value: Tconv

tag: condition

value: Experimental autoimmune encephalomyelitis (EAE)


title: control_148

status: Public on Oct 12 2022

type: genomic

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis Guide. Annotation and library downloaded from Taiwan Biobank (https://www.biobank.org.tw/fd.php)
processed data file includes: SNP ID: dbSNP_RS_ID and affy_snp_id; SNP Call: AA, AB, BB, and NoCall; SNP Annotation: Allele_A, Allele_B, Ref_Allele and Alt_Allele; SNP Quality: CR(Call Rate), ConversionType; SNP frequency: n_AA, n_AB, n_BB, n_NC and MinorAlleleFrequency.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral white blood cells

label_protocol: Type 2 diabetes mellitus (DM) was defined as a fasting glucose larger than 126 mg/dL, a glycosylated hemoglobin larger than 6.5, or the use of hypoglycemic medications. CKD was defined using the National Kidney Foundation: Kidney Disease Outcomes Quality Initiative classification with a persistent proteinuria or an eGFR of less than 60 mL/min/1.73 m2, as determined by the abbreviated Modification of Diet in Renal Disease equation. DKD was diagnosed if subjects fulfilled both DM criteria and CKD criteria at the same time.

growth_protocol: Peripheral venous blood was obtained after an overnight fast.

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

tag: tissue

value: peripheral white blood cells

tag: diagnosis

value: control

tag: Sex

value: male


title: control_147

scan_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

value: female


title: control_143


title: control_145


title: control_146


title: Tconv EAE CNS 2

type: RNA

description:
Roc238_CNS_GFP_neg
Tconv cells in CNS of mice at peak of EAE.

molecule: total RNA

organism: Mus musculus

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturer's instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

tag: strain

value: Female


title: Tconv EAE CNS 1

description:
Roc231_CNS_GFP_neg
Tconv cells in CNS of mice at peak of EAE.


title: Treg EAE CNS 3

description:
DJK60_CNS_GFP_pos
Treg cells in CNS of mice at peak of EAE.

source_name: CD4+FOXP3+ T cells from the CNS of EAE mice

value: Treg


title: Treg EAE CNS 2

description:
Roc240_CNS_GFP_pos
Treg cells in CNS of mice at peak of EAE.


title: Tconv EAE spleen 2

description:
Roc240_spl_GFP_neg
Tconv cells in spleen of mice at peak of EAE.

source_name: CD4+FOXP3- T cells from the spleen of EAE mice

value: Spleen


title: Tconv EAE spleen 3

description:
DJK60_spl_GFP_neg
Tconv cells in spleen of mice at peak of EAE.


title: control_141


title: control_140


title: Treg EAE CNS 1

description:
Roc231_CNS_GFP_pos
Treg cells in CNS of mice at peak of EAE.


title: control_139


title: control_138


title: control_136


title: control_142


title: Treg EAE spleen 3

description:
Roc240_spl_GFP_pos
Treg cells in spleen of mice at peak of EAE.

source_name: CD4+FOXP3+ T cells from the spleen of EAE mice


title: Tconv EAE CNS 3

description:
Roc240_CNS_GFP_neg
Tconv cells in CNS of mice at peak of EAE.


title: control_135


title: Treg EAE spleen 2

description:
Roc238_spl_GFP_pos
Treg cells in spleen of mice at peak of EAE.


title: Treg EAE spleen 4

description:
DJK60_spl_GFP_pos
Treg cells in spleen of mice at peak of EAE.


title: Treg EAE spleen 1

description:
Roc231_spl_GFP_pos
Treg cells in spleen of mice at peak of EAE.


title: 41977-Input-pool_5

type: SRA

city: Duarte

first: WEI

last: CHEN

state: CA

address: 1500 E Duarte Rd

country: USA

institute: City of Hope National Medical Center

library_source: genomic

data_processing:
Paired-end  reads were aligned to mm10 reference using Bowtie2 with the default settings.
Samtools was implemented on transforming the aligned sam files into bam files.
Samtools was applied to sorting and indexing the transformed bam files.
MACS2 was run for the peak-calling process to generate narrowPeaks and bigWig files with the most default settings and two customized options: --mfold 5 50, --extsize 200.
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeaks

source_name: Bone Marrow

extract_protocol: genomic DNA was sonicated with Covais with the peak setting of 300bp. The DNA fragments were ligated with IDT Stubby adapters with KAPA DNA Hyperprep kit, the ligated DNA was pooled and underwent Immunoprecipitation (IP) , the final IP prodoucts were amplified with Hotstart 2x master mix (from KAPA DNA Hyper Prep kit) with IDT index primers.

value: Bone Marrow

value: c-kit+ cells

tag: genotype

tag: chip antibody


title: Tconv naive spleen 1

description:
GFP_neg_4
Tconv cells in spleen of naive mice.

source_name: CD4+FOXP3- T cells from the spleen of naive mice

value: Naive


title: Treg naive spleen 3

description:
GFP_plus_3
Treg cells in spleen of naive mice.

source_name: CD4+FOXP3+ T cells from the spleen of naive mice


title: Tconv naive spleen 2

description:
GFP_neg_5
Tconv cells in spleen of naive mice.


title: Tconv naive spleen 3

description:
GFP_neg_6
Tconv cells in spleen of naive mice.


title: control_134


title: Treg naive spleen 2

description:
GFP_plus_2
Treg cells in spleen of naive mice.


title: 41977-Input-pool_3


title: Tconv EAE spleen 1

description:
Roc231_spl_GFP_neg
Tconv cells in spleen of mice at peak of EAE.


title: 41980-IP-pool-3_7


title: RNA-seq of adult Tribolium castaneum testis [Tca_Testis_b]

city: Barcelona

first: Federica

last: Mantica

address: Dr. Aiguader 88

country: Spain

institute: CRG

description: Pooled testis from adult individuals

library_source: transcriptomic

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

molecule: polyA RNA

organism: Tribolium castaneum

source_name: Adult testis

extract_protocol:
Trizol
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Testis

tag: genome build

tag: gtf

value: Tcas5.2 GTF (enriched from Ensembl metazoa v45)


title: 41977-Input-pool_1


title: RNA-seq of adult Tribolium castaneum testis [Tca_Testis_a]

description: Pooled testis from adult individuals


title: control_137


title: control_133


title: 41980-IP-pool-3_5


title: 41977-Input-pool_7


title: 41980-IP-pool-3_3


title: control_132


title: 41980-IP-pool-3_1


title: control_130


title: RNA-seq of adult Tribolium castaneum muscle [Tca_Muscle_b]

description: Pooled muscle from adult individuals

source_name: Adult muscle

value: Muscle


title: 41979-IP-pool-2_7


title: RNA-seq of adult Tribolium castaneum ovaries [Tca_Ovary_b]

description: Pooled ovaries from adult individuals

source_name: Adult ovaries

value: Ovaries


title: 41979-IP-pool-2_1


title: 41979-IP-pool-2_3


title: 41979-IP-pool-2_5


title: control_129


title: control_128


title: 41978-IP-pool-1_7


title: 41978-IP-pool-1_5


title: 41978-IP-pool-1_3


title: RNA-seq of adult Tribolium castaneum muscle [Tca_Muscle_a]

description: Pooled muscle from adult individuals


title: RNA-seq of adult Tribolium castaneum malpighian tubes [Tca_MalpighianTubes_b]

description: Pooled malpighian tubes from adult individuals

source_name: Adult malpighian tubes

value: Malpighian tubes


title: control_127


title: NHD13/Tet2-KO rep4

data_processing:
Initial WES was carried out to identify mutations in gene exomes. Three NHD13/Tet2fl/fl and five NHD13/Tet2fl/fl/Mx1-Cre mice from the same pair of breeders (NHD13/Tet2fl/fl and Tet2fl/fl/Mx1-Cre) were used to exclude the confounding results of germline mutations
Genomic DNA was captured with the Agilent SureSelect all mouse exon probes according to the manufacturer’s protocol. 100-bp paired-end sequencing was performed using an Illumina HiSeq 2500 system
Raw sequencing reads were mapped to the whole mouse genome (mm10) using PEMapper/PECaller (https://github.com/wingolab-org/pecaller) with default settings, and variant bases were annotated with SeqAnt (http://seqant.genetics.emory.edu/
Post to the removal of adapters using Trimmomatic, reads were aligned back to mouse mm10 reference genome using BWA
samtools was used to pileup depth from the post-processing alignment, while VarScan to call variants and indels with the following options, --min-reads2 3 --min-var-freq 0.005 --p-value 1.0.

extract_protocol:
precapture libraries were prepared with KAPA DNA Hyper prep kit, capture probe was SureSelext XT Mouse All exon kit (Agilent)
WES seq

tag: age

value: 20 weeks old


title: control_131


title: control_126


title: NHD13/Tet2-KO rep3


title: NHD13/Tet2-KO rep2


title: NHD13/Tet2-KO rep1


title: RNA-seq of adult Tribolium castaneum ovaries [Tca_Ovary_a]

description: Pooled ovaries from adult individuals


title: RNA-seq of adult Tribolium castaneum guts [Tca_Gut_c]

description: Pooled guts from adult individuals

source_name: Adult guts

value: Guts


title: control_125

value: peripheral white blood cells


title: NHD13/Tet2-WT rep3


title: control_144

value: control


title: RNA-seq of adult Tribolium castaneum guts [Tca_Gut_a]

description: Pooled guts from adult individuals


title: NHD13/Tet2-WT rep2


title: NHD13/Tet2-WT rep1


title: control_124

value: male


title: aortae from Favine/ApoE DKO mice_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: aortae from apoE knockout mice without Favine

data_processing:
Sequencing was performed on an Illumina HiSeq2500 platform in a 75-base single-end mode.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: aortae from Favine/ApoE DKO mice

extract_protocol:
Total RNA was isolated from the liver tissues using the Rneasy® Mini Kit (QIAGEN, Hilden, Germany)。
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cell line

value: aortae

value: Favine/ApoE DKO


title: NHD13/Tet2-KO rep5


title: 41978-IP-pool-1_1


title: control_123


title: control_122

value: female


title: aortae from Favine/ApoE DKO mice_rep1


title: RNA-seq of adult Tribolium castaneum fat body [Tca_FatBody_a]

description: Pooled fat body from adult individuals

source_name: Adult fat body

value: Fat body


title: RNA-seq of adult Tribolium castaneum malpighian tubes [Tca_MalpighianTubes_a]


title: aortae from ApoE KO mice_rep3

description: aortae from apoE knockout mice with Favine

source_name: aortae from ApoE KO mice

value: ApoE KO


title: RNA-seq of adult Tribolium castaneum epidermis [Tca_Epithelium_b]

description: Pooled epidermis from adult individuals

source_name: Adult epidermis

value: Epidermis


title: control_121


title: aortae from ApoE KO mice_rep2


title: aortae from ApoE KO mice_rep1


title: control_120


title: deltaRing1A/B EPC. rep3

city: Yokohama

first: Osamu

last: Masui

address: 1-7-22 Suehirocho, Tsurumi

department: IMS

institute: RIKEN

data_processing:
Allele specific RNA-seq analysis was performed as described previously (Sakata et al., 2017) by constructing the B6-ChrXTMSM specific reference. After trimming away any portion of the SMARTer adaptor sequences and the first two bases of read 1 (an error-prone stretch caused by random hexamer priming during library preparation), paired-end reads were mapped to the custom reference as single-end reads. For each gene, the number of B6 (maternal) and MsM (paternal) allele-specific reads were counted and ratios of expression from paternal alleles were calculated. We considered genes with more than 10 allele-specific reads as informative. In initial analysis, we noticed that Tmsb4x and Tsix showed aberrant data due to a error-prone variant and incompleteness of strand specificity, respectively. Therefore, those two genes were omitted from further analysis.
The numbers of maternal and paternal allele-specific reads for each gene were counted using custom scripts.
Gene expression was quantified in a non-allelic manner using Cufflinks v2.2.1 cuffdiff with option '--library-type ff-firststrand --multi-read-correct'.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes patRatio (the ratio of the number of paternal reads to the number of total allele specific reads), asReads (the total number of allele-specific reads), and FPKM values for each sample.

source_name: Ectoplacental cone

extract_protocol:
Dissected ectoplacental cones of E7.5 embryos either from control (Ring1A-/-, Ring1Bfl/fl) or ∆Ring1A/B (Ring1A-/-, Ring1Bdl/dl were used for total RNA extraction using All-prep DNA/RNA micro kit (Qiagen).
RNA-seq libraries were prepared with the SMARTer Stranded Total RNA-seq Kit v2 using 10 ng total RNA and sequenced by the HiSeq 2500 as 100 bp paired-end.

treatment_protocol: Tamoxifen was intraperitoneally injected to pregnant mother at E5.5 to induce CreERT2-dependent Ring1B inactivation.

value: C57BL/6 B6-ChrXT^MSM

tag: developmental stage

tag: tissues

value: Ectoplacental cone


title: RNA-seq of adult Tribolium castaneum epidermis [Tca_Epithelium_a]

description: Pooled epidermis from adult individuals

value: Tcas5.2 GTF (enriched from Ensembl metazoa v45)


title: deltaRing1A/B EPC. rep2


title: control_119

source_name: peripheral white blood cells


title: RNA-seq of adult Tribolium castaneum fat body [Tca_FatBody_b]

description: Pooled fat body from adult individuals


title: RNA-seq of adult Tribolium castaneum brain [Tca_Brain_e]

description: Pooled brains from adult individuals

source_name: Adult brain

value: Brain


title: Control EPC. rep3


title: RNA-seq of adult Tribolium castaneum brain [Tca_Brain_d]

description: Pooled brains from adult individuals


title: control_118


title: deltaRing1A/B EPC. rep1


title: Control EPC. rep2


title: aortae from Favine/ApoE DKO mice_rep2


title: control_117


title: RF_plate3_B03_S15

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

library_source: transcriptomic single cell

data_processing:
Reads were aligned to hg19 (Gencode v21) using Top Hat and estimated counts and transcripts per million (TPM) matrices generated using RSEM. Any samples with fewer than 5x10E5 or more than 6x10E6 aligned reads or fewer than 10,000 uniquely ex-pressed genes were removed from subsequent analysis.
Assembly: hg19
Supplementary files format and content: Tab-separated gene-by-cell TPM matrix

source_name: tonsil

extract_protocol:
Libraries were prepared using a modified SMART-Seq2 protocol as previously reported . In brief, based on FACS analysis (BD FACSAria™), single cells of Tetramer+ (HIV or CMV-specific), and tetramer- cells (bulk/total CD8+ T-cells), were sorted into wells onto 96-well plates with lysis buffer, which contained 1 µl 10 mM dNTP mix, 1 µL 10 µM oligo dT primer, 1.9 µl 1% Triton X-100 (Sigma) plus 0.1 µl 40 U/µl RNase Inhibitor.
The sealed plates were stored frozen at -80°C. Thawed plate is incubated for 3 min at 72°C and placed on ice. Next, SMART-Seq2 Whole Transcriptome Amplification (WTA) was performed: 7 µL of RT mix was added to each well and RT was carried out; then, 14 µL of PCR mix was added to each well and PCR was performed. Thereafter a cDNA cleanup was performed using 0.6x and 0.8x volumes of Agencourt AMPure XP SPRI beads (Beckman Coulter) to eliminate short fragments (less than 500 bp). Libraries were then quantified using a Qubit dsDNA HS Assay Kit (Life Technologies). Library size and quality were measured by Bioanalyzer using a High Sensitivity DNA Analysis Kit (Agilent Technologies). Sequencing libraries were prepared from WTA products using Nextera XT (Illumina). After library construction, a final AMPure XP SPRI clean-up (0.8 volumes) was conducted. Library concentration and size were measured with the KAPA Library Quantification kit (KAPA Biosystems) and a Tape Station (Agilent Technologies), respectively. Library was then constructed using Nextera XT DNA library preparation kit (Illumina FC-131-1096) using index primer. After library construction, sequences were purified using a 0.8X SPRI ratio yielding library sizes with an average distribution of 500-750 pb in length as determined using an Agilent hsD5000 Screen Tape System (Agilent Genomics). Finally, samples were sequenced on a NextSeq500 (30 bp paired-end reads) to an average depth of 5 million reads.

value: T cell

tag: disease state

value: HIV

value: tonsil


title: RF_plate6_F02_S158


title: RF_plate6_H07_S187


title: Treg naive spleen 1

description:
GFP_plus_1
Treg cells in spleen of naive mice.

value: Female

value: Spleen

value: Treg

value: Naive


title: control_116

value: peripheral white blood cells

value: control

value: male


title: RNA-seq of adult Monodelphis domestica skin [Mdo_Skin_a]

description: Epidermis from an adult individual

organism: Monodelphis domestica

source_name: Adult skin

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: monDom5 GTF (enriched from Ensembl v86)


title: RF_plate6_F01_S157


title: RF_plate6_H04_S184


title: RNA-seq of adult Aede aegypti muscle [Aae_Muscle_a]

description: Pooled muscle from adult individuals

organism: Aedes aegypti

value: Muscle

value: AaegL5 GTF (enriched from Ensembl Metazoa v46)


title: RNA-seq of adult Aedes aegypti epidermis [Aae_Epidermis_a]

description: Pooled epidermis from adult individuals

value: Epidermis


title: control_114

value: female


title: RF_plate6_H01_S181


title: RF_plate6_F12_S168


title: RF_plate6_H05_S185


title: RF_plate3_B07_S19


title: RF_plate6_D12_S144


title: Control EPC. rep1

value: C57BL/6 B6-ChrXT^MSM

value: Ectoplacental cone


title: RF_plate3_A01_S1

value: T cell


title: RF_plate6_E01_S145

value: HIV


title: RF_plate6_F07_S163

value: tonsil


title: control_111


title: control_112


title: RF_plate6_G11_S179


title: RNA-seq of adult Monodelphis domestica skin [Mdo_Skin_b]

description: Epidermis from an adult individual


title: RF_plate6_B10_S118


title: RF_plate6_G05_S173


title: control_110


title: control_115


title: RF_plate6_G04_S172


title: control_109


title: RF_plate6_E08_S152


title: control_113


title: control_108


title: RF_plate3_B04_S16


title: RF_plate6_F04_S160


title: control_107


title: RF_plate6_F03_S159


title: RF_plate3_A08_S8


title: control_106


title: control_105


title: RF_plate6_B07_S115


title: RF_plate3_A10_S10


title: RF_plate6_E03_S147


title: RF_plate3_A12_S12


title: control_104


title: RF_plate6_G03_S171


title: RF_plate6_G01_S169


title: RF_plate6_E02_S146


title: control_103


title: RF_plate6_A03_S99


title: control_102


title: RF_plate6_E12_S156


title: RF_plate6_H08_S188


title: control_101


title: RF_plate6_C12_S132


title: RF_plate6_A02_S98


title: RF_plate6_A05_S101


title: RF_plate6_B04_S112


title: control_99


title: control_100


title: RF_plate6_A06_S102


title: LT48

city: Hamburg

first: Krystian

middle: Daniel

last: Fita

address: Martinistrasse 52

department: Department of Neurosurgery

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
spinal MNG tumor DNA from FFPE sections
spinal MNG

hyb_protocol: Bisulfite treatment, whole-genome DNA amplification, hybridization and single-base extension, fluorescence staining and scanning of the chips were performed following the manufacturer´s instructions (Illumina).

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

data_processing: For methylation profiling, loading and normalization was performed using the R package chAMP (v. 2.24.0). The BMIQ method was used for normalization. 850K data sets were merged with 450K data sets. For genomic copy number variation profiling, the R packages minfi (v. 1.40.0) and conumee (v. 1.28.0, parameter undo.SD = 1.5) were used for loading and processing.

label: Cy3 and Cy5

source_name: spinal meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Sample DNA was extracted from FFPE sections according to the manufacturer´s instructions (Illumina).

value: f

tag: histology

value: psammomatous

value: int-A

value: yes


title: RF_plate6_E11_S155


title: RF_plate6_E04_S148


title: LT49

value: transitional


title: RF_plate3_A05_S5


title: control_98

value: peripheral white blood cells

value: control


title: RF_plate6_G06_S174


title: control_97


title: LT46


title: RF_plate6_B11_S119


title: control_96


title: spRef07

value: atypical

value: subtotal

value: no


title: LT44


title: spRef06

value: m

value: mal


title: LT47

value: meningotheliomatous


title: LT45

value: angiomatous


title: RF_plate6_H06_S186

value: T cell


title: RF_plate6_B09_S117

value: HIV


title: control_93

value: male


title: spRef05

tag: recurrence


title: RF_plate6_G08_S176

tag: cell type

value: tonsil


title: RF_plate6_B06_S114


title: control_92


title: SMH38

value: f

value: psammomatous


title: SMH37

value: yes


title: RF_plate6_H03_S183


title: SMH36


title: RF_plate6_E09_S153


title: SMM34

value: complete

value: int-A


title: control_94

value: peripheral white blood cells

value: control


title: SMH39


title: spRef04


title: RF_plate3_A04_S4


title: control_91


title: RF_plate6_A01_S97


title: SMM32


title: SMM35


title: control_90


title: RF_plate6_F11_S167


title: RF_plate3_A06_S6


title: RF_plate6_C10_S130


title: RF_plate6_E05_S149


title: control_95

value: female


title: control_89


title: RF_plate6_A04_S100


title: RF_plate6_F08_S164


title: RF_plate6_F09_S165


title: control_88


title: control_87


title: RF_plate3_B05_S17


title: RF_plate3_B01_S13


title: RF_plate3_B06_S18


title: control_86


title: RF_plate6_G07_S175


title: RF_plate6_G02_S170


title: RF_plate6_E06_S150


title: RF_plate6_F05_S161


title: SMM29

value: no


title: control_84


title: RF_plate3_A03_S3


title: RF_plate3_A02_S2


title: RF_plate6_H02_S182


title: SMM27

value: m


title: RF_plate3_B02_S14


title: SMM30


title: SMM31


title: RF_plate6_F06_S162


title: SMM25


title: SMM28


title: plate1_E07_S55


title: RF_plate6_E07_S151


title: control_82


title: plate4_C05_S221


title: plate4_F02_S254


title: control_81


title: control_83


title: plate5_G11_S371


title: control_80


title: control_85


title: plate2_D02_S134


title: SMM33


title: plate1_E03_S51


title: SMM23


title: plate2_C11_S131


title: control_79


title: control_78


title: plate1_E05_S53


title: plate5_A02_S290


title: SMM24


title: SMM21


title: plate1_E01_S49


title: control_77


title: plate4_F06_S258


title: SMM22


title: plate2_A04_S100


title: plate4_G03_S267


title: control_76


title: SMM26


title: RF_plate3_A07_S7


title: SMH19


title: plate2_C10_S130


title: control_75


title: plate1_D05_S41


title: control_74


title: plate1_A09_S9


title: control_73


title: plate1_A01_S1


title: control_72


title: plate5_F06_S354


title: plate2_C07_S127


title: plate5_E02_S338


title: SMH17

value: atypical


title: SMH16


title: plate4_F08_S260


title: control_71


title: SMH15

value: meningotheliomatous


title: plate2_D12_S144


title: plate5_F11_S359


title: control_70


title: plate2_G02_S170


title: plate4_D03_S231


title: control_69


title: plate4_G09_S273


title: SMH14


title: plate4_A04_S196


title: SMH13rec

description:
spinal MNG tumor DNA from FFPE sections
spinal MNG recurrence

value: transitional


title: SMH18

value: fibroblastic


title: plate4_D09_S237

value: T cell

value: HIV


title: control_67


title: plate5_C03_S315

value: tonsil


title: plate4_F01_S253


title: control_66


title: plate2_A12_S108


title: SMH12

value: f


title: SMH08


title: plate4_G12_S276


title: plate4_F12_S264


title: plate5_G02_S362


title: plate1_G04_S76


title: plate4_E11_S251


title: control_64


title: SMH11


title: 4th_Eff_Male_3

city: Beijing

first: Jinchun

last: Wu

address: No. 5, Yiheyuan street

country: China

institute: Peking University

data_processing:
Libraries were analyzed by PEM-Q pipeline as described in Liu et al., 2021.
Assembly: mm10_pSIN, which combined the retrovirus genome to mm10
Supplementary files format and content: tab files as described in Liu et al., 2021

source_name: intestine

growth_protocol: T cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 100 mM non-essential amino acids (NEAA), 50 U/mL penicillin, 50 mg/mL streptomycin, and 50 mM b-mercaptoethanol without further indication.

extract_protocol:
cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted and transfected into Rag1-/- recipient mice, after 21 days, recipients were sacrificed and inflammatory T cells from intestine were sorted by CD90.1 and extract DNA
20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).

treatment_protocol: For retroviral vector (RV) experiment, TCR transgenic naïve CD4+ T cells were sorted from an HH7-2tg Cas9 mouse, then activated under TH0 condition with plated coated a-mouse CD3e (0.25 mg/mL, BioXcell) and a-mouse CD28 (1 mg/mL, BioXcell) for 2 days, the medium was supplemented with 1 mg/mL a-mouse IFNg (BioXcell), 1 mg/mL a-mouse IL-4 (BioXcell), 20 U/mL hIL-2 (Peprotech) and 1 mg/ml a-TGFβ (BioXcell) to prevent TH1, TH2 or TH17 polarization. Activated T cells were transfected with pST-sgRNA RV in the presence of 8 mg/mL polybrene during spin infection (2,000 g for 120 min at 33 ºC) and then rested for 3 days in medium containing 20 U/mL hIL-2 (Peprotech), 1 mg/mL a-TGFβ (BioXcell), 5 ng/mL mouse IL-7 (Sinobio), 1 mg/mL a-mouse IFNg (BioXcell) and 1 mg/mL a-mouse IL-4 (BioXcell). CD90.1 positive activated T cells were sorted and transferred into Rag1–/– recipient mice, with 300,000 cells for 1 recipient through i.v. tail. After 21 days, recipients were sacrificed and dissected to get intestinal tissues. Intestinal tissues were washed by PBS with 1 mM DTT for 10 min, followed by 5 mM EDTA for 20 min to remove epithelial cells, then treated by RPMI with collagenase (1 mg/mL collagenase; Roche), DNase I (100 μg/mL; Sigma), dispase (0.05 U/mL; Worthington) and 10% FBS at 37ºC for 60 min with constant mixing. Leukocytes were collected by 40-80% Percoll gradient. Inflammatory T cells were sorted with CD45.1+ and CD90.1+ for PEM-seq analysis.

tag: transfection

value: pST-sgRNA

tag: treatment

value: Rag1-/- NM


title: control_68

tag: tissue

tag: diagnosis


title: SMH10

tag: Sex

value: complete

value: yes


title: plate4_F05_S257


title: 4th_Eff_Male_2

tag: strain

value: activated by a-CD3/CD28, a-IFNg, and a-IL-4

tag: genotype


title: control_63

value: peripheral white blood cells

value: control


title: plate2_H07_S187


title: SMH07

value: psammomatous

value: no


title: 4th_Eff_Male_1


title: SMH06

value: int-A


title: 4th_Eff_Female_4


title: plate2_C03_S123


title: plate1_F04_S64


title: plate5_B12_S312


title: control_61

value: male


title: plate2_E01_S145


title: control_59


title: SMH05rec


title: plate1_C01_S25


title: control_58

value: female


title: plate2_D06_S138


title: 4th_Eff_Female_3


title: SMH05

value: transitional

value: subtotal

value: int-B


title: 4th_Eff_Female_2


title: control_60


title: plate4_H05_S281

value: T cell

value: HIV

value: tonsil


title: plate2_C08_S128


title: plate2_F03_S159


title: SMH02

value: m

value: meningotheliomatous


title: SMH09

value: f

value: clear cell

value: complete


title: control_57

value: peripheral white blood cells

value: control


title: control_56


title: plate2_F09_S165


title: plate5_C12_S324


title: SMH06rec

value: yes


title: SMH01

value: psammomatous

value: no

value: int-A


title: control_55

value: female


title: plate5_G08_S368


title: 2nd_Eff_2months_11

extract_protocol:
cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted and transfected into Rag1-/- recipient mice, after 2 months, recipients were sacrificed and inflammatory T cells from intestine were sorted by CD90.1 and extract DNA
20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).

value: pST-sgRNA

value: Rag1-/- NM


title: control_54


title: 2nd_Eff_2months_9

value: activated by a-CD3/CD28, a-IFNg, and a-IL-4


title: plate1_B08_S20

value: T cell

value: HIV


title: control_53


title: plate1_E09_S57

value: tonsil


title: plate4_E10_S250


title: control_62


title: control_65


title: 2nd_Eff_3weeks_7


title: plate5_E04_S340


title: 2nd_Eff_3weeks_6


title: plate5_B04_S304


title: plate4_E05_S245


title: plate2_D09_S141


title: plate2_C04_S124


title: 2nd_Eff_3weeks_5


title: plate4_F09_S261


title: 2nd_Eff_2months_10


title: SMH03

value: meningotheliomatous


title: plate4_B09_S213


title: 2nd_Eff_2months_8


title: control_50


title: control_51


title: 2nd_Activated_T

source_name: spleen

extract_protocol:
cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted, and extract DNA
20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).

value: HH7-tg Cas9 CD45.1


title: control_52

value: male


title: plate5_H03_S375


title: plate1_A04_S4


title: plate1_A10_S10


title: control_49


title: 3rd_Naive_T_myc6

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted and transcfected into Rag1-/- recipient mice, after 21 days,recipients were sacrificed and inflammentory T cells from gut were sorted by CD90.1 and extract DNA

data_processing:
Libraries were analized by PEM-Q pipeline as described in Liu et al., 2021.
Assembly: mm10_pSIN, which combined the retrovirus genome to mm10
Supplementary files format and content: tab files as described in Liu et al. ,2021

extract_protocol: 20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).


title: 3rd_Effector_Female_2

source_name: gut


title: plate2_F06_S162


title: plate1_C06_S30


title: control_48


title: plate5_B01_S301


title: 3rd_Effector_Female_1


title: plate2_E04_S148


title: control_47


title: control_46


title: plate5_F08_S356


title: plate2_E08_S152


title: 3rd_Activated_T_myc6_rp2

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted, and extract DNA

value: Activated by a-CD3/CD28, a-IFNg, and a-IL-4


title: plate5_D01_S325


title: plate4_C09_S225


title: plate2_H01_S181


title: plate2_G11_S179


title: 1st_Effector_T_4_cMyc

extract_protocol:
cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, activated by a-CD3/CD28, a-IFNg, and a-IL-4 for 2days, and transfected with retrovirus with pST-sgRNA for 3days, CD90.1 positive activated T cells were sorted and transcfected into Rag1-/- recipient mice, after 21 days,recipients were sacrificed and inflammentory T cells from gut were sorted by CD90.1 and extract DNA
20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).


title: control_44

value: peripheral white blood cells


title: plate4_D06_S234


title: control_43

value: control


title: plate4_H03_S279


title: control_42


title: plate5_G09_S369


title: plate1_C02_S26


title: 3rd_Activated_T_myc6_rp1

description: cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, and extract DNA


title: 1st_Effector_T_1_cMyc


title: 1st_Effector_T_3_cMyc


title: 1st_Effector_T_2_cMyc


title: plate4_E08_S248


title: control_41


title: plate5_G12_S372


title: 1st_Naïve_T_primer_control_cMyc

extract_protocol:
cells sorted by CD3+ CD4+ CD45.1+ TCR-Vb6+ CD62L+ CD44- CD25-, and extract DNA
20 mg of genomic DNA from the naïve, activated, and inflammatory T cells was fragmented to be 300 bp in size by sonication. DNA fragments were applied to a Bst polymerase 3.0 (NEB) mediated one-round of liner primer extension with a biotinylated primer targeting the on-target site in the first intron of c-Myc. After that, the excessive biotinylated primers were removed by AxyPrep Mag PCR Clean-Up beads (Axygen). DNA was denatured at 95℃ for 5 min, immediately chilled on ice for 3 min, and incubated with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) for 2-4 hours. The C1 beads were thoroughly washed by 1x B&W buffer (5 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA), 10 mM NaOH, 10 mM Tris-HCl, and then subjected to be ligated with a bridge adapter containing random molecular barcodes. After overnight incubation, the ligated DNA on C1 beads was thoroughly washed by 1x B&W buffer and 10 mM Tris-HCl, and tagged with Illumina adapter sequences. DNA ranging from 300-700 bp were recovered and sequenced on a Hiseq platform (2 x 150 bp).


title: control_45


title: 1st_Activated_T_cMyc


title: plate2_A03_S99


title: control_40


title: control_39


title: plate1_A03_S3


title: plate5_G05_S365


title: plate1_B01_S13


title: plate4_D07_S235


title: plate2_C06_S126


title: control_38


title: plate5_B02_S302


title: Uterus, Restf/f amhr2+/Cre - rep 4

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
base calling was performed using Illumina’s bcl2fastq2 software
the RNA-Seq reads were mapped to the mouse reference genome (GRCm38) using STAR-2.5.2b.
transcript abundance estimates were calculated uing Cufflinks 2.2.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file of FPKM values for each Sample

source_name: Uterus

extract_protocol:
RNA isolation from whole uteri of Restf/f Amhr2+/cre cKO (n=3) and restf/f mice (n=3) aged 4 months was performed using phenol: chloroform extraction.
Total RNA was used to construct RNA-seq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (cat#RS-122-2001/RS-122-2002) according to manufacturer's instructions

tag: tisue

value: Uterus

value: Restf/f amhr2+/Cre


title: plate2_A10_S106


title: Uterus, Restf/f amhr2+/Cre - rep 3


title: plate4_H04_S280


title: plate4_H02_S278


title: plate1_B10_S22


title: plate2_C01_S121


title: Uterus, Restf/f amhr2+/Cre - rep 2


title: control_37


title: plate5_A04_S292


title: plate2_E12_S156


title: control_36


title: Uterus, restf/f - rep 4

value: restf/f


title: plate1_F06_S66


title: plate4_E02_S242


title: 4th_Eff_Female_1


title: plate2_D11_S143


title: Uterus, restf/f - rep 3


title: plate4_C02_S218


title: Uterus, restf/f - rep 2


title: control_33


title: mupi-serum-3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Klebsiella_pneumoniae_NJST258_2_and_plasmids_from_NJST258_1 using Bowtie2
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2  (Love et al., 2014)
Assembly: Klebsiella_pneumoniae_NJST258_2_and_plasmids_from_NJST258_1
Supplementary files format and content: normalized_counts.txt are from deseq2 in matrix format

organism: Klebsiella pneumoniae

source_name: Klebsiella pneumoniae NJST258

growth_protocol: All strains were routinely cultured in Luria-Bertani (LB) broth.

extract_protocol:
Total RNA was isolated from the samples using the RNeasy Mini kit (Qiagen).
RNA was prepared for NGS sequencing using the Illumina Stranded Total RNA Prep Ligation with Qiagen FastSelect -5s/16s/23s

value: Klebsiella pneumoniae NJST258

value: Mupirocin + serum


title: plate4_C04_S220


title: control_32

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

value: female


title: plate5_B09_S309


title: doxy-serum-3

value: Doxycycline + serum


title: plate1_B07_S19


title: LB-serum-3

value: LB + serum


title: plate2_A09_S105

value: T cell


title: control_30


title: control_35


title: control_29


title: plate2_G05_S173

value: HIV


title: doxy-3

value: Doxycycline


title: plate4_B02_S206

value: tonsil


title: control_28


title: plate4_H07_S283


title: plate1_A07_S7


title: control_34


title: plate4_B05_S209


title: LB-3

value: LB


title: plate4_C08_S224


title: control_27

value: male


title: plate2_E11_S155


title: mupi-serum-2


title: plate2_G04_S172


title: control_26


title: plate2_C12_S132


title: control_25


title: plate5_B07_S307


title: plate5_C02_S314


title: control_31


title: control_24


title: mupi-3

value: Mupirocin


title: LB-serum-2


title: plate4_H12_S288


title: plate4_C06_S222


title: mupi-2


title: plate2_B09_S117


title: plate1_F02_S62


title: doxy-2


title: control_22

value: peripheral white blood cells


title: LB-2


title: plate2_B10_S118


title: plate4_H06_S282


title: plate5_G01_S361


title: plate4_G07_S271


title: plate4_D01_S229


title: control_21

value: control


title: mupi-serum-1


title: plate4_A09_S201


title: control_20


title: plate4_D12_S240


title: plate1_F01_S61


title: doxy-serum-1


title: plate2_B12_S120


title: control_23


title: plate2_F01_S157


title: LB-serum-1


title: control_18


title: mupi-1


title: plate4_D02_S230


title: plate4_D04_S232


title: plate5_B11_S311


title: plate4_A01_S193


title: control_17


title: doxy-1


title: plate1_F10_S70


title: plate1_B05_S17


title: plate2_H09_S189


title: WCS365DcolR_media_rep3

city: Vancouver

first: Chrisitna

middle: L

last: Wiesmann

state: British Columbia

address: 1365 - 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: The University of British Columbia

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

organism: Pseudomonas fluorescens

source_name: plant growth promoting Pseudomonas bacteria

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions and stored in RNAprotect Bacteria Reagent (Qiagen) if extraction was not perfomed immediately.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.

tag: background strain

value: grown in M9 minimal media


title: plate2_H05_S185


title: control_15


title: control_13


title: plate4_G01_S265


title: plate4_A06_S198


title: control_14


title: WCS365DcolR_media_rep2


title: control_19


title: WCS365DcolR_media_rep1


title: plate2_G07_S175


title: control_12


title: control_16


title: control_11


title: LB-1


title: plate1_B03_S15


title: plate2_A06_S102


title: WCS365DcolR_plant_rep3

value: grown in Arabidopsis rhizosphere


title: WCS365DcolR_plant_rep2


title: plate2_F04_S160


title: WCS365DcolR_plant_rep1


title: control_9


title: plate2_F05_S161


title: plate1_A05_S5


title: plate2_C05_S125


title: plate1_G08_S80


title: plate2_C09_S129


title: plate4_H08_S284


title: control_8


title: control_7


title: WCS365WT_media_rep3

value: wild-type


title: WCS365WT_media_rep2


title: plate4_E09_S249


title: plate2_E02_S146


title: plate5_B10_S310


title: WCS365WT_media_rep1


title: doxy-serum-2

value: Klebsiella pneumoniae NJST258


title: plate2_B08_S116


title: plate4_D08_S236


title: WCS365WT_plant_rep3


title: plate1_C04_S28


title: control_5


title: plate4_G08_S272


title: control_6


title: WCS365WT_plant_rep2


title: control_4


title: plate4_G10_S274


title: plate4_F04_S256


title: plate4_C12_S228


title: WCS365WT_plant_rep1


title: plate5_A03_S291


title: control_3


title: CBP dsRNA Pho IP  Rep 2

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: CBP dsRNA Pho IP  Rep 2

data_processing:
ChIP-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. Duplicated and unmapped reads were removed using Picard. RPKM normalized ChIP-seq coverage tracks were generated using the deepTools. Bigwig files of the mean RPKM were produced using the deepTools comparebigwig tool.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage

organism: Drosophila melanogaster

source_name: Schneider 2 (S2) cells

growth_protocol: S2 cells were cultured at 25°C in Schneider's Drosophila medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 15 min at room temperature, quenched with 0.16 M glycine for 5 min at 4°C and washed in cold PBS. Crude nuclear extracts were obtained by sequentially washes with ChIP buffer A (10 mM HEPES pH 7.6, 10 mM EDTA pH 8.0, 0.5mM EGTA pH 8.0 and 0.25% Triton X-100) followed by ChIP buffer B (10mM HEPES pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 and 0.01% Triton X-100) to isolate nuclei. Nuclei were resuspended in Sonication buffer (15 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.1% sodium deoxycholate and 1% Triton X-100), with Complete Mini EDTA-Free protease inhibitor tablets, Roche) supplemented with 0.5% SDS and 0.2% n-lauroylsarcosine, at a final concentration of 5 – 10 x 107 cells/ml and sonicated in a Bioruptor (Diagenode) using high power settings to obtain an average fragment size distribution of 200–500 bp. The concentration of chromatin was quantified. Immunoprecipitations were performed by incubating 10 μg of chromatin with anti-CBP (homemade),  anti-E(z) (kind gift of Richard Jones, Southern Methodist University, USA) and anti-Pho (kind gift of Judith Kassis, National Institute of Health, USA) overnight. Chromatin-antibody complexes were bound to Protein A and G Dynabeads (Invitrogen) and washed sequentially with Wash A (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100), Wash B (Wash A adjusted to 500 mM NaCl), Wash C (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Sodium Deoxycholate and 0.5% IGEPAL CA-630) and Tris-EDTA (TE). Beads were resuspended in 100 μl TE, treated with RNase A (20 μg/ml) at 55°C for 30 min, supplemented with SDS (0.75%) and Tris (50 mM). and crosslinks reversed at 65°C overnight. Eluted ChIP DNA was treated with Proteinase K at 55°C for 2 h and purified using the ChIP DNA Clean & Concentrator kit (ZymoResearch, D5205).
Libraries were constructed from ChIP samples (2-5 ng) with the NEBNext Ultra II DNA Library Prep Kit (NEB) and single-end (1x75 bp) sequenced on an Illumina NextSeq 550 platform at the BEA core facility, Stockholm.

treatment_protocol: Experiments were conducted on cells at 80-90% confluency.Cells were resuspended in FCS free media and incubated with 37 nM of CBP or GFP dsRNA for 1 hr. FCS-containing media was added to the cells to achieve a final concentration of 10% FCS. Cells were incubated for 72 hr then treated with a second dose of dsRNA and incubated for a further 72 hr (D6).

value: Oregon R

value: Late embryonic stage

tag: antibody

value: rabbit anti-Pho (from Judith Kassis)

tag: spike-in


title: control_1

value: female


title: plate4_C10_S226

value: T cell


title: plate4_C11_S227

value: HIV


title: plate1_F03_S63


title: plate1_E10_S58


title: CBP dsRNA Pho IP  Rep 1

description: CBP dsRNA Pho IP  Rep 1

tag: developmental stage


title: plate5_A08_S296


title: plate4_B10_S214


title: plate4_B04_S208


title: RNA-seq of adult Octopus bimaculoides testis [Obi_Testis_H]

description: Testis from an adult individual

organism: Octopus bimaculoides

source_name: Adult testis

extract_protocol:
N/A
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Testis

tag: genome build

tag: gtf

value: PRJNA270931 enriched GTF


title: plate5_C05_S317

tag: disease state

value: tonsil


title: CBP dsRNA Ez IP  Rep 1

description: CBP dsRNA Ez IP  Rep 1

value: rabbit anti-E(z) (from Richard Jones)


title: plate1_C05_S29


title: CBP dsRNA Input  Rep 2

description: CBP dsRNA Input  Rep 2


title: RNA-seq of adult Octopus bimaculoides skin [Obi_Skin_H]

description: Skin from an adult individual

value: Skin


title: plate2_D03_S135


title: plate2_B11_S119


title: plate4_G05_S269


title: CBP dsRNA Input  Rep 1

description: CBP dsRNA Input  Rep 1


title: RNA-seq of adult Octopus bimaculoides kidneys [Obi_Kidney_H]

description: Kidney from an adult individual

source_name: Adult kidneys

value: Kidney


title: plate4_E12_S252


title: plate1_C07_S31


title: control_2

value: peripheral white blood cells

value: control

value: male


title: RNA-seq of adult Octopus bimaculoides guts [Obi_Gut_H]

description: Guts from an adult individual

source_name: Adult guts

value: Guts


title: CBP dsRNA CBP IP  Rep 2

description: CBP dsRNA CBP IP  Rep 2

value: rabbit anti-CBP (homemade)


title: plate4_F11_S263


title: plate2_B07_S115


title: CBP dsRNA CBP IP  Rep 1

description: CBP dsRNA CBP IP  Rep 1

value: Oregon R


title: plate4_C03_S219


title: plate4_A03_S195


title: plate4_B03_S207


title: GFP dsRNA Pho IP  Rep 2

description: GFP dsRNA Pho IP  Rep 2

value: Late embryonic stage


title: RNA-seq of Epysirphus balteatus testis [Eba_Testis_a]

description: Pooled testis from adult individuals

organism: Episyrphus balteatus

extract_protocol:
Trizol
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: JAGTYB010000000 enriched GTF


title: plate2_D10_S142


title: GFP dsRNA Pho IP  Rep 1

description: GFP dsRNA Pho IP  Rep 1

value: rabbit anti-Pho (from Judith Kassis)


title: plate5_E06_S342

value: T cell


title: GFP dsRNA Ez IP  Rep 2

description: GFP dsRNA Ez IP  Rep 2


title: plate4_G11_S275

value: HIV


title: RNA-seq of adult Octopus bimaculoides muscle [Obi_Muscle_H]

description: Muscle from an adult individual

source_name: Adult muscle

value: Muscle


title: CBP dsRNA Ez IP  Rep 2

description: CBP dsRNA Ez IP  Rep 2


title: RNA-seq of Epysirphus balteatus ovaries [Eba_Ovary_Mat_b]

description: Pooled ovaries from adult individuals

source_name: Adult ovaries

value: Ovary


title: plate4_A11_S203

value: tonsil


title: GFP dsRNA Ez IP  Rep 1

description: GFP dsRNA Ez IP  Rep 1

value: rabbit anti-E(z) (from Richard Jones)


title: RNA-seq of Epysirphus balteatus ovaries [Eba_Ovary_a]

description: Pooled ovaries from adult individuals


title: plate4_E04_S244


title: plate2_F12_S168


title: plate4_E06_S246


title: control_10

source_name: peripheral white blood cells


title: GFP dsRNA Input  Rep 1

description: GFP dsRNA Input  Rep 1


title: plate1_C12_S36


title: plate1_D04_S40


title: GFP dsRNA Input  Rep 2

description: GFP dsRNA Input  Rep 2


title: GFP dsRNA CBP IP  Rep 2

description: GFP dsRNA CBP  Rep 2


title: RNA-seq of Epysirphus balteatus muscle [Eba_Muscle_a]

description: Pooled muscle from adult individuals


title: plate5_A09_S297


title: plate4_C01_S217


title: RNA-seq of Epysirphus balteatus testis [Eba_Testis_b]

description: Pooled testis from adult individuals

value: Testis


title: plate5_F07_S355


title: plate2_E10_S154


title: GFP dsRNA CBP IP  Rep 1

description: GFP dsRNA CBP IP  Rep 1


title: plate2_B06_S114


title: plate1_F09_S69


title: RNA-seq of Epysirphus balteatus immature ovaries [Eba_Ovary_Inmat_b]

description: Pooled immature ovaries


title: RNA-seq of Epysirphus balteatus muscle [Eba_Muscle_b]

description: Pooled muscle from adult individuals


title: RNA-seq of Epysirphus balteatus guts [Eba_Gut_b]

description: Pooled guts from adult individuals

value: Gut


title: RNA-seq of Epysirphus balteatus malpighian tubes [Eba_MalpighianTubes_a]

description: Pooled malphighian tubes from adult individuals

source_name: Adult malpighian tubes

value: Malphighian tubes


title: plate4_C07_S223

source_name: tonsil


title: ATAC C646 4 h Rep 1

description: ATAC C646 4 h Rep 1

data_processing:
ATAC-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. Duplicated and unmapped reads were removed using Picard. To obtain the spike-in reads, we mapped the reads to the  Drosophila virilis (dvir_caf1) genome assembly and the D. melanogaster reads were normalized based on the ratio of D. virilis reads. From the spike-in adjusted data,  RPKM normalized ATAC-seq coverage tracks were generated using the deepTools. Bigwig files of the mean RPKM were produced using the deepTools comparebigwig tool.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage

extract_protocol:
Crude nuclear extracts were isolated from 100,000 untreated and C646-treated S2 cells by resuspension in ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1& IGEPAL CA-630) and centrifugation at 700 g for 10 min. 10,000 spike-in nuclei from 2-4 h D. virilis embryos  (dechorionated and crude nuclear extracts prepared by manual homogenization with a pestle in ATAC lysis buffer) were added to the S2 nuclear pellets which were resuspended in 22.5 μl ATAC lysis buffer, 2.5 μl Tn5 (Tagment DNA Enzyme 1(TDE1) (Illumina)) and 25 μl Tagment DNA Buffer (Illumina). Tagmentation was performed at 37°C for 30 min on a thermomixer at 1,000 rpm. The transposition reaction was stopped by addition of 1% SDS and DNA purified by the addition of Agencourt AMPure XP beads (Beckman Coulter A63881) at a 2:1 ratio of beads to sample. Purification was performed following the manufacturer’s instructions.
Tagmented DNA was PCR amplified using 1x Phusion® High-Fidelity PCR Master Mix with GC Buffer (NEB), 1.25 μM PCR Primer Cocktail (Illumina) and 1.25 μM Nextera PCR primers i5 and i7 (Nextera® Index Kit (Illumina)). PCR amplification conditions were: 72°C for 5 min, followed by 10 cycles of 98°C 10 seconds, 65°C 1 min and 15 seconds, then 72°C for 1 min. Amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter A63881) using a 1:5:1 ratio of bead to sample volume. Libraries were sequenced paired-end (2x 37 bp) on the Illumina NextSeq 550 platform at the BEA core facility, Stockholm.

treatment_protocol: Experiments were conducted on cells at 80-90% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 for 1 hr or 4 hr.

value: Drosophila virilis


title: ATAC C646 4 h Rep 2

description: ATAC C646 4 h Rep 2


title: plate4_F07_S259

extract_protocol:
Libraries were prepared using a modified SMART-Seq2 protocol as previously reported . In brief, based on FACS analysis (BD FACSAria™), single cells of Tetramer+ (HIV or CMV-specific), and tetramer- cells (bulk/total CD8+ T-cells), were sorted into wells onto 96-well plates with lysis buffer, which contained 1 µl 10 mM dNTP mix, 1 µL 10 µM oligo dT primer, 1.9 µl 1% Triton X-100 (Sigma) plus 0.1 µl 40 U/µl RNase Inhibitor.
The sealed plates were stored frozen at -80°C. Thawed plate is incubated for 3 min at 72°C and placed on ice. Next, SMART-Seq2 Whole Transcriptome Amplification (WTA) was performed: 7 µL of RT mix was added to each well and RT was carried out; then, 14 µL of PCR mix was added to each well and PCR was performed. Thereafter a cDNA cleanup was performed using 0.6x and 0.8x volumes of Agencourt AMPure XP SPRI beads (Beckman Coulter) to eliminate short fragments (less than 500 bp). Libraries were then quantified using a Qubit dsDNA HS Assay Kit (Life Technologies). Library size and quality were measured by Bioanalyzer using a High Sensitivity DNA Analysis Kit (Agilent Technologies). Sequencing libraries were prepared from WTA products using Nextera XT (Illumina). After library construction, a final AMPure XP SPRI clean-up (0.8 volumes) was conducted. Library concentration and size were measured with the KAPA Library Quantification kit (KAPA Biosystems) and a Tape Station (Agilent Technologies), respectively. Library was then constructed using Nextera XT DNA library preparation kit (Illumina FC-131-1096) using index primer. After library construction, sequences were purified using a 0.8X SPRI ratio yielding library sizes with an average distribution of 500-750 pb in length as determined using an Agilent hsD5000 Screen Tape System (Agilent Genomics). Finally, samples were sequenced on a NextSeq500 (30 bp paired-end reads) to an average depth of 5 million reads.


title: ATAC C646 1 h Rep 2

description: ATAC C646 1 h Rep 2


title: RNA-seq of Epysirphus balteatus guts [Eba_Gut_a]

description: Pooled guts from adult individuals


title: RNA-seq of Epysirphus balteatus fat body [Eba_FatBody_b]

description: Pooled fat bodies from adult individuals

source_name: Adult fat body

value: Fat body


title: plate1_A02_S2


title: plate4_D05_S233


title: RNA-seq of Epysirphus balteatus fat body [Eba_FatBody_a]


title: plate1_E02_S50


title: ATAC C646 1 h Rep 1

description: ATAC C646 1 h Rep 1


title: plate5_F04_S352


title: RNA-seq of Epysirphus balteatus malpighian tubes [Eba_MalpighianTubes_b]


title: plate2_F08_S164


title: ATAC NT Rep 2

description: ATAC NT Rep 2


title: ATAC NT Rep 1

description: ATAC NT Rep 1


title: plate4_G02_S266


title: plate1_D07_S43


title: plate1_A06_S6


title: RNA-seq of Epysirphus balteatus epidermis [Eba_Epidermis_a]

description: Pooled epidermis from adult individuals

source_name: Adult epidermis

value: Epidermis


title: plate1_F05_S65


title: plate1_C11_S35


title: C646 Input PcGs Rep 2

description:
C646 Input PcGs Rep 2
C646_R1_INPUT_PcGs_S4

data_processing:
ChIP-seq reads from each sequenced library were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 with the default parameters. Duplicated and unmapped reads were removed using Picard. To obtain the spike-in reads, we mapped the reads to the  Drosophila virilis (dvir_caf1) genome assembly and the D. melanogaster reads were normalized based on the ratio of D. virilis reads. From the spike-in adjusted data,  RPKM normalized ChIP-seq coverage tracks were generated using the deepTools. Bigwig files of the mean RPKM were produced using the deepTools comparebigwig tool.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for coverage

extract_protocol:
Cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 15 min at room temperature, quenched with 0.16 M glycine for 5 min at 4°C and washed in cold PBS. Crude nuclear extracts were obtained by sequentially washes with ChIP buffer A (10 mM HEPES pH 7.6, 10 mM EDTA pH 8.0, 0.5mM EGTA pH 8.0 and 0.25% Triton X-100) followed by ChIP buffer B (10mM HEPES pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 and 0.01% Triton X-100) to isolate nuclei. Nuclei were resuspended in Sonication buffer (15 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.1% sodium deoxycholate and 1% Triton X-100), with Complete Mini EDTA-Free protease inhibitor tablets, Roche) supplemented with 0.5% SDS and 0.2% n-lauroylsarcosine, at a final concentration of 5 – 10 x 107 cells/ml and sonicated in a Bioruptor (Diagenode) using high power settings to obtain an average fragment size distribution of 200–500 bp. The concentration of chromatin was quantified and spike-in chromatin from Drosophila virilis cells was added. Immunoprecipitations were performed by incubating 10 μg of chromatin with anti-CBP (homemade), anti-dRING (kind gift of Yuri Schwartz, Umeå Universitet, Sweden), anti-E(z) (kind gift of Richard Jones, Southern Methodist University, USA) and anti-Pho (kind gift of Judith Kassis, National Institute of Health, USA) overnight. Chromatin-antibody complexes were bound to Protein A and G Dynabeads (Invitrogen) and washed sequentially with Wash A (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 0.1% SDS, 0.1% Sodium Deoxycholate and 1% Triton X-100), Wash B (Wash A adjusted to 500 mM NaCl), Wash C (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% Sodium Deoxycholate and 0.5% IGEPAL CA-630) and Tris-EDTA (TE). Beads were resuspended in 100 μl TE, treated with RNase A (20 μg/ml) at 55°C for 30 min, supplemented with SDS (0.75%) and Tris (50 mM). and crosslinks reversed at 65°C overnight. Eluted ChIP DNA was treated with Proteinase K at 55°C for 2 h and purified using the ChIP DNA Clean & Concentrator kit (ZymoResearch, D5205).
Libraries were constructed from ChIP samples (2-5 ng) with the NEBNext Ultra II DNA Library Prep Kit (NEB) and single-end (1x75 bp) sequenced on an Illumina NextSeq 550 platform at the BEA core facility, Stockholm.

treatment_protocol: Experiments were conducted on cells at 80-90% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 or the inactive analog C37 for 30 minutes.


title: RNA-seq of Epysirphus balteatus brain [Eba_Brain_a]

description: Pooled brains from adult individuals

source_name: Adult brain

value: Brain


title: RNA-seq of Epysirphus balteatus brain [Eba_Brain_b]

description: Pooled brains from adult individuals


title: plate2_D04_S136


title: plate2_A11_S107


title: plate5_H06_S378


title: C646 Input PcGs Rep 1

description:
C646 Input PcGs Rep 1
C646_R1_INPUT_PcGs_S2

value: Oregon R


title: C646 Pho Rep 2

description:
C646 Pho Rep 2
C646_R2_Pho_S16

value: Late embryonic stage


title: plate4_E07_S247


title: plate1_F11_S71


title: C646 Pho Rep 1

description:
C646 Pho Rep 1
C646_R1_Pho_S14


title: RNA-seq of Epysirphus balteatus epidermis [Eba_Epidermis_b]

description: Pooled epidermis from adult individuals

value: JAGTYB010000000 enriched GTF


title: plate2_A02_S98


title: RNA-seq of adult Callorhinchus milii muscle [Cmi_Muscle_b]

description: Muscle from an adult individual

organism: Callorhinchus milii

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
polyA-selected stranded RNA-seq; RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cmi 6.1.3 GTF (enriched from Ensembl v99)


title: C646 E(z) Rep 2

description:
C646 E(z) Rep 2
C646_R2_Ez_S8


title: plate1_A11_S11

value: T cell


title: plate5_D02_S326

value: HIV


title: C646 E(z) Rep 1

description:
C646 E(z) Rep 1
C646_R1_Ez_S6


title: RNA-seq of adult Callorhinchus milii kidney [Cmi_Kidney_b]

description: Kidney from an adult individual

source_name: Adult kidney

value: Kidney


title: plate4_A12_S204


title: plate2_G10_S178


title: plate4_D10_S238


title: plate1_B09_S21


title: RNA-seq of adult Callorhinchus milii ovaries [Cmi_Ovary_b]

description: Ovary from an adult individual

value: Ovary


title: RNA-seq of adult Callorhinchus milii skin [Cmi_Epithelium_b]

description: Skin from an adult individual

source_name: Adult skin

value: Epithelium


title: RNA-seq of adult Callorhinchus milii brain [Cmi_Brain_b]

description: Brain from an adult individual

value: Neural


title: plate2_G08_S176

value: tonsil


title: plate4_G04_S268


title: C646 dRING Rep 2

description:
C646 dRING Rep 2
C646_R2_dRING_S12

value: rabbit anti-dRING (from Yuri Schwartz)


title: RNA-seq of adult Cloeon fat body [Cdi_FatBody_b]

organism: Cloeon dipterum

value: Fatbody


title: C646 dRING Rep 1

description:
C646 dRING Rep 1
C646_R1_dRING_S10

value: Drosophila virilis


title: C646 Input CBP Rep 2

description:
C646 Input CBP Rep 2
C646_R2_INPUT_S4


title: plate5_G07_S367


title: plate2_B02_S110


title: C646 Input CBP Rep 1

description:
C646 Input CBP Rep 1
C646_R1_INPUT_S2


title: RNA-seq of adult Cloeon fat body [Cdi_FatBody_a]


title: plate5_C04_S316


title: plate5_F09_S357


title: plate5_E01_S337


title: plate1_B06_S18


title: plate5_B03_S303


title: plate1_D10_S46


title: plate4_H09_S285


title: C646 CBP Rep 2

description:
C646 CBP Rep 2
C646_R2_CBP_S8

value: rabbit anti-CBP (homemade)


title: C646 CBP Rep 1

description:
C646 CBP Rep 1
C646_R1_CBP_S6


title: C37 Input PcGs Rep 2

description:
C37 Input PcGs Rep 2
C37_R2_INPUT_PcGs_S3


title: RNA-seq of adult Cloeon dipterum epidermis [Cdi_Epidermis_a]

description: Pooled epidermis from adult individuals

value: Epidermis


title: C37 Input PcGs Rep 1

description:
C37 Input PcGs Rep 1
C37_R1_INPUT_PcGs_S1


title: plate4_F10_S262


title: HCMV AD169 infected MRC5, dUL91 virus, MOI = 3, 72 HPI, rep 3

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

data_processing:
To process the RNA-seq data, a combined reference genome was generated from the X17403.1 HCMV genome and the human GRCh38 (release 104 ensembl) reference genome.
The RNAsik pipeline was run with the following parameters: ‘-align star -counts -paired -all’ and used the combined fasta file and gtf file as input for the ‘-fastaRef’ and ‘-gtfFile’ parameters.
Data quality control, filtering and differential expression (DE) analysis was performed using DEBrowser Shiny user interface (v1.21.1) (Kucukural et al., 2019) in R Studio (v4.1.1).
Low count filtering parameters were set to CPM < 3 in all 14 samples and normalised using Trimmed Mean of M-values (TMM). Batch effect correction was set to “none”. Relative log expression was plotted using the complete dataset with default settings.
DE analysis was performed between the 5 WT replicates and 3 replicates of each vPIC mutant sample with DE method: “Limma”, Normalization: “TMM”, Fit Type: “Is” and Norm. Bet. Arrays: “none” set.
Assembly: X17403.1 (HCMV), GRC38 ensembl release 104 (human)
Supplementary files format and content: NonStrandedCounts-withNames_hcmv_human.txt (counts table)

organism:
Homo sapiens
Human betaherpesvirus 5

growth_protocol: See manuscript

extract_protocol:
Samples were lysed in TRIzol at 72 HPI and total RNA extracted using the Direct-Zol MiniPrep kit (Zymo, R2050)
Sequencing libraries were prepared using an MGIEasy stranded mRNA kit
MGITech MGISEQ2000RS sequencer

treatment_protocol: See manuscript

value: fibroblast

tag: cell line

value: WT

tag: infection

value: dUL91 HCMV infected


title: HCMV AD169 infected MRC5, dUL91 virus, MOI = 3, 72 HPI, rep 2

tag: cell type


title: plate5_D09_S333


title: HCMV AD169 infected MRC5, dUL91 virus, MOI = 3, 72 HPI, rep 1


title: plate4_F03_S255


title: plate4_H01_S277


title: plate2_G12_S180


title: plate2_B01_S109


title: C37 Pho Rep 2

description:
C37 Pho Rep 2
C37_R2_Pho_S15

value: Oregon R

value: Late embryonic stage

value: rabbit anti-Pho (from Judith Kassis)


title: HCMV AD169 infected MRC5, dUL87 virus, MOI = 3, 72 HPI, rep 3

value: dUL87 HCMV infected


title: plate1_B04_S16

value: T cell

value: HIV


title: RNA-seq of adult Cloeon dipterum epidermis [Cdi_Epidermis_b]

description: Pooled epidermis from adult individuals


title: plate5_G10_S370


title: C37 E(z) Rep 2

description:
C37 E(z) Rep 2
C37_R2_Ez_S7

value: rabbit anti-E(z) (from Richard Jones)


title: HCMV AD169 infected MRC5, dUL87 virus, MOI = 3, 72 HPI, rep 2


title: C37 Pho Rep 1

description:
C37 Pho Rep 1
C37_R1_Pho_S13


title: plate1_B02_S14


title: plate4_A05_S197


title: C37 E(z) Rep 1

description:
C37 E(z) Rep 1
C37_R1_Ez_S5


title: HO44_PATOM_16 (biol rep 1)

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files of single-end RNA-Seq reads were aligned with STAR 2.6.0a  to the reference genome GRCh38 with 2-pass mode.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of gene level counts

source_name: Primary Tumor

extract_protocol:
mRNA extracted using the Qiagen Rneasy Micro Kit. 200 ng of total RNA according to manufacturers instructions for Illumina TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary Tumor

value: Pancreatic Ductal Adenocarcinoma

tag: treatment

value: PaTOM Media


title: HO107_WNT_P12 (biol rep 1)

source_name: Liver Metastasis

value: Liver Metastasis

value: WNT Media


title: HCMV AD169 infected MRC5, dUL54 virus, MOI = 3, 72 HPI, rep 3

value: dUL54 HCMV infected


title: plate4_D11_S239

tag: tissue

value: tonsil


title: HCMV AD169 infected MRC5, dUL54 virus, MOI = 3, 72 HPI, rep 2

value: fibroblast


title: C37 dRING Rep 2

description:
C37 dRING Rep 2
C37_R2_dRING_S11

value: rabbit anti-dRING (from Yuri Schwartz)

value: Drosophila virilis


title: plate2_C02_S122


title: HO228_WNT_PAX300_P21 (biol rep 1)

source_name: Patient-Derived Xenograft

value: Patient-Derived Xenograft


title: plate4_H10_S286


title: HCMV AD169 infected MRC5, dUL49 virus, MOI = 3, 72 HPI, rep 1

value: WT

value: dUL49 HCMV infected


title: HO228_WNT_PAX300_P23 (biol rep 3)


title: HCMV AD169 infected MRC5, dUL87 virus, MOI = 3, 72 HPI, rep 1

value: dUL87 HCMV infected


title: plate4_A10_S202

value: T cell


title: C37 Input CBP Rep 1

description:
C37 Input CBP Rep 1
C37_R1_INPUT_S1

source_name: Schneider 2 (S2) cells

value: Oregon R

value: Late embryonic stage


title: plate2_E07_S151

value: HIV


title: HCMV AD169 infected MRC5, dUL49 virus, MOI = 3, 72 HPI, rep 3


title: C37 CBP Rep 1

description:
C37 CBP Rep 1
C37_R1_CBP_S5

value: rabbit anti-CBP (homemade)


title: HO219_PATOM_PAX300_P18 (biol rep 1)

value: Pancreatic Ductal Adenocarcinoma

value: PaTOM Media


title: HCMV AD169 infected MRC5, WT virus, MOI = 3, 72 HPI, rep 5

value: WT HCMV infected


title: plate2_B04_S112


title: HCMV AD169 infected MRC5, WT virus, MOI = 3, 72 HPI, rep 4


title: Tonsil, CD3 sorted, Donor 2, scRNAseq

description: SeqWell

data_processing:
Raw sequencing data were converted to demultiplexed FASTQ files using bcl2fastq2 based on Nextera N700 indices corresponding to individual arrays. Reads were then aligned to hg19 genome assembly and aligned using the Dropseq-tools pipeline on Terra (app.terra.bio).
Assembly: hg19
Supplementary files format and content: Tab-separated cell-by-gene count matrices

extract_protocol:
Single cell suspensions were obtained from fresh biopsies of tonsils. Blood samples were processed from fresh peripheral blood  mononuclear cells (PBMCs) purified using Ficoll separation
Samples were prepared using  Seq-Well S3. Briefly,  15,000 cells in 200 mL RPMI + 10% FBS were loaded onto one  PDMS array preloaded with barcoded mRNA capture beads  (ChemGenes) and settled by gravity into distinct wells. The  loaded arrays were washed with PBS and sealed using a  polycarbonate membrane with a pore size of 0.01 µm, which  allows for exchange of buffers but retains biological molecules  within each nanowell. Arrays were sealed in a dry 37°C oven for  40 min and submerged in a lysis buffer containing guanidium  thiocyanate (Sigma), EDTA, 1% beta-mercaptoethanol and  sarkosyl (Sigma) for 20 min at room temperature. Arrays were  transferred to hybridization buffer containing NaCl (Fisher  Scientific) and supplemented with 8% (v/v) polyethylene glycol  (PEG, sigma) and agitated for 40 min at room temperature,  mRNA capture beads with mRNA hybridized were collected  from each Seq-Well array, and beads were resuspended in a  master mix for reverse transcription containing Maxima H  Minus Reverse Transcriptase (ThermoFisher EP0753) and  buffer, dNTPs, RNase inhibitor, a 50 template switch  oligonucleotide, and PEG for 30 min at room temperature,  and overnight at 52°C with end-over-end rotation.  Exonuclease I treatment (New England Biolabs M0293L) was  used to remove excess primers. After exonuclease digestion,  bead-associated cDNA denatured for 5 min in 0.2 mM NaOH  with end over end rotation. Next, beads were washed with TE +  0.01% tween-20, and second strand synthesis was carried out by  resuspending beads in a master mix containing Klenow  Fragment (NEB), dNTPs, PEG, and the dN-SMRT  oligonucleotide to enable random priming off of the beads.  PCR amplification was carried out using KAPA HiFi PCR  Mastermix (Kapa Biosystems KK2602) with 2.00 beads per 50 µL reaction volume. Post-whole transcriptome amplification,  libraries were then pooled in sets of six (12,000 beads) and  purified using Agencourt AMPure XP SPRI beads (Beckman  Coulter, A63881) by a 0.6x volume ratio, followed by a 0.8x.  Libraries size was analysed using an Agilent Tapestation  hsD5000 kit (Agilent Genomics) with an expected peak at  1000 bp and absence of smaller primer peaks. Libraries were  quantified using Qubit High-Sensitivity DNA kit and  preparation kit and libraries were constructed using Nextera  XT DNA tagmentation (Illumina FC-131-1096) using 800 pg of  pooled cDNA library as input using index primers with format  as in Gierahn et al. Amplified final libraries were purified twice  with AMpure XP SPRI beads as before, with a volume ratio of  0.6x followed by 0.8x yielding library sizes with an average  distribution of 650-750 pb. Libraries were pooled and sequenced  together using a Illumina NovaSeq 6000 S2 Reagent kit v1.5 (100  cycles) using a paired end read structure with custom read 1  primer: read 1: 20 bases with a 12 bases cell barcode and 8 bases  unique molecular identifier (UMI). Read 2: 82 bases of transcript  information, index 1 and index 2: 8 bases.

value: CD3+ cells

value: Tonsil


title: Tonsil, untouched, Donor 2, scRNAseq

description: SeqWell

source_name: Tonsil


title: HO219_PATOM_PAX300_P19 (biol rep 2)


title: HCMV AD169 infected MRC5, WT virus, MOI = 3, 72 HPI, rep 3

value: fibroblast


title: HO219_WNT_PAX300_P18 (biol rep 1)

value: WNT Media


title: plate1_G05_S77

value: tonsil


title: plate4_E01_S241


title: HCMV AD169 infected MRC5, WT virus, MOI = 3, 72 HPI, rep 1


title: HO219_WNT_PAX300_P19 (biol rep 2)

value: Patient-Derived Xenograft


title: HCMV AD169 infected MRC5, WT virus, MOI = 3, 72 HPI, rep 2

value: WT


title: Tonsil, CD3 sorted, Donor 3, scRNAseq

description: SeqWell


title: Tonsil, untouched, Donor 3, scRNAseq

description: SeqWell


title: C37 dRING Rep 1

description:
C37 dRING Rep 1
C37_R1_dRING_S9

value: rabbit anti-dRING (from Yuri Schwartz)

value: Drosophila virilis


title: PBMC, donor 2190, scRNAseq

description: SeqWell

source_name: Blood

value: Blood


title: C37 Input CBP Rep 2

description:
C37 Input CBP Rep 2
C37_R2_INPUT_S3

value: Oregon R


title: plate2_G03_S171

value: T cell


title: plate2_F02_S158

value: HIV


title: HO219_WNT_PAX300_P20 (biol rep 3)


title: plate1_A08_S8


title: HCMV AD169 infected MRC5, dUL54 virus, MOI = 3, 72 HPI, rep 1

value: dUL54 HCMV infected


title: plate4_A08_S200


title: RNA-seq of adult Bombyx mori testis [Bmo_Testis_H]

description: Pooled testis from adult individuals

data_processing:
Estimated counts and TPMs were computed by Kallisto (v0.44.0)
Supplementary files format and content: Tab-delimited file with length, effective length, estimated counts and transcript per million (TPM) for all species protein coding genes in the relative GTF

organism: Bombyx mori

source_name: Adult testis

value: Testis

value: ASM15162v1 GTF (enriched from Ensembl Metazoa v45)


title: HO228_PATOM_PAX300_P21 (biol rep 1)

value: Pancreatic Ductal Adenocarcinoma

value: PaTOM Media


title: HO228_WNT_PAX300_P22 (biol rep 2)


title: HCMV AD169 infected MRC5, dUL49 virus, MOI = 3, 72 HPI, rep 2

value: dUL49 HCMV infected


title: C37 CBP Rep 2

description:
C37 CBP Rep 2
C37_R2_CBP_S7

value: Late embryonic stage

value: rabbit anti-CBP (homemade)


title: RNA-seq of adult Bombyx mori muscle [Bmo_Muscle_H]

description: Pooled muscle from adult individuals

source_name: Adult muscle

value: Muscle


title: HO44_PATOM_17 (biol rep 2)

value: Primary Tumor


title: PBMC, donor 2127, scRNAseq

description: SeqWell


title: plate1_G06_S78

value: tonsil


title: HO44_WNT_P16 (biol rep 2)

value: WNT Media


title: plate1_A12_S12


title: plate4_B07_S211


title: RNA-seq of adult Bombyx mori brain [Bmo_Brain_H]

description: Pooled brains from adult individuals

value: Brain


title: plate4_B06_S210


title: PBMC, donor 2142, scRNAseq

description: SeqWell

value: Blood


title: Uveal melanoma cell-METTL14-3

city: Shanghai

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: hg38
Supplementary files format and content: *.txt: HTseq

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Uveal melanoma cell

value: GNAQ mutation

value: Transfected with lentivirus to overexpress METTL14

tag: time

value: 72 hours


title: HO44_WNT_P17 (biol rep 3)


title: HO44_WNT_P15 (biol rep 1)


title: plate2_A07_S103

value: T cell

value: HIV


title: Normal_2

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Province

address: nanshan street

institute: Tsinghua University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited csv files include read count values for each Sample

source_name: skin tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular

value: skin tissue

value: skin cells

value: WT

value: normal growth


title: Normal_1


title: Normal_3


title: HO107_PATOM_P10 (biol rep 1)

value: Liver Metastasis

value: Pancreatic Ductal Adenocarcinoma

value: PaTOM Media


title: Uveal melanoma cell-NC-3

value: Transfected with vector


title: plate2_E05_S149

value: tonsil


title: HO107_WNT_P13 (biol rep 2)

value: WNT Media


title: HDB_15mm_3

value: skin cells and mesenchymal stem cells

value: mesenchymal stem cell-laden matrigel microspheres implantation


title: HDB_15mm_2


title: plate5_E10_S346


title: HO163_WNT_PAX4_P6 (biol rep 1)

value: Patient-Derived Xenograft


title: Uveal melanoma cell-NC-1

value: Uveal melanoma cell

value: GNAQ mutation


title: Uveal melanoma cell-NC-2

value: 72 hours


title: plate2_G09_S177

value: T cell

value: HIV


title: Uveal melanoma cell-METTL14-2

value: Transfected with lentivirus to overexpress METTL14


title: HO163_PaTOM_PAX4_P8 (biol rep 3)


title: HDB_15mm_1

value: skin tissue

value: WT


title: plate4_H11_S287


title: HDB_10mm_3


title: Uveal melanoma cell-METTL14-1


title: HO107_PATOM_P17 (biol rep 2)

value: Liver Metastasis


title: HO163_PaTOM_PAX4_P7 (biol rep 2)

value: Pancreatic Ductal Adenocarcinoma


title: plate5_A07_S295


title: HO163_PaTOM_PAX4_P6 (biol rep 1)

value: PaTOM Media


title: HDB_10mm_2


title: plate4_G06_S270


title: M28Z-BOE_multiround_2

first: Xingying

last: Zhang

address: No. 5, Yard 1, Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: total mRNA

data_processing:
RNA-seq:
The library samples were sequenced on the Illumina NovaSeq sequencer with 150 bp paired-end reads.
RNA sequencing reads of CAR-T cells and OT-1 cells were aligned to human reference sequence GRCh38 and mouse reference sequence GRCm39 separately using STAR (2.7.0f).
Read counts and FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated using RSEM (1.3.2).
ChIP-seq:
The obtained FASTQ files were performed quality control with FastQC (0.11.9). Sequenced reads were aligned to the human reference sequence GRCh38 with BWA (0.7.17) software to obtain the SAM files which were converted to BAM files by SAMtools (1.3.1) software.
Then BAM files were sorted with the SAMtools and were deduplicated with Picard (2.24.0).
Binding sites (peaks) are called using MACS2 (2.2.7.1) relative to a control input library and q-value threshold was set as 0.05.
The deduplicated BAM files were converted to bigwig files using bamCoverage command of deeptools (3.3.0) software and viewed using for IGV (2.7.0) visualization software.
Assembly: GRCh38 (human), GRCm39 (mouse)
Supplementary files format and content: *_readcounts_FPKM.xlsx: Excel files include read counts and FPKM values.
Supplementary files format and content: bigwig format for visualization in IGV.

source_name: blood

extract_protocol:
Total RNA was isolated from CAR-T cells and mRNA was enriched with Oligo (dT) and broken randomly, then mRNA was reversed by random hexamers to cDNA.
Terminal of the double-stranded cDNA was added sequencing adaptors and utilized PCR amplification to produce the cDNA library.

value: blood

value: Primary T cells

value: CAR-T BATF overexpression

value: three rounds tumor challenge


title: M28Z-BOE_multiround_3

description: total mRNA


title: HDB_10mm_1

value: skin cells and mesenchymal stem cells

value: mesenchymal stem cell-laden matrigel microspheres implantation


title: HO163_WNT_PAX4_P7 (biol rep 2)

value: Patient-Derived Xenograft

value: WNT Media


title: M28Z-BOE_multiround_1

description: total mRNA


title: plate2_B03_S111

data_processing:
Reads were aligned to hg19 (Gencode v21) using Top Hat and estimated counts and transcripts per million (TPM) matrices generated using RSEM. Any samples with fewer than 5x10E5 or more than 6x10E6 aligned reads or fewer than 10,000 uniquely ex-pressed genes were removed from subsequent analysis.
Assembly: hg19
Supplementary files format and content: Tab-separated gene-by-cell TPM matrix

value: tonsil


title: Acellular beads_15mm_3

value: skin cells

value: matrigel microspheres implantation


title: M28Z-BKO_multiround_1

description: total mRNA

value: CAR-T BATF knockout


title: M28Z-BKO_multiround_2

description: total mRNA


title: Acellular beads_15mm_1

value: skin tissue


title: plate2_D05_S137

value: T cell

value: HIV


title: HO163_WNT_PAX4_P12 (biol rep 4)

value: Pancreatic Ductal Adenocarcinoma


title: Acellular beads_15mm_2

value: WT


title: plate4_E03_S243


title: Acellular beads_10mm_3


title: M28Z_multiround_3

description: total mRNA

value: blood

value: CAR-T WT


title: HO163_PaTOM_PAX4_P12 (biol rep 4)

value: PaTOM Media


title: plate2_B05_S113


title: plate2_D01_S133


title: HO228_PATOM_PAX300_P23 (biol rep 3)


title: Acellular beads_10mm_2


title: M28Z-BKO_multiround_3

description: total mRNA

value: Primary T cells

value: three rounds tumor challenge


title: plate2_E09_S153


title: M28Z_multiround_1

description: total mRNA


title: HO163_WNT_PAX4_P8 (biol rep 3)


title: Acellular beads_10mm_1


title: HO228_PATOM_PAX300_P24 (biol rep 4)


title: HO219_PATOM_PAX300_P20 (biol rep 3)


title: M28Z-IKO_3

description: total mRNA

value: CAR-T IRF4 knockout

value: co-culture with NCI-H226-luciferase at E:T=0.1:1 for 7 days


title: M28Z-IKO_2

description: total mRNA


title: plate2_G01_S169


title: plate1_B12_S24


title: HO44_PATOM_P25 (biol rep 3)

value: Primary Tumor