title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 46

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: amplicon sequencing


title: Chern_City_50

status: Public on Dec 14 2022

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

country: USA

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: location

value: Chernobyl City

tag: tissue

value: Whole Blood

tag: breed

value: Mixed Breed


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG4hr_rep2

type: SRA

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and E.coli genome (hg19 and ecK12MG1655) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the DESeq2 size factors using Deeptools.
Genome_build: hg19 and ecK12MG1655
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

organism: Homo sapiens

source_name: Rh30 cell line

growth_protocol: Cells were cultured in RPMI-1640 containing 10% FetalPlex and supplemented with 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
Cells were collected and incubated with Concanavalin A-coated beads. Antibodies were used to bind targeted DNA-associated proteins. pAG-Mnase was used to digest targeted regions of the genome. DNA was then extracted using phenol-chloroform
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: DMSO, 500 nM dTAG47

tag: treatment

value: 500nM dTAG47

tag: antibody

value: Anti-HA (Cell Signaling, (C29F4) #3724)


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 49

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: To grow Arabidopsis plants for protoplast preparation, Col-0 and fwa-4 epi-mutant plants were grown under a 12-hour light/12-hour dark photoperiod and with low light condition for 3-4 weeks. To grow maize plants for protoplast isolation, B73 seeds were soaked in water overnight and planted in half peat moss and half vermiculite. After three days of light incubation, emerged seedlings were transferred to dark until the 2nd leaf was 10-15 cm long.   Transgenic T1 plants were screened with half MS plates with 40 μg/ml hygromycin B. For 28 °C treatment of T1 plants, stratified seeds on half MS plates with hygromycin B were incubated at 28 °C and resistant T1 plants were transferred to soil after about a week, and put back to 28 °C for a total of two weeks incubation at 28 °C. T1 plants were then moved to a greenhouse (23 °C) for the rest of the life cycle.  To support the growth of albino seedlings in T2 generation, 3% sucrose was supplemented to half MS plates when needed.

extract_protocol:
Amplicon sequencing: DNA was extracted from protoplast samples and leaves of transgenic plants with Qiagen DNeasy plant mini kit. The amplicon was obtained using two rounds of PCR. Amplification primers for the first round of PCR were designed to have the 3’ sequence of the primers flanking a 200-300 bp fragment of the genomic area targeted by the guide RNA of interest. The 5’ part of the primer contained a sequence which will be bound by common sequencing primers. After 25 cycles of the first round of PCR amplification, the reaction was purified using 1x Ampure XP beads (Beckman Coulter A63881). The eluate was used as template for the second round of PCR using the Phusion enzyme and 12 cycles of amplification. The second round of PCR was designed so that indexes were added to each sample. The samples were then purified using 0.8x Ampure XP beads. Part of the purified libraries were run on a 2% agarose gel to check for size and absence of primer dimer (fragments below 200 bp considered as primer dimer). Then amplicons were sent for sequencing with NovaSeq 6000 or iSeq 100 platform.
Whole genome sequencing: DNA from single Arabidopsis seedlings was extracted with the Qiagen DNeasy plant mini kit and sheared to 300 bp size with a Covaris. Library preparation was performed with Tecan Ovation Ultralow V2 DNA-seq kit. The libraries were sequenced with the NovaSeq 6000 platform.

value: leaf tissue

tag: developmental stage

value: 3-4 weeks

tag: strain

tag: background genotype

tag: target locus


title: 151_ATACseq_RAW_shSMRT_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

organism: Mus musculus

growth_protocol:
ChIP-Seq: WT RAW264.7 cells, lentivirus-medicated knockdown cells and GPS2 CRISPR KO cells were maintained normal 10% FBS DMEM medium.
ATAC-Seq: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.
RNA-Seq: BMDM cells were maintained normal 10% FBS DMEM medium supplement with 30% L929 medium for one week.
Cut&Tag: WT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
ChIP-Seq: Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
ATAC-Seq: WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×10^5 cells one day before the experiments. Cells were harvested with IL4 1h treatment, washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
RNA-Seq: 2×10^5 WT and GPS2 KO BMDM cells were seeded one day before the treatment. The next day the cells were treatment with IL4 6h and the total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
Cut&Tag: 2×10^5 shGFP and shKDM1A RAW cells were seeded one day before.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
ChIP-Seq: RAW264.7 cells were treated with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
ATAC-Seq: RAW264.7 cells were treated IL4 (20ng/ml) for 1h .
RNA-Seq: BMDM cells were treated with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

tag: cell type

value: Macrophage

value: BALB/c

value: Control

tag: chip antibody

value: No antibody

tag: chip antibody vendor

value: No

tag: chip antibody cat.


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG4hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 45


title: Chern_City_49


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 44


title: 150_ATACseq_RAW_shNCOR_rp3


title: 149_ATACseq_RAW_shNCOR_rp2


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG2hr_rep2


title: Chern_City_47


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_dTAG2hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 43


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_DMSO_rep2

value: DMSO


title: 148_ATACseq_RAW_shNCOR_rp1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 42


title: 147_ATACseq_RAW_shGFP_rp3


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_Xlink_DMSO_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 41


title: Chern_City_45


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_nonXlink_DMSO_rep2

description: 6035-P3F-HA-DMSO-merge_macs2q0.01_peaks.narrowPeak


title: 146_ATACseq_RAW_shGFP_rp2


title: Chern_City_46


title: 145_ATACseq_RAW_shGFP_rp1


title: Chern_City_44


title: Rh30_PAX3-FOXO1-FKBP cells CUT&RUN_P3F_nonXlink_DMSO_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 40


title: Chern_City_43


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_DMSO_Input_rep2

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and Drosophila genome (hg19 and dm3) using Bowtie2.
Peaks were called using MACS2.
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using counts per million mapped reads.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext Ultra II DNA Library Prep Kit


title: Chern_City_42


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 38


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_DMSO_Input_rep1


title: Chern_City_48


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 37


title: 126_RAW_cut_tag_shKDM1A_H3K4me1_rp2

data_processing:
Library strategy: Cut & Tag
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition. Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

value: Abcam


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 36


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG24hr_rep2

value: anti-H3K27ac (Abcam, #ab4729)

tag: time point


title: Chern_City_40


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG24hr_rep1


title: 125_RAW_cut_tag_shKDM1A_H3K4me1_rp1


title: Chern_City_39


title: 124_RAW_cut_tag_shGFP_H3K4me2_rp2


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG4hr_rep2


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 35


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 34


title: Chern_City_38


title: 123_RAW_cut_tag_shGFP_H3K4me2_rp1


title: 128_RAW_cut_tag_shKDM1A_H3K4me2_rp2


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG4hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 39


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 33


title: Chern_City_37


title: 122_RAW_cut_tag_shGFP_H3K4me1_rp2


title: Chern_City_36


title: 127_RAW_cut_tag_shKDM1A_H3K4me2_rp1


title: 121_RAW_cut_tag_shGFP_H3K4me1_rp1


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG2hr_rep2


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_dTAG2hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 32


title: Chern_City_35


title: Chern_City_41


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 31


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_DMSO_rep2


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 30


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 29


title: Chern_City_33


title: Chern_City_32


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 27


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 28


title: Chern_City_31


title: Islet_Tead1KO_Rep3

type: RNA

city: Pittsburgh

first: Vijay

middle: K.

last: Yechoor

state: PA

address: 200 Lothrop Street, BST 1058W

institute: University of Pittsburgh

hyb_protocol: Following fragmentation 12mcg of aRNA was used fro hybridization. 16 hours at 45 °C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip® Fluidics Station 450. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control metrics recorded using Affymetrix Command Console software version 3.0.0.

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

label: biotin

molecule: total RNA

label_protocol: Biotin labelled aRNA was fragmented and then hybridized

growth_protocol: 12 week old male flox and KO mice

extract_protocol: total RNA was extracted by Trizol and then purified by Qiagen RNA prep kits along with DNAse digestion on column.

treatment_protocol: islets were isolated bu collagenase digestion of pancreas in situ and purifoed by density centrifugation and then by hand picking.

tag: Sex

value: male

tag: age

value: 12 weeks

tag: genotype/variation

value: Tead1 beta cell-specific KO

value: islet


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 26


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG1hr_rep1

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.32).
Paired end reads were aligned to a concatenated human and Drosophila genome (hg19 and dm3) using Bowtie2.
Peaks were called using Genrich (v. 0.6.1).
Differential analysis was performed using DiffBind and DESeq2.
BigWig files were generated and normalized using the DESeq2 size factors using Deeptools.
Genome_build: hg19 and dm3
Supplementary_files_format_and_content: bigWig file
Supplementary_files_format_and_content: peak file

extract_protocol:
ATAC-Seq Kit (Active Motif, catalog No.53150)
ATAC-Seq Kit (Active Motif, catalog No.53150)


title: Chern_City_30

tag: location

value: Chernobyl City

value: Whole Blood

value: Mixed Breed


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG1hr_rep2

value: 500nM dTAG47


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep1


title: Chern_City_29

tag: tissue


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 25

value: leaf tissue

value: 3-4 weeks


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 24


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG0.5hr_rep2


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG0.5hr_rep1


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 23


title: Chern_City_34

tag: breed


title: Rh30_PAX3-FOXO1-FKBP cells ChIP-seq_DMSO_rep1

tag: treatment


title: Chern_City_27


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep2


title: Islet_Tead1KO_Rep1


title: Islet_Flox_Rep3

value: Flox


title: Islet_Tead1KO_Rep2


title: Islet_Flox_Rep1


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep2


title: Islet_Flox_Rep2


title: Chern_City_26


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 21


title: 6211-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep1


title: Chern_City_28


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 22


title: Chern_City_25


title: Chern_City_24


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG24hr_rep1


title: P10-CD11B-positive-IL1B-rep5

city: Paris

first: Anne-Laure

last: Schang

state: Select Option

address: 4, Avenue de l'Observatoire

department: Faculté de Pharmacie

country: France

institute: Université Paris Cité

description: Gene expression at post-natal day (P) 5 in brain CD11B+ cells after twice daily injection of IL1B (10ng/g) from P1 to P10

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent W hole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The las t washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 5

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). Samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: Male swiss mice were injected intra-peritoneally with PBS or IL1B (10ng/g) from post-natal (P) 1 to P4 and once at P5. 2h after the last injection and 5 days later at P10, six mice of each group (PBS or IL1B) were sacrificed, brain were collected and dissociated; O4+ oligodendrocytes and CD11B+ microglia were sequentially isolated by Magnetic Activated Cell Sorting (MACS technology, Miltenyi). Cell pellets were frozen.

value: swiss

value: Brain CD11B+ microglia

tag: gender


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 20

tag: developmental stage


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG4hr_rep1


title: P10-CD11B-positive-IL1B-rep4

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 4

tag: strain


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 19

tag: background genotype


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 18

tag: target locus


title: P10-CD11B-positive-IL1B-rep6

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 6

tag: cell type


title: P10-CD11B-positive-IL1B-rep3

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 3


title: Chern_City_22


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep2


title: Chern_City_20


title: Chern_City_21


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG24hr_rep2


title: Chern_City_23


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 16


title: Chern_City_19


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 15


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG2hr_rep1


title: P10-CD11B-positive-PBS-rep6

description: Gene expression at post-natal day (P) 5 in brain CD11B+ cells after twice daily injection of PBS from P1 to P10

source_name: Brain CD11B-positive cells, P10, PBS, replicate 6

value: PBS


title: P10-CD11B-positive-IL1B-rep2

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 2


title: P10-CD11B-positive-IL1B-rep1

source_name: Brain CD11B-positive cells, P10, IL1B, replicate 1


title: P10-CD11B-positive-PBS-rep5

source_name: Brain CD11B-positive cells, P10, PBS, replicate 5


title: P10-CD11B-positive-PBS-rep4

source_name: Brain CD11B-positive cells, P10, PBS, replicate 4


title: Chern_City_18


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_dTAG4hr_rep2


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 14


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep1

value: DMSO


title: Chern_City_17


title: Chern_City_16


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 17


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 13


title: SPECTRUM-OV-118_S1_CD45P_RIGHT_ADNEXA

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

description:
matrix.h5
GEO_cells.tsv

library_source: transcriptomic

data_processing:
Mapping and QC with cellranger 3.1.0
Cell type assignment with cellassign 0.99.2
Batch correction with harmony 0.1
Clustering with Seurat v3
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.h5:raw UMI count matrix with cell_ids in columns and genes in rows
Supplementary_files_format_and_content: GEO_cells.tsv:annotation table with cell_ids in rows and meta data in columns

molecule: polyA RNA

source_name: Adnexa

growth_protocol: Primary samples.

extract_protocol:
Dissociation: Tumor tissue was immediately processed for tissue dissociation. Fresh tissue was cut into 1 mm pieces and dissociated at 37°C using the Human Tumor Dissociation Kit (Miltenyi Biotec) on a gentleMACS Octo Dissociator. After dissociation, single cell suspensions were filtered and washed with ACK (Ammonium-Chloride-Potassium) Lysing Buffer. Cells were stained with Trypan Blue and cell counts and viability were assessed using the Countess II Automated Cell Counter (ThermoFisher) (for detailed protocol see 40). Sorting: Freshly dissociated cells were stained with a mixture of GhostRed780 live/dead marker (TonBo Biosciences) and Human TruStain FcX™ Fc Receptor Blocking Solution (BioLegend). The stained samples were then incubated and stained with Alexa Fluor® 700 anti-human CD45 Antibody (BioLegend). Post staining, they were washed and resuspended in RPMI + 2% FCS and submitted for cell sorting. The cells were sorted into CD45 positive and negative fractions by fluorescence assisted cell sorting (FACS) on a BD FACSAria™ III flow cytometer (BD Biosciences). Positive and negative controls were prepared and used to set up compensations on the flow cytometer. Cells were sorted into tubes containing RPMI + 2% FCS for sequencing.
Flow sorted tumor cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip B (10x Genomics PN 2000060). GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,400-5,000 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics PN 1000075) according to the manufacturer’s protocol. cDNA amplification included 12 cycles and 0.4-419ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR.

tag: sort


title: SPECTRUM-OV-118_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 11


title: SPECTRUM-OV-118_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Chern_City_15


title: 6086-Rh30_PAX3-FOXO1-FKBP cells ATAC-seq_DMSO_rep2


title: P10-CD11B-positive-PBS-rep1

source_name: Brain CD11B-positive cells, P10, PBS, replicate 1


title: P10-CD11B-positive-PBS-rep2

source_name: Brain CD11B-positive cells, P10, PBS, replicate 2


title: Chern_City_14


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 10


title: P5-CD11B-positive-IL1B-rep6

description: Gene expression at post-natal day (P) 5 in brain CD11B+ cells after twice daily injection of IL1B (10ng/g) from P1 to P5

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 6


title: P5-CD11B-positive-IL1B-rep5

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 5


title: P10-CD11B-positive-PBS-rep3

source_name: Brain CD11B-positive cells, P10, PBS, replicate 3


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 12

source_name: Arabidopsis leaf tissue


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 09


title: SPECTRUM-OV-118_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Chern_City_13

source_name: Whole Blood


title: SPECTRUM-OV-118_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-118_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 08


title: Chern_City_12


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 07


title: CNPP_58

value: Chernobyl Nuclear Power Plant


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 06


title: CNPP_57


title: SPECTRUM-OV-116_S1_CD45P_RIGHT_PARACOLIC_GUTTER

description:
matrix.h5
GEO_cells.tsv

source_name: Other


title: SPECTRUM-OV-116_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: P5-CD11B-positive-IL1B-rep4

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 4


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 05


title: P5-CD11B-positive-IL1B-rep3

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 3


title: P5-CD11B-positive-IL1B-rep2

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 2


title: P5-CD11B-positive-IL1B-rep1

source_name: Brain CD11B-positive cells, P5, IL1B, replicate 1


title: CNPP_56


title: SPECTRUM-OV-116_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: CNPP_55


title: P5-CD11B-positive-PBS-rep5

description: Gene expression at post-natal day (P) 5 in brain CD11B+ cells after twice daily injection of PBS from P1 to P5

source_name: Brain CD11B-positive cells, P5, PBS, replicate 5


title: CNPP_53


title: SPECTRUM-OV-116_S1_CD45N_RIGHT_PARACOLIC_GUTTER

description:
matrix.h5
GEO_cells.tsv


title: CNPP_54


title: SPECTRUM-OV-116_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: SPECTRUM-OV-116_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 03


title: CNPP_52


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 01


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 02


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 41


title: CNPP_51


title: SPECTRUM-OV-116_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P5-CD11B-positive-PBS-rep4

source_name: Brain CD11B-positive cells, P5, PBS, replicate 4


title: Fig5A rdr6 background version2 vcasphi U6gR10 T1 plant 04


title: P5-CD11B-positive-PBS-rep3

source_name: Brain CD11B-positive cells, P5, PBS, replicate 3


title: P5-CD11B-positive-PBS-rep6

source_name: Brain CD11B-positive cells, P5, PBS, replicate 6


title: P5-CD11B-positive-PBS-rep1

source_name: Brain CD11B-positive cells, P5, PBS, replicate 1


title: SPECTRUM-OV-116_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: CNPP_50


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 40


title: P5-CD11B-positive-PBS-rep2

source_name: Brain CD11B-positive cells, P5, PBS, replicate 2


title: P10-O4-positive-IL1B-rep6

description: Gene expression at post-natal day (P) 5 in brain O4+ cells after twice daily injection of IL1B (10ng/g) from P1 to P10

source_name: Brain O4-positive cells, P10, IL1B, replicate 6

value: Brain O4+ oligodendrocytes


title: CNPP_49


title: SPECTRUM-OV-115_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 39

source_name: Arabidopsis leaf tissue


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 38


title: SPECTRUM-OV-115_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: P10-O4-positive-IL1B-rep5

source_name: Brain O4-positive cells, P10, IL1B, replicate 5

value: male


title: CNPP_48

source_name: Whole Blood


title: CNPP_47


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 37


title: SPECTRUM-OV-115_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-115_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 36


title: CNPP_46


title: SPECTRUM-OV-115_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 35


title: CNPP_45


title: CNPP_44


title: P10-O4-positive-IL1B-rep4

source_name: Brain O4-positive cells, P10, IL1B, replicate 4


title: SPECTRUM-OV-115_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: P10-O4-positive-IL1B-rep2

source_name: Brain O4-positive cells, P10, IL1B, replicate 2


title: SPECTRUM-OV-115_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 34


title: P10-O4-positive-IL1B-rep3

source_name: Brain O4-positive cells, P10, IL1B, replicate 3


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 33


title: P10-O4-positive-PBS-rep6

description: Gene expression at post-natal day (P) 5 in brain O4+ cells after twice daily injection of PBS from P1 to P10

source_name: Brain O4-positive cells, P10, PBS, replicate 6


title: CNPP_43


title: P10-O4-positive-IL1B-rep1

source_name: Brain O4-positive cells, P10, IL1B, replicate 1


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 32


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 31


title: SPECTRUM-OV-115_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: SPECTRUM-OV-112_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: CNPP_42


title: CNPP_41


title: SPECTRUM-OV-112_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: CNPP_40


title: CNPP_39


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 30


title: P10-O4-positive-PBS-rep4

source_name: Brain O4-positive cells, P10, PBS, replicate 4


title: SPECTRUM-OV-112_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P10-O4-positive-PBS-rep5

source_name: Brain O4-positive cells, P10, PBS, replicate 5


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 29


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 28


title: SPECTRUM-OV-112_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: SPECTRUM-OV-112_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 27


title: CNPP_37


title: SPECTRUM-OV-112_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: CNPP_36


title: P10-O4-positive-PBS-rep2

source_name: Brain O4-positive cells, P10, PBS, replicate 2


title: P10-O4-positive-PBS-rep1

source_name: Brain O4-positive cells, P10, PBS, replicate 1


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 26


title: CNPP_35


title: SPECTRUM-OV-112_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P5-O4-positive-IL1B-rep5

description: Gene expression at post-natal day (P) 5 in brain O4+ cells after twice daily injection of IL1B (10ng/g) from P1 to P5

source_name: Brain O4-positive cells, P5, IL1B, replicate 5


title: P5-O4-positive-IL1B-rep4

source_name: Brain O4-positive cells, P5, IL1B, replicate 4


title: SPECTRUM-OV-110_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: P5-O4-positive-IL1B-rep6

source_name: Brain O4-positive cells, P5, IL1B, replicate 6


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 25

source_name: Arabidopsis leaf tissue


title: SPECTRUM-OV-112_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: CNPP_34

source_name: Whole Blood


title: P5-O4-positive-IL1B-rep3

source_name: Brain O4-positive cells, P5, IL1B, replicate 3


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 24


title: CNPP_33


title: CNPP_38


title: SPECTRUM-OV-110_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 22


title: P5-O4-positive-IL1B-rep1

source_name: Brain O4-positive cells, P5, IL1B, replicate 1


title: P5-O4-positive-IL1B-rep2

source_name: Brain O4-positive cells, P5, IL1B, replicate 2


title: CNPP_31


title: P5-O4-positive-PBS-rep6

description: Gene expression at post-natal day (P) 5 in brain O4+ cells after twice daily injection of PBS from P1 to P5

source_name: Brain O4-positive cells, P5, PBS, replicate 6


title: P10-O4-positive-PBS-rep3

source_name: Brain O4-positive cells, P10, PBS, replicate 3


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 21


title: P5-O4-positive-PBS-rep5

source_name: Brain O4-positive cells, P5, PBS, replicate 5


title: SPECTRUM-OV-110_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 23


title: YPD2

city: Belo Horizonte

first: GUSTAVO JOSE

middle: COTA

last: DE FREITAS

state: MG

address: Av. Presidente Antônio Carlos  6627, Instituo de Ciencias Biológicas

department: MICROBIOLOGIA

country: Brazil

institute: UNIVERSIDADE FEDERAL DE MINAS GERAIS

data_processing:
Quality reads were filtered using the FastQC software, and adapters were removed by the Trimmomatic v.0.36 (Bolger, Lohse, & Usadel, 2014). Trimmed reads were mapped to the C. neoformans H99 or the Mus musculus GRCm38 reference genomes, both available on ENSEMBL, using the STAR aligner v.2.5.2b (Dobin et al., 2013). STAR aligner detects splice junctions incorporating them to align the entire read sequences and generates the BAM files. Supplementary Table S18 and S19 show the statistics of genome mapping. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2 (Liao, Smyth, & Shi, 2014), and unique reads that fell within exon regions were counted. Differentially expressed genes (DEGs) were obtained using a 5% false discovery rate (FDR), using the DESeq2 Bioconducter package (Love, Huber, & Anders, 2014).
Fungal DEGs were functionally categorized using Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes), using the FungiDB ((http://fungidb.org/fungidb/) and FungiFun2 (https://elbe.hki-jena.de/fungifun/). Mouse DEGs were categorized using the ShinyGO v0.75 database (Ge, Jung, & Yao, 2020). Highly represented categories under each condition were determined by enrichment analysis.
FastQC v0.11.7 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.36 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the C. neoformans h99/ mus musculus reference genomes using the STAR v2.5.2b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.5 (upregulation) or <= -1.5 (downregulation) were called as differentially expressed.
Assembly: Broad C. neoformans h99/ Mus musculus GRCm38 reference genomes
Supplementary files format and content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism: Cryptococcus neoformans

source_name: Culture

growth_protocol: C. neoformans H99 was cultured on Yeast extract Peptone Dextrose (YPD) for 48h/72h (stationary phase) at 37°C for experiment.

extract_protocol:
C57BL/6 mice were infected intratracheally with 1x10e5 cells the H99 strain to analyze the transcriptome. After 6h or 240h of infection, BALF obtained from 6 mice of each condition were pooled together, generating two replicates of 6h and 240h (10d). BALF was centrifuged at 1200 x g and resuspended in 1mL TRIzol Reagent (Invitrogen Life Technologies) for RNA isolation, according to the manufactures' protocol. RNA from H99 yeasts grown in YPD was used as control.
RNA quality, library preparation, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ Inc (South Plainfield, NJ). RNA samples were quantified by fluorometry (Qubit 2.0, Thermo Fisher Scientific–Life Technologies), and RNA integrity was checked with 2100 Bioanalyzer (Agilent Technologies). Transcriptome sequencing was performed via rRNA depletion using the Illumina HiSeq platform (Illumina, USA) in the 2 x 150 bp Paired-End configuration.

value: Culture


title: P5-O4-positive-PBS-rep4

source_name: Brain O4-positive cells, P5, PBS, replicate 4


title: SPECTRUM-OV-110_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: 10x D185 (scRNA-seq)

city: Seattle

first: Amy

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Illumina Nextseq 2000, Illumina Nextseq 550
cds_joint_annotated_220712.RDS

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv), Monocle3 cds object (RDS file)

molecule: nuclear RNA

source_name: ES cell line-derived retinal organoid

growth_protocol: hECSs were differentiated into EBs and then organoids following the protocol from Fligor et al. (2020). Differentiation of retinal organoids from human pluripotent stem cells. Methods Cell Biol. 159, 279–302.

extract_protocol:
5-10 organoids per well were added to a 96-well v-bottom plate. The organoids were washed in dPBS and resuspended in 100 uL papain  at 37C. Every 5-10 minutes the samples were pipetted up and down  until minimal cell clusters were observed by bright phase microscopy (15-20 minutes). The papain was deactivated with 100 uL of Ovomucoid.
Dissociated cells were subjected to the standard 10x workflow for Single Cell 3' v3.1 Dual Index Gene Expression kit.
single Cell RNA sequencing library prepared from whole cells using a 10x 3' v3.1 Dual Index Gene Expression kit.

treatment_protocol: BMP4 (1.5 nM) was added on Day 6 and diluted by half every 2 days until Day 12

value: ES cell line-derived retinal organoid

tag: cell line

value: WA09 (H9) hESC with NRL-GFP

value: 185 days

tag: fraction

value: nuclear polyA RNA


title: CNPP_32

value: Whole Blood

value: Mixed Breed


title: SPECTRUM-OV-110_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 19

value: leaf tissue


title: P5-O4-positive-PBS-rep3

source_name: Brain O4-positive cells, P5, PBS, replicate 3


title: SPECTRUM-OV-110_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 17

value: 3-4 weeks


title: 10x D78 (scRNA-seq)

value: 78 days


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 16


title: SPECTRUM-OV-107_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: SPECTRUM-OV-107_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 20


title: P5-O4-positive-PBS-rep2

source_name: Brain O4-positive cells, P5, PBS, replicate 2

value: swiss


title: Tumor, Sephin1, day 15, replicate 1, scRNAseq, TCR enriched

city: Shanghai

first: Rongjing

last: Wang

state: Select One...

address: 320 Yueyang Road, Shanghai, China

institute: Shanghai Institute of Nutrition and Health, CAS

description:
10x Genomics
TS1d15V5-T

data_processing:
After obtaining all 12 expression sequencing datasets and 12 TCR enrichment sequencing datasets, we first analyzed the data using CellRanger (version 6.0.0) software from 10X Genomics. The single-cell expression data were then imported into R and integrated with Seurat (version 3.2.3). To minimize information loss and filter out low-quality and duplicated cells at the same time, genes expressed in at least 2 cells were kept, and cells with more than 100 but less than 4000 genes were kept. In addition, violin plot was made by the percentage of mitochondrial genes, and cells that were discrete in the violin plot were filtered out. The filtered cells were then integrated, normalized, scaled and clustered with Seurat. Cell type annotation was then performed using classic immune cell markers.
The filtered TCR contig matrix was analyzed and integrated using scRepertoire (version 1.2.1) (83) and then integrated with the gene expression data. TCRs were separated and annotated by their distribution in one sample. If the percentage of the clone number of one clonotype in all clones of the sample was between 0.1 and 1, the clonotype was classified as “hyperexpanded”; if the percentage was between 0.01 and 0.1, the classification was “large”. “medium” was used to denote a percentage between 0.001 and 0.01, and “small” indicated a percentage between 〖10〗^(-4) and 0.001. Separated TCRs were then integtated with the expression data. The integration process was scripted and performed on Python (version 2.7.5) and R (version 3.6.3) platforms. Cells were matched between the TCR enrichment data and expression data according to their specific barcode sequence. Plots of different TCR types were made with ggplot2 (version 3.3.5).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Peripheral blood samples were collected from the mouse eyes. Each sample was first mixed with 200 μl EDTA and then mixed with PBS in an equal volume. Equal volumes of Ficoll-Paque PREMIUM (Amersham/GE, 17544602) and the blood-EDTA-PBS solution were added to a 15 ml centrifuge tube and centrifuged at 400 × g for 20 min. The peripheral blood mononuclear cells (PBMCs) were collected, and the erythrocytes were removed with ACK lysing buffer (ThermoFisher, A1049201). The remaining cells were filtered with a 30 μm MACS SmarterStrainer (Miltenyi/MACS, 130-110-915), washed with PBS 1-2 times, and resuspended in PBS to a proper volume. The cells were stained with AO/PI (Nexcelom Bioscience, CS2-0106-5mL) and quantified using a Cellometer K2 (Nexcelom Bioscience).Tumor tissues were collected and cut into small pieces (approximately 1-2 mm). Then, we digested the tumor tissues with a mouse tumor dissociation kit (Miltenyi/MACS, 130-096-730) following the standard procedure. After that, the cell suspension was filtered with a 30 μm MACS SmarterStrainer. Then, we performed either FACS analysis or FACS sorting (sorting for CD45+ and live cells).
The cell suspension samples we obtained with this procedure were used for single-cell library construction. We performed single-cell immune profiling following the standard procedure from 10X Genomics. The library construction kit we used included the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 (16 rxns, PN-1000165), Chromium Single Cell 5’ Library Construction Kit (16 rxns, PN-1000020), Chromium Single Cell V(D)J Enrichment Kit (Mouse T cell, 96 rxns, PN-1000071), Chromium Next GEM Chip G Single Cell Kit (48 rxns, PN-1000120) and Single Index Kit T Set A (96 rxns, PN-1000213).

value: Immune cells

value: Tumor

value: 10-12 weeks old


title: SPECTRUM-OV-107_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: 10x D28 (scRNA-seq)

extract_protocol:
5-10 organoids per well were added to a 96-well v-bottom plate. The organoids were washed in dPBS and resuspended in 100 uL accutase at 37C. Every 5-10 minutes the samples were pipetted up and down  until minimal cell clusters were observed by bright phase microscopy (30-45 minutes). The accutase was deactivated with 20 uL of FBS.
Dissociated cells were subjected to the standard 10x workflow for Single Cell 3' v3.1 Dual Index Gene Expression kit.
single Cell RNA sequencing library prepared from whole cells using a 10x 3' v3.1 Dual Index Gene Expression kit.

value: 28 days


title: Tumor, normal, day 15, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
TN2d15V5-T


title: SPECTRUM-OV-107_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: Tumor, Sephin1, day 15, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
TS2d15V5-T


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 18

source_name: Arabidopsis leaf tissue


title: P5-O4-positive-PBS-rep1

source_name: Brain O4-positive cells, P5, PBS, replicate 1

value: PBS

value: Brain O4+ oligodendrocytes


title: YPD1

value: Culture


title: EO, Cre negative, (Control2)

city: Saskatoon

first: Raed Samir

last: Said

state: SK

address: University of Saskatchewan 107 Wiggins Road, S7N 5E5 Saskatoon, Canada

country: Canada

institute: University of Saskatchewan

data_processing:
Quality control of raw sequencing reads was performed using FastQC and Low-quality reads were removed and PHRED score and sequence duplication levels were calculated using the Galaxy platform
Trimmed paired-end reads were aligned to the mouse genome using STAR ultrafast universal RNA-seq aligner
To calculate transcript abundances, we converted raw reads to TPM values and differential expression analysis was performed using DESeq2 package.
Principal component analysis and distribution analysis were used to identify outlier samples
Supplementary files format and content: CSV file include RPKM values for each Sample

source_name: Enamel organ

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Enamel organ

value: Ameloblasts

tag: genotype

value: Stim1 fl/fl Cre-

value: No deletion of Stim1


title: Tumor, normal, day 15, replicate 1, scRNAseq, TCR enriched

description:
10x Genomics
TN1d15V5-T


title: EO, Stim1 Het (Control1)

value: Stim1 fl/wt Cre+

value: Partial deletion of Stim1


title: Blood, Sephin1, day 15, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
BS2d15V5-T

source_name: Peripheral Blood

value: Peripheral Blood


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 14

value: leaf tissue

value: 3-4 weeks


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 13


title: SPECTRUM-OV-107_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-107_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 15


title: Blood, Sephin1, day 15, replicate 1, scRNAseq, TCR enriched

description:
10x Genomics
BS1d15V5-T


title: Mouse islets Srrm3+/+ female 12 week-old

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: polyA-selected RNA

data_processing:
Raw reads were mapped with vast-tools align v2.5.1.
Assembly: hg38 (GRCh38), mm10 (GRCm38), rn6 (Rnor_6.0)
Supplementary files format and content: *.cRPKM.txt: Files with raw read counts and cRPKMs for each human, mouse or rat gene in Ensembl.

source_name: Islets

extract_protocol:
Total RNA extraction was performed using RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Illumina strand-specific
Strand-specific polyA-selected

value: Pancreatic islets

value: 12 weeks

tag: Sex

value: female


title: EO, Stim1 cKO

value: Stim1 fl/fl Cre+

value: Complete deletion of Stim1


title: Mouse islets Srrm3-/- female 12 week-old

description: polyA-selected RNA

tag: age


title: Blood, normal, day 15, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
BN2d15V5-T

value: Immune cells

value: 10-12 weeks old


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 12


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 11


title: Blood, normal, day 15, replicate 1, scRNAseq, TCR enriched

description:
10x Genomics
BN1d15V5-T


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 10


title: SPECTRUM-OV-107_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Mouse islets Srrm3+/+ male 10 week-old

description: polyA-selected RNA

value: 10 weeks

value: male


title: Blood, Sephin1, day 0, replicate 1, scRNAseq, TCR enriched

description:
10x Genomics
BS1d0V5-T

value: 8-10 weeks old


title: SPECTRUM-OV-105_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 08


title: SPECTRUM-OV-105_S1_CD45P_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

source_name: UQ


title: Blood, Sephin1, day 0, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
BS2d0V5-T


title: Mouse islets Srrm3+/+ female 10 week-old

description: polyA-selected RNA


title: SPECTRUM-OV-105_S1_CD45P_BLADDER

description:
matrix.h5
GEO_cells.tsv

source_name: Other


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 07


title: Mouse islets Srrm3+/- female 12 week-old

description: polyA-selected RNA


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 09


title: SPECTRUM-OV-105_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-107_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: Blood, normal, day 0, replicate 2, scRNAseq, TCR enriched

description:
10x Genomics
BN2d0V5-T


title: Blood, normal, day 0, replicate 1, scRNAseq, TCR enriched

description:
10x Genomics
BN1d0V5-T


title: Mouse islets Srrm3-/- male 10 week-old

description: polyA-selected RNA


title: Tumor, Sephin1, day 15, replicate 2, scRNAseq

description:
10x Genomics
TS2d15V5

value: Tumor


title: SPECTRUM-OV-105_S1_CD45N_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: Mouse islets Srrm3-/- female 10 week-old

description: polyA-selected RNA


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 05


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 04


title: SPECTRUM-OV-105_S1_CD45N_BLADDER

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-105_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Mouse islets Srrm3+/- male 10 week-old

description: polyA-selected RNA


title: Tumor, Sephin1, day 15, replicate 1, scRNAseq

description:
10x Genomics
TS1d15V5


title: SPECTRUM-OV-105_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 02


title: Mouse islets Srrm3+/- female 10 week-old

description: polyA-selected RNA


title: SI_sh2

city: Changsha

first: Chaxiang

last: Guan

state: Hunan

address: 87 Xiangya Road

department: Department of Physiology, School of Basic Medical Science

institute: Central South University

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 1 containing ploy-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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene and every sample

source_name: MLE12 cell

growth_protocol: Mouse lung alveolar epithelial cells (MLE12 cells, ATCC CRL-2110) were maintained in HITES medium (DMEM/F12 medium modified to contain hydrocortisone, insulin, transferrin, estradiol and selenium) containing 2% fetal bovine serum (Gibco, USA) and 1% (v/v) penicillin/streptomycin (Solarbio) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from control and Slc25a1 plus Idh3α-deficient MLE12 cells using RNAiso Plus (TaKaRa, Japan) according to the manufacturer's instructions.
The transcriptome library for sequencing was generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations. The index codes were added to attribute sequences to each sample. After the quality of sequencing libraries was confirmed on the Agilent 2100 system, clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, CA, USA) according to the manufacturer’s instructions. The library preparations were then sequenced on an Illumina Hiseq 2500 platform (Illumina, San Diego, CA, USA), and paired-end reads were generated. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set to default.

treatment_protocol: MLE12 cells were transfected simultaneously with shIdh3a lentivirus (MOI: 50) and shSlc25a1 lentivirus (MOI: 50) and negative control (shCtrl lentivirus, MOI: 50) in the presence of 1´HitransG P (Lot: REVG005, GeneChem). Empty construct was used as control for all experiments. The cells were washed with fresh complete medium 16 h later and then cultivated for an additional 80 h. The efficiency of Idh3a and Slc25a1 knockdown (or overexpression) was assessed by immunoblotting.

value: Simultaneous infections with an Idh3α-silencing lentivirus (Idh3α shRNA) and an Slc25a1-silencing lentivirus


title: SPECTRUM-OV-090_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Blood, Sephin1, day 15, replicate 2, scRNAseq

description:
10x Genomics
BS2d15V5


title: Tumor, normal, day 15, replicate 2, scRNAseq

description:
10x Genomics
TN2d15V5


title: SI_sh1


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 03


title: SI_sh3


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 06


title: Tumor, normal, day 15, replicate 1, scRNAseq

description:
10x Genomics
TN1d15V5


title: Ctrl_sh3

value: infections with lentivirus( empty LV vectors )


title: Fig5A rdr6 background version2 ncasphi U6gR10 T1 plant 01


title: Blood, Sephin1, day 15, replicate 1, scRNAseq

description:
10x Genomics
BS1d15V5


title: Blood, normal, day 15, replicate 2, scRNAseq

description:
10x Genomics
BN2d15V5


title: SPECTRUM-OV-090_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Fig4D pUB10 ribozyme A form PDS3gR10 vCasphi rep1

source_name: Arabidopsis mesophyll protoplast

value: mysophyll protoplast

value: wild type


title: Blood, normal, day 15, replicate 1, scRNAseq

description:
10x Genomics
BN1d15V5

value: Peripheral Blood


title: Fig4D pUB10 ribozyme A form PDS3gR10 nCasphi rep2

value: 3-4 weeks


title: Ctrl_sh2


title: Blood, Sephin1, day 0, replicate 2, scRNAseq

description:
10x Genomics
BS2d0V5


title: Ctrl_sh1


title: Fig4D pUB10 ribozyme A form PDS3gR10 nCasphi rep1


title: SPECTRUM-OV-090_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: L4_RNA-seq

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Reference genome sequence data from Mus musculus were obtained from the NCBI Genome database (assembly ID: GRCm38). Reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
The read counts per million fragments mapped (CPM) value of each sample was measured in the RNA-seq data.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text format with CPM values of mRNA

source_name: C2C12 cell

extract_protocol:
Total RNA was extracted from C2C12 myotubes using easy-BLUETM total RNA extraction kit according to the manufacturer’s instructions (iNtRON). RNA quality was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands), and RNA quantification was performed using ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
Libraries were prepared from total RNA using the NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK). The isolation of mRNA was performed using the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for the cDNA synthesis and shearing, following manufacture’s instruction. Indexing was performed using the Illumina indexes 1- 12. The enrichment step was carried out using of PCR. Subsequently, libraries were checked using the Agilent 2100 bioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was performed using the library quantification kit using a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed paired-end reads (2 × 100 bp) using HiSeq 2500 (Illumina, Inc., USA).

value: C2C12 cell line

tag: electrical pulse stimulation

value: treated by electrical pulse stimulation


title: Blood, Sephin1, day 0, replicate 1, scRNAseq

description:
10x Genomics
BS1d0V5


title: SPECTRUM-OV-083_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: Fig4D pUB10 ribozyme A form PDS3gR10 vCasphi rep2

data_processing:
Amplicon sequencing:  Reads were first quality and adaptor trimmed using Trim Galore and then mapped to the target genomic region by the BWA aligner. Sorted and indexed bam files were used as input files for further analysis by the CrispRvariants R package. Each mutation pattern with corresponding read counts was exported by the CrispRvariants R package. After assessing all control samples, a criterion to classify reads as edited reads was established: only reads with a >= 3 bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 100 read counts from a sample were counted as edited reads. This criterion is established due to the observation of 1 bp indels and occasionally 2 bp indels with read numbers >100 in control samples. Also, larger indels that occur at very low frequencies (much lower than 100 reads) were observed in control samples. These observations indicate that occasional PCR inaccuracy and low-quality sequencing in a small fraction of reads can result in the indel patterns with corresponding read number ranges as stated above in control samples with the typical sequencing depth in our experiments (1-5 million reads/sample). By employing such stringent criteria, it is believed that the editing signals counted are true signals indicating editing events. Additionally, for FWA gRNA5 and gRNA6 targeted regions, there are long stretches of adenines near these target regions. Due to the high error rate of polymerases amplifying long stretches of adenines, reads with indels only within these stretches of adenines were not counted as true deletions. For amplicon sequencing result analysis of maize protoplast, the criterion to classify reads as edited reads was established: only reads with a >= 3bp deletion or insertion (indel, mainly as deletions) of the same pattern (indels of same size starting at the same location) with >= 10 read counts from a sample were counted as edited reads. The adjustment of the criterion was based on the fact that these amplicon sequencing was of less depth (performed by the iSeq 100) compared to the amplicon libraries of Arabidopsis protoplasts.
Whole genome sequencing for off-target analysis: For variant calling, whole genome sequencing reads were aligned to the TAIR10 reference genome using BWA mem (v0.7.17)53 with default parameters. GATK (4.2.0.0)39 MarkDuplicatesSpark was used to remove PCR duplicate reads. Then GATK HaplotypeCaller was used to call raw variants. Raw SNPs were filtered with QD < 2.0, FS > 60.0, MQ < 40.0, and SOR > 4.0. Raw InDels were filtered with QD < 2.0, FS > 200.0, and SOR > 10.0 and used for base quality score recalibration. The recalibrated bam file was further applied to GATK and Strelka (v2.9.2)40 for SNPs/InDel calling. Only SNPs/InDels called by both GATK and Strelka were used for further analysis. The intersection of GATK and Strelka  SNPs/InDels were filtered by removing identical SNPs/InDels in the rdr6-15 background by BedTools (v2.26.0)54. Variants with coverage lower than 30 reads were removed. Variant loci at which the ratio of the reads with the WT allele over the reads with variant allele larger than three were removed. For heterozygous alleles, at a coverage level of 30 reads, the chance of observing WT reads /mutation allele reads >3 is 0.26% (binomial distribution, one-tailed P=0.0026).
Assembly: tair10
Supplementary files format and content: Crispvariant_result, with detected SNV and indels in amplicon sequencing  vcf, raw variants called with GATK or strelka2 comparing to tair10 reference genome sequence
Library strategy: amplicon sequencing


title: Fig4D pUB10 ribozyme A form PDS3gR10 WTCasphi rep2


title: Fig4D pUB10 ribozyme A form PDS3gR10 WTCasphi rep1


title: SPECTRUM-OV-083_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: L2_RNA-seq


title: SPECTRUM-OV-083_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Blood, normal, day 0, replicate 2, scRNAseq

description:
10x Genomics
BN2d0V5


title: Blood, normal, day 0, replicate 1, scRNAseq

description:
10x Genomics
BN1d0V5


title: L1_RNA-seq


title: SPECTRUM-OV-090_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: CL4_RNA-seq

value: No treatment


title: Fig4D pUB10 A form PDS3gR10 WTCasphi rep1


title: SPECTRUM-OV-083_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4D pUB10 A form PDS3gR10 WTCasphi rep2


title: SPECTRUM-OV-083_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: CL3_RNA-seq


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 vCasphi rep2


title: CL1_RNA-seq


title: SPECTRUM-OV-083_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 vCasphi rep1


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 nCasphi rep2


title: SPECTRUM-OV-082_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: L3_RNA-seq


title: SPECTRUM-OV-082_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: β-Tead1-KO#2 rep1

description:
1yrb-Tead1-_-6587_S4_L001
1yrb-Tead1-_-6587_S4_L001

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using default parameters in CLC genomics workbench 12
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using default dettings in CLC genomics workbench 12
Genome_build: mm10
Supplementary_files_format_and_content: microsoft Excel files include RPKM values for each Sample

extract_protocol:
islets were isolated after collagenase digestion and density gradient purification and then hand picked for purity, flash frozen in liquid nitrogen, and RNA was harvested using column purification.Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: islets


title: SPECTRUM-OV-082_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-083_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: β-Tead1-KO#2 rep2

description:
1yrb-Tead1-_-6587_S4_L002
1yrb-Tead1-_-6587_S4_L002

tag: tissue


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 nCasphi rep1


title: β-Tead1-KO#1 rep2

description:
1yrb-Tead1-_-6584_S3_L002
1yrb-Tead1-_-6584_S3_L002


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 WTCasphi rep2


title: Fig4D CmYLCVp A form PDS3gR10 WTCasphi rep2


title: SPECTRUM-OV-082_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Flox#2 rep1

description:
1yTead1F_F-6582_S2_L001
1yTead1F_F-6582_S2_L001

value: Flox/Flox


title: Fig4D CmYLCVp A form PDS3gR10 WTCasphi rep1


title: KOI5

city: Gainesville

first: Robert

middle: John

last: Cousins

state: FL

address: 572 Newell Drive

department: Food Science/Nutrition

institute: University of Florida

data_processing:
The ten RNA-seq libraries were sequenced on an Illumina Nova Seq 6000 Platform at Novogene Corporation Inc.
FastQC v0.11.9 was used to determine sequence quality and low-quality reads and adapters were removed by the Trimmomatic
Paired end reads with quality score of >20 and sequence lengths >30bp were mapped to the mouse genome GRCm38 using HiSat2 (2.0.4) and SAMtools (1.3.1), and performed differential expression analysis (DEGs) with DESeq2 (1.14.1).
Assembly: mm10

source_name: proximal Intestine

extract_protocol:
Total RNA was extracted from  frozen proximal intestinal segments pre-treated with RNAlater™, using TRI Reagent® (Sigma).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: proximal Intestine

value: KO

tag: treatment

value: 8-10 weeks


title: Fig4D CmYLCVp ribozyme A form PDS3gR10 WTCasphi rep1

extract_protocol:
Amplicon sequencing: DNA was extracted from protoplast samples and leaves of transgenic plants with Qiagen DNeasy plant mini kit. The amplicon was obtained using two rounds of PCR. Amplification primers for the first round of PCR were designed to have the 3’ sequence of the primers flanking a 200-300 bp fragment of the genomic area targeted by the guide RNA of interest. The 5’ part of the primer contained a sequence which will be bound by common sequencing primers. After 25 cycles of the first round of PCR amplification, the reaction was purified using 1x Ampure XP beads (Beckman Coulter A63881). The eluate was used as template for the second round of PCR using the Phusion enzyme and 12 cycles of amplification. The second round of PCR was designed so that indexes were added to each sample. The samples were then purified using 0.8x Ampure XP beads. Part of the purified libraries were run on a 2% agarose gel to check for size and absence of primer dimer (fragments below 200 bp considered as primer dimer). Then amplicons were sent for sequencing with NovaSeq 6000 or iSeq 100 platform.
Whole genome sequencing: DNA from single Arabidopsis seedlings was extracted with the Qiagen DNeasy plant mini kit and sheared to 300 bp size with a Covaris. Library preparation was performed with Tecan Ovation Ultralow V2 DNA-seq kit. The libraries were sequenced with the NovaSeq 6000 platform.


title: Flox#2 rep2

description:
1yTead1F_F-6582_S2_L002
1yTead1F_F-6582_S2_L002


title: SPECTRUM-OV-082_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: KOI4


title: Flox#1 rep2

description:
1yTead1F_F-6580_6585_S1_L002
1yTead1F_F-6580_6585_S1_L002


title: SPECTRUM-OV-082_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-082_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast vCasphi plasmid FWAgR6 rep1

value: FWA


title: Flox#1 rep1

description:
1yTead1F_F-6580_6585_S1_L001
1yTead1F_F-6580_6585_S1_L001


title: KOI2


title: SPECTRUM-OV-081_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast vCasphi plasmid FWAgR5 rep2


title: β-Tead1-KO#1 rep1

description:
1yrb-Tead1-_-6584_S3_L001
1yrb-Tead1-_-6584_S3_L001


title: SPECTRUM-OV-081_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-082_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Donor 1, scRNAseq, rep2

city: Brno

first: Radim

last: Jaroušek

state: Česká republika

address: Kotlářská 2

department: Immunology and experimental biology

country: Czech Republic

institute: Masaryk university

description:
3' mRNA library: Tcell_FSK_barcodes.tsv file contains cell barcode and UMI; Tcell_FSK_features.tsv file contains transcript;  Tcell_FSK_matrix.mtx contains cell counts
TCell_FSK_barcodes.tsv.gz
TCell_FSK_features.tsv.gz
TCell_FSK_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis,visualisation).
Assembly: GRCh38.p13
Supplementary files format and content: 10x Genomics output files: _barcodes.tsv.gz, _features.tsv.gz, _matrix.mtx.gz

source_name: Healthy donor blood

growth_protocol: Sorted Th naive cells (CD4+CD45RA+CD25-) were cultivated in ) RPMI 1640 containing 10 % (v/v) low endotoxin fetal bovine serum and 1% penicillin-streptomycin .

extract_protocol:
Cells were stained with TotalSeq-B cell feature barcode antibody to barcode each sample for multiplexing. Cells from each sample were pooled in equal cell numbers and loaded into a Chromium Controller (10X Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
Naïve CD4+ T cells were seeded activated with combination of plate-coated anti-CD3 (1 µg/ml) and soluble anti-CD28 antibody (10 ng/ml) for 30 min. Activated cells were incubated for 5 days in the presence of t  IL-12 (25 ng/ml) for Th1 differentiation; IL-4 (10 ng/mL) for Th2 differentiation; and IL-6 (25 ng/ml), IL-23 (25 ng/ml), IL-1β (25 ng/ml), TGF-β (0.25 ng/ml) for Th17 differentiation.
AC activator forskolin (10 µM) was added 20 h after activation and differentiation treatments, and treated cells were incubated for 5 days altogether.

value: T cells

value: Healthy donor blood

tag: library type

value: mRNA

value: not specified


title: Donor 1, HTO-derived cDNA, rep2

description:
Cell Hashing library:  file contains cell barcode and UMI; file contains Hashtag Antibody Derived Tag reads
TCell_FSK_barcodes.tsv.gz
TCell_FSK_features.tsv.gz
TCell_FSK_matrix.mtx.gz

library_source: other

molecule: protein

value: HTO


title: KOI1


title: SPECTRUM-OV-081_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast vCasphi plasmid FWAgR4 rep2

value: mysophyll protoplast

tag: developmental stage

value: wild type


title: WTI4

value: WT


title: Donor 1, HTO-derived cDNA, rep1


title: Fig4C WT protoplast vCasphi plasmid FWAgR6 rep2

value: 3-4 weeks

tag: strain


title: WTI5


title: SPECTRUM-OV-081_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast vCasphi plasmid FWAgR1 rep2

tag: background genotype


title: hashtags_1h_inf_with_Staph

first: Itai

last: Yanai

address: 430 East 29th St., Office 510

department: Biochemistry and Molecular Pharmacology

institute: New York University, School of Medicine

data_processing:
Basecalls was done using cellranger mkfastq V3.0.0
alignment, filtering, counting and umi counting was doe using cellranger count V3.0.0
hashing umi count was done using CITE-Seq v1.4.2
Assembly: human GRCh38-3.0.0
Supplementary files format and content: expression matrix of umi ocunts

source_name: Human monocytes derived macrophages

growth_protocol: human monocytes were isolated from PBMCs isolated from human blood by CD14+ expression, and incubated for 4 days with GM-CSF to differentiate into macrophages

extract_protocol:
macrophages were harvested by vigorously washing the cells using cold PBS supllemented with EDTA, washed and tagged according to the cell hashing protocol
10X single cell RNA seq V3

treatment_protocol: macrophages were infected with Staphylococcus at MOI 5 and infected for 1h

value: MDM


title: KOI3


title: Donor 1, scRNAseq, rep1


title: WTI2


title: 1h_inf_with_Staph


title: Fig4C WT protoplast vCasphi plasmid FWAgR1 rep1

tag: target locus


title: WTI3


title: SPECTRUM-OV-081_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-081_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast nCasphi plasmid FWAgR6 rep2


title: SPECTRUM-OV-080_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: pSS_13 cDC2s

city: Utrecht

first: Ana

middle: Pinheiro

last: Lopes

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq.
Variance stabilizing transformation (VST) was applied to obtain normalized gene counts.
Assembly: GrCh38 (v79)
Supplementary files format and content: Matrix table with normalized gene counts (VST) for every gene across all samples_Discovery
Supplementary files format and content: Matrix table with normalized gene counts (VST) for every gene across all samples_Replication

source_name: peripheral blood

extract_protocol:
CD1c-expressing cDC2s were isolated from peripheral blood mononuclear cells with the CD1c (BDCA-1)+ Dendritic Cell Isolation Kit (Miltenyi) according to manufacturer's instruction. Cells were lysed in RLTplus buffer (Qiagen) supplemented with beta-mercaptoethanol (1%). Total RNA was purified using AllPrep Universal Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was measured by capillary electrophoresis using a Bioanalyzer (Agilent), and the RNA 6000 Nano Kit (Agilent Technologies); all samples had RIN-score >7.0.
RNA libraries were prepared according to the standard Illumina protocols

tag: gender

value: Female

tag: group

value: primary Sjogren's syndrome

tag: cohort type

value: Discovery


title: Fig4C WT protoplast vCasphi plasmid FWAgR5 rep1


title: Fig4C WT protoplast nCasphi plasmid FWAgR5 rep2


title: Fig4C WT protoplast nCasphi plasmid FWAgR6 rep1


title: SPECTRUM-OV-081_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

tag: sort


title: Fig4C WT protoplast vCasphi plasmid FWAgR4 rep1


title: pSS_14 cDC2s

value: Male


title: pSS_12 cDC2s


title: P200_20.1_ELS_LPS

city: Amsterdam

first: Aniko

last: Korosi

state: Noord Holland

address: Sciencepark 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v2.10.
For each sample, the trimmed reads were mapped to the mouse genome GRCm39 using a short-read aligner based on Burrows—Wheeler Transform (STAR2 v2.5.4) with default settings.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0. Only unique reads that fall within exonic regions were counted.
Assembly: GRCm39
Supplementary files format and content: A count file containing gene counts per sample.

source_name: hippocampus

extract_protocol:
RNA was isolated with the RNeasy Micrro Kit (Qiagen, 74034) according to manufacturer’s instructions.
NEBNext Low Input RNA Library Prep Kit for Illumina (NEB #E6420S/L)

treatment_protocol: Microglia from ELS or control animals at P9 and at P200 after LPS or PBS treatment.

tag: condition

value: ELS

value: LPS

value: mouse microglia


title: pSS_11 cDC2s


title: pSS_10 cDC2s


title: Fig4C WT protoplast nCasphi plasmid FWAgR4 rep1

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

institute: University of California, Los Angeles

value: FWA


title: P200_17.2_ELS_PBS

value: PBS


title: Fig4C WT protoplast nCasphi plasmid FWAgR5 rep1


title: Fig4C WT protoplast nCasphi plasmid FWAgR1 rep2


title: SPECTRUM-OV-080_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: SPECTRUM-OV-080_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P200_20.2_ELS_PBS


title: Fig4C WT protoplast nCasphi plasmid FWAgR4 rep2


title: SPECTRUM-OV-080_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: pSS_09 cDC2s


title: SPECTRUM-OV-080_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-080_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P200_17.1_ELS_PBS


title: SPECTRUM-OV-080_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast control for FWAgR6


title: pSS_08 cDC2s


title: Fig4C WT protoplast nCasphi plasmid FWAgR1 rep1


title: WTI1

value: proximal Intestine

tag: genotype

value: 8-10 weeks


title: P200_4.2_ELS_LPS

tag: age


title: SPECTRUM-OV-077_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: P200_11.2_ELS_LPS


title: P200_11.1_ELS_PBS


title: P200_4.1_ELS_PBS


title: pSS_05 cDC2s


title: SPECTRUM-OV-080_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: pSS_07 cDC2s


title: Fig4C WT protoplast control for FWAgR4


title: P200_17.3_ELS_LPS


title: pSS_06 cDC2s


title: Fig4C WT protoplast control for FWAgR5


title: SPECTRUM-OV-077_S1_CD45P_CECUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast WTCasphi plasmid FWAgR6 rep2


title: P200_2.2_ELS_LPS


title: P200_18.3_CTR_LPS

value: CTR


title: P200_2.1_ELS_PBS


title: pSS_03 cDC2s


title: pSS_02 cDC2s


title: pSS_04 cDC2s


title: SPECTRUM-OV-077_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-077_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast control for FWAgR1

value: mysophyll protoplast


title: P200_18.1_CTR_PBS


title: SPECTRUM-OV-077_S1_CD45N_CECUM

description:
matrix.h5
GEO_cells.tsv


title: P200_18.2_CTR_PBS


title: pSS_01 cDC2s


title: Fig4C WT protoplast WTCasphi plasmid FWAgR6 rep1

value: wild type


title: nSS_09 cDC2s

value: non-Sjogren's sicca


title: Fig4C WT protoplast WTCasphi plasmid FWAgR5 rep2

value: 3-4 weeks


title: nSS_08 cDC2s


title: P200_15.1_CTR_PBS


title: SPECTRUM-OV-075_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-077_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P200_15.2_CTR_LPS


title: Fig4C WT protoplast WTCasphi plasmid FWAgR5 rep1


title: SPECTRUM-OV-077_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P200_8.3_CTR_LPS


title: nSS_06 cDC2s


title: P200_8.2_CTR_LPS


title: SPECTRUM-OV-077_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: nSS_07 cDC2s


title: Fig4C WT protoplast WTCasphi plasmid FWAgR4 rep2


title: Fig4C WT protoplast WTCasphi plasmid FWAgR1 rep2


title: Fig4C WT protoplast WTCasphi plasmid FWAgR4 rep1


title: nSS_05 cDC2s


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR6 rep2


title: nSS_03 cDC2s


title: SPECTRUM-OV-075_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4C WT protoplast WTCasphi plasmid FWAgR1 rep1


title: SPECTRUM-OV-075_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-075_S1_CD45P_LEFT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-075_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: nSS_04 cDC2s


title: SPECTRUM-OV-075_S1_CD45N_LEFT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: P200_8.1_CTR_PBS


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR6 rep1


title: P200_5.2_CTR_PBS


title: P200_5.3_CTR_LPS


title: nSS_01 cDC2s


title: nSS_02 cDC2s


title: SPECTRUM-OV-075_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P200_5.1_CTR_PBS


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR5 rep2


title: P200_1.2_CTR_LPS


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR5 rep1


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR4 rep2


title: HC_08 cDC2s

value: healthy control


title: HC_07 cDC2s

value: Female


title: SPECTRUM-OV-071_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-075_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: HC_06 cDC2s


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR4 rep1


title: P200_1.1_CTR_PBS


title: SPECTRUM-OV-071_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: HC_04 cDC2s


title: P9_58.2_CTR


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR1 rep2


title: SPECTRUM-OV-071_S1_CD45P_PELVIC_PERITONEAL_TUMOUR

description:
matrix.h5
GEO_cells.tsv


title: HC_05 cDC2s


title: Fig4AandSupFig6C fwa protoplast vCasphi plasmid FWAgR1 rep1


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR6 rep1


title: P9_52.2_CTR


title: P9_58.1_CTR


title: SPECTRUM-OV-071_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-071_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR6 rep2


title: P9_51.3_CTR


title: HC_03 cDC2s


title: P9_52.1_CTR


title: P200_1.3_CTR_LPS


title: SPECTRUM-OV-071_S1_CD45N_PELVIC_PERITONEAL_TUMOUR

description:
matrix.h5
GEO_cells.tsv


title: HC_02 cDC2s


title: HC_01 cDC2s


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep2

city: Boston

first: Susu

last: Zhang

address: 360 Longwood Ave, LC6102

institute: Dana-Farber Cancer Institute

description:
biotinylated RNA
4855-dTAG-2B.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-2B.4e7norm.minus.ucsc.bedgraph.gz.tdf

data_processing:
Library strategy: PRO-seq
Adaptors were trimmed and short/low quality sequence filtered by Trimmomatic-0.32: ILLUMINACLIP:adaptor.txt:2:30:7 TRAILING:15 MINLEN:15
Reverse complement sequence was generated using fastx_reverse_complement from the FASTX toolkit(v 0.0.13)
Reverse complement sequences were aligned to the human genome (hg19)+ S2 genome  using bowtie2 (v2.2.2)
samtools -view  generated .bam file with hg19 chromosomes
Differential transcript analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - pause_PROseq.pl with DESeq normalization
Differential eRNA analysis was carried out using the Nascent RNA Sequencing Analysis (NRSA) pipeline - eRNA.pl
Genome_build: hg19
Supplementary_files_format_and_content: Homer-generated bedgraph files, differential gene transcription analysis generated by NRSA

source_name: Rh30 cell line

extract_protocol:
following nuclear run-on, total RNA was isolated by Trizol extraction and biotinylated RNA isolated by streptavidin bead binding
follwing hydrolysis of RNA, 3'adaptors were ligated to biotinylated RNA fragments. After 5'Cap removal and end repair, 5' adaptors were also ligated. Adaptor-ligated RNA fragments were reverse transcribed and cDNA libraries amplified using indexed primers.

treatment_protocol: 500 nM dTAG47

value: 500nM dTAG47


title: P9_51.2_CTR


title: SPECTRUM-OV-071_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv

extract_protocol:
Dissociation: Tumor tissue was immediately processed for tissue dissociation. Fresh tissue was cut into 1 mm pieces and dissociated at 37°C using the Human Tumor Dissociation Kit (Miltenyi Biotec) on a gentleMACS Octo Dissociator. After dissociation, single cell suspensions were filtered and washed with ACK (Ammonium-Chloride-Potassium) Lysing Buffer. Cells were stained with Trypan Blue and cell counts and viability were assessed using the Countess II Automated Cell Counter (ThermoFisher) (for detailed protocol see 40). Sorting: Freshly dissociated cells were stained with a mixture of GhostRed780 live/dead marker (TonBo Biosciences) and Human TruStain FcX™ Fc Receptor Blocking Solution (BioLegend). The stained samples were then incubated and stained with Alexa Fluor® 700 anti-human CD45 Antibody (BioLegend). Post staining, they were washed and resuspended in RPMI + 2% FCS and submitted for cell sorting. The cells were sorted into CD45 positive and negative fractions by fluorescence assisted cell sorting (FACS) on a BD FACSAria™ III flow cytometer (BD Biosciences). Positive and negative controls were prepared and used to set up compensations on the flow cytometer. Cells were sorted into tubes containing RPMI + 2% FCS for sequencing.
Flow sorted tumor cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Chip B (10x Genomics PN 2000060). GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,400-5,000 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics PN 1000075) according to the manufacturer’s protocol. cDNA amplification included 12 cycles and 0.4-419ng of the material was used to prepare sequencing libraries with 8-14 cycles of PCR.


title: SPECTRUM-OV-071_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: P9_51.1_CTR


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR4 rep2

city: Los Angeles


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep1

description:
biotinylated RNA
4855-dTAG-2A.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-2A.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: SPECTRUM-OV-070_S1_CD45P_PELVIS

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR5 rep2


title: P9_55.3_ELS


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR1 rep2


title: SPECTRUM-OV-070_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR4 rep1


title: P9_55.2_ELS


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR1 rep1


title: P9_55.1_ELS


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG1hr_rep1

description:
biotinylated RNA
4855-dTAG-1A.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-1A.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG0.5hr_rep2

description:
biotinylated RNA
4855-dTAG-0.5B.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-0.5B.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: SPECTRUM-OV-070_S1_CD45P_HEPATIC_SURFACE

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-070_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C fwa protoplast nCasphi plasmid FWAgR5 rep1


title: Fig4AandSupFig6C fwa protoplast control for FWAgR6


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG0.5hr_rep1

description:
biotinylated RNA
4855-dTAG-0.5A.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-0.5A.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: Fig4AandSupFig6C fwa protoplast control for FWAgR5


title: SPECTRUM-OV-070_S1_CD45N_PELVIS

description:
matrix.h5
GEO_cells.tsv


title: P9_53.3_ELS


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep2

description:
biotinylated RNA
4855-dTAG-0B.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-0B.4e7norm.minus.ucsc.bedgraph.gz.tdf

value: DMSO


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG1hr_rep2

description:
biotinylated RNA
4855-dTAG-1B.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-1B.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: Fig4AandSupFig6C fwa protoplast control for FWAgR4


title: SPECTRUM-OV-070_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P9_53.2_ELS


title: 4855-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep1

description:
biotinylated RNA
4855-dTAG-0A.4e7norm.plus.ucsc.bedgraph.gz.tdf
4855-dTAG-0A.4e7norm.minus.ucsc.bedgraph.gz.tdf


title: SPECTRUM-OV-070_S1_CD45N_HEPATIC_SURFACE

description:
matrix.h5
GEO_cells.tsv


title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG4hr_rep2

description:
biotinylated RNA
5161-dTAG4-Comb.3e7norm.plus.ucsc.bedgraph.gz.tdf
5161-dTAG-4Comb.3e7norm.minus.ucsc.bedgraph.gz.tdf