title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG4hr_rep1


title: P9_17.3_CTR

status: Public on Dec 14 2022

type: SRA

city: Amsterdam

first: Aniko

last: Korosi

state: Noord Holland

address: Sciencepark 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

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: strain

tag: condition

value: CTR

tag: treatment

tag: age

tag: tissue

value: mouse microglia


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR6 rep1

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

library_source: genomic

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

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis mesophyll protoplast

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: mysophyll protoplast

tag: developmental stage

value: 3-4 weeks

tag: background genotype

tag: target locus

value: FWA


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR6 rep2


title: Fig4AandSupFig6C fwa protoplast control for FWAgR1


title: SPECTRUM-OV-068_S1_CD45P_INFRACOLIC_OMENTUM

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

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

organism: Homo sapiens

source_name: Omentum

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: P9_17.2_CTR


title: SPECTRUM-OV-068_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: P9_17.1_CTR


title: P9_53.4_ELS

value: ELS


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR5 rep2


title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep1

city: Boston

first: Susu

last: Zhang

state: MA

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
biotinylated RNA
5161-dTAG2-Comb.3e7norm.plus.ucsc.bedgraph.gz.tdf
5161-dTAG-2Comb.3e7norm.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

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

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: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR5 rep1


title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep2

description:
biotinylated RNA
5161-dTAG0-Comb.3e7norm.plus.ucsc.bedgraph.gz.tdf
5161-dTAG-0Comb.3e7norm.minus.ucsc.bedgraph.gz.tdf

value: DMOS


title: P9_15.2_CTR


title: P9_15.1_CTR


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR4 rep2


title: SPECTRUM-OV-068_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-067_S1_CD45P_RIGHT_OVARY_AND_TUBE

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: P9_53.1_ELS


title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_DMSO_rep1


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR4 rep1


title: input_UT

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

data_processing:
Raw reads quality control perfomed with Fastqc (version 0.11.5)
Reads alignment with BWA (0.7.16a) on hg38 human genome version
Bigwig files were generated using deeptools bamCoverage and bigwigCompare and normalized byRPGC, then by the correponding input using SES normalization
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

source_name: HeLa

growth_protocol: HeLa cells were routinely maintained in DMEM medium supplemented with 10% FBS and 2% glutamine

extract_protocol:
Cells were then crosslinked, collected and lysed according to the "ChIP-IT High Sensitivity" kit (Active Motif). Sheared chromatin was obtained using a probe sonicator and used for ChIP experiments using RNAPII and YTHDC1 antibodies.
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Control cells were kept at 37°C, stressed cells were incubated at a temperature of 43°C for 60 minutes in a water-bath

tag: cell type

value: HeLa (cervix adenocarcinoma from American Type Culture Collection, VA, USA)

tag: passages

tag: chip antibody


title: SPECTRUM-OV-067_S1_CD45N_LARGE_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: 5161-Rh30_PAX3-FOXO1-FKBP cells PRO-seq_dTAG2hr_rep2


title: SPECTRUM-OV-068_S1_CD45P_LARGE_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: P9_19.2_ELS


title: SPECTRUM-OV-068_S1_CD45N_LARGE_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C fwa protoplast WTCasphi plasmid FWAgR1 rep2


title: YTHDC1_UT


title: SPECTRUM-OV-065_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: P9_19.1_ELS


title: Fig4AandSupFig6C fwa protoplast WTCashi plasmid FWAgR1 rep1


title: input_HS

value: Heat shock


title: Fig4AandSupFig6C WT protoplast vCasphi plasmid PDS3gR8 rep2

value: wild type


title: P9_9.3_ELS


title: YTHDC1_HS


title: SPECTRUM-OV-067_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast vCasphi plasmid PDS3gR8 rep1


title: P9_9.2_ELS


title: hashtags_4h_inf_mut_donor_B

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
Genome_build: 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 densitiy gradient, 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 different bacteria at different MOI to get to 50% infection after 4 hours

value: MDM

tag: infection

value: WT Group B Streptococcus, cpsE Group B Streptococcus mutant and cylE Group B Streptococcus mutant


title: P9_19.3_ELS


title: Fig4AandSupFig6C WT protoplast vCasphi plasmid PDS3gR10 rep2


title: SPECTRUM-OV-065_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: P9_9.1_ELS


title: SPECTRUM-OV-065_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Pan02 whole tumor, TGFb-vaccine, mouse 3 [Tumor_27]

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned to mm10 using STAR
Reads at genes were quantified by featureCount
Supplementary files format and content: Count_table.txt

source_name: Subcutaneous whole tumor

growth_protocol:
Pan02 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.
Mice were injected subcutaneously (s.c.) on the right flank with 0.5 million  Pan02 cancer cells.

extract_protocol:
Tumor fragments (≤ 20 mg) in RNAlater (Invitrogen) were transferred to RLT buffer (Qiagen) and mechanically homogenized with a Tissue Lyser (Qiagen). RNA was extracted with the RNEasy Plus Mini Kit (Qiagen),
500ng purified RNA (RIN score > 7) was enriched for polyadenylated mRNA followed by fragmentation. Random primmed cDNA synthesis was performed using NEBNext kits. This was followed by hairpin adaptor ligation and PCR mediated indexing (NEBNext). The library was size selected using AMPure beads and quantified by KAPA (Roche).

treatment_protocol: Mice were vaccinated on day 10 and 17 post-inoculation with a TGFb-derived multi-peptide vaccine adjuvanted with Montanide.

tag: Sex

value: female

value: Subcutaneous whole tumor

tag: cell line

value: pancreatic ductal adenocarcinoma

tag: genotype

value: WT

value: TGFb-vaccine


title: SPECTRUM-OV-065_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast vCasphi plasmid PDS3gR10 rep1


title: Fig4AandSupFig6C WT protoplast nCasphi plasmid PDS3gR8 rep2


title: hashtags_4h_inf_donor_K

value: Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Group B Streptococcus, Yersinia pseudotuberculosis, Shigella flexneri and Salmonella enterica


title: hashtags_4h_inf_mut_donor_A


title: SPECTRUM-OV-065_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Pan02 whole tumor, TGFb-vaccine, mouse 2 [Tumor_26]


title: SPECTRUM-OV-065_S1_CD45N_RIGHT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: hashtags_4h_inf_donor_J


title: Pan02 whole tumor, TGFb-vaccine, mouse 1 [Tumor_25]


title: hashtags_2h_inf_donor_J


title: Pan02 whole tumor, untreated, mouse 4 [Tumor_24]

value: Untreated


title: Fig4AandSupFig6C WT protoplast nCasphi plasmid PDS3gR10 rep2

value: mysophyll protoplast

value: 3-4 weeks


title: SPECTRUM-OV-065_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast nCasphi plasmid PDS3gR8 rep1


title: SPECTRUM-OV-054_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: hashtags_4h_inf_donor_H


title: Fig4AandSupFig6C WT protoplast nCasphi plasmid PDS3gR10 rep1


title: SPECTRUM-OV-054_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast control for PDS3gR8


title: Pan02 whole tumor, untreated, mouse 2 [Tumor_22]


title: hashtags_2h_inf_donor_H


title: Fig4AandSupFig6C WT protoplast control for PDS3gR10


title: SPECTRUM-OV-054_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Pan02 whole tumor, untreated, mouse 3 [Tumor_23]


title: SPECTRUM-OV-054_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: hashtags_4h_inf_donor_D1


title: hashtags_4h_inf_donor_D2


title: Pan02 whole tumor, untreated, mouse 1 [Tumor_21]


title: KP_6

city: Lexington

first: Yifan

last: Kong

state: Kentucky

address: 760 Press Avenue, HKRB, Room 334

institute: University of Kentucky

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads filtering is as follows: (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
STAR software is used to accomplish the mapping. The alignment by STAR performs precise and effective in positioning junction reads for RNA sequencing data analysis.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads
HTSeq v0.6.1 was used to count the read numbers mapped of 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, Reads Per Kilobase of exon model per Million mapped reads, 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
Assembly: mm10
Supplementary files format and content: Exel. Raw read counts and fkpm

source_name: lung tumor

extract_protocol:
Total RNA was isolated from tumors with the RNeasy® mini kit ((#74104, Qiagen) according to the manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was synthesized using  random hexamer primers followed by the second strand cDNA synthesis. The library  was ready after end repair, A-tailing, adapter ligation, size selection, amplification,  and purification.

value: lung tumor

value: loxP-STOP-loxP (LSL)-KrasG12D; p53fl/fl

value: harvested at 12 weeks post Ad-Cre delivery


title: Fig4AandSupFig6C WT protoplast WTCasphi plasmid PDS3gR8 rep2


title: SPECTRUM-OV-053_S1_CD45P_RIGHT_DIAPHRAGM

description:
matrix.h5
GEO_cells.tsv

source_name: UQ


title: SPECTRUM-OV-053_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast WTCasphi plasmid PDS3gR10 rep2


title: hashtags_2h_inf_donor_K


title: KP_4


title: Fig4AandSupFig6C WT protoplast WTCasphi plasmid PDS3gR8 rep1


title: hashtags_4h_inf_donor_C2


title: hashtags_4h_inf_donor_C1


title: hashtags_4h_inf_donor_A


title: KP_5


title: KPP_6

value: loxP-STOP-loxP (LSL)-KrasG12D; p53fl/fl ;Rosa26LSL-Plk1/+


title: SPECTRUM-OV-053_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig4AandSupFig6C WT protoplast WTCasphi plasmid PDS3gR10 rep1


title: hashtags_4h_inf_donor_B1


title: Fig3D pUB10 A form rep1


title: KPP_5


title: SPECTRUM-OV-053_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_mut_donor_A


title: Fig3D CmYLCVp ribozyme A form rep2


title: KP_1


title: Fig3D pUB10 A form rep2


title: Fig3D pUB10 ribozyme A form rep2


title: SPECTRUM-OV-053_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-053_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_mut_donor_B


title: SPECTRUM-OV-053_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: KP_3


title: KPP_3


title: hashtags_4h_inf_donor_B2


title: KPP_1


title: KPP_4


title: 4h_inf_donor_K


title: KP_2


title: SPECTRUM-OV-052_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Fig3D CmYLCVp ribozyme A form rep1


title: Fig3D pUB10 ribozyme A form rep1


title: SPECTRUM-OV-053_S1_CD45N_RIGHT_DIAPHRAGM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-052_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: KPP_2


title: 2h_inf_donor_K


title: Fig3D 2x35Sp ribozyme A form rep2


title: Fig3Cand3D CmYLCVp A form rep1


title: LAMS HTGTS-seq setx-/- cut biol rep 2

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

description: digested to enrich for translocation

data_processing:
For LAMS-HTGTS, sequences were processed and analyzed as detailed in (Crowe et al., 2018; Hu et al., 2016; https://github.com/robinmeyers/transloc_pipeline) with minor adjustments. Briefly, sequences were aligned to custom genomes, substituting the mm9 sequence from (114, 494, 415–114, 666, 816) with sequence from the NG_005838.1 (Genbank accession no. NG_005838.1) C57BL/6 IgH sequence on chr 12 (to 11,172 to 183,818), or sequence from the AJ851868.3 (GenBank accession no AJ851868.3) 129 IgH sequence (1,415,966– 1,592,715).Junctions were analyzed by comparing sequences to both C57BL/6 and S129 backgrounds. A consensus genome was generated between C57BL/6 and S129, and if reads fell into either category they were deemed not mutated—this eliminated over-estimation of insertions, deletions, and mismatch mutations. Of note, no junctions aligned to S129 on one side and C57BL/6. Deletions are defined as regions missing nucleotides adjacent to prey-break site but having 100% homology in flanking regions. Insertions are defined as regions containing nucleotides that map to neither the bait nor the prey-break site. Microhomologies (MHs) are defined as regions of 100% homology between the bait and the prey-break site. Blunt junctions are considered to have no MHs or insertions. Additional scripts used to analysis can be found in github (https://github.com/srhartono/TCseqplus).
For DRIP-seq, raw sequencing reads were trimmed with fastq-mcf v2.4.4 and mapped to mm9 genome with bowtie2 v2.2.6. Wig files were generated using bedtools genomecov and converted into bigWig using wigToBigWig; scores indicate tag per million (x30). Peak bed files were generated using HMM as previously described in (Sanz et al., 2016) and converted into bigBed using bedToBigBed.
Assembly: mm9
Supplementary files format and content: bigWig, bigBed, and tlx (tab-separated files containing translocation coodinates and information)
Library strategy: LAMS-HTGTS

source_name: Spleen

growth_protocol: Setx-/- , Rnaseh2bf/f, and CD19cre mice were previously described and used to generate Setx-/- Rnaseh2bf/f CD19cre mice (Becherel et al., 2013; Hiller et al., 2012; Rickert et al., 1997)

extract_protocol:
For LAMS-HTGTS, genomic DNA was isolated from WT, Setx-/- , Rnaseh2bf/f , and Setx-/- Rnaseh2bf/f cells 72 hours after stimulation to switch to IgG1 with 72 h LPS/IL-4/α-RP105.
For DRIP-seq, genomic DNA was gently extracted by SDS/Proteinase K treatment at 37°C followed by phenol-chloroform extraction and ethanol precipitation. The extracted genomic DNA was fragmented with restriction enzyme (Hindlll, Xbal, EcoRI, SspI, BrsGI), 4 micrograms of digested DNA were incubated with 2 micrograms of S9.6 antibody overnight at 4 ℃ in DRIP buffer (10 mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100). In vitro RNase H digestion was used to generate a negative control. After incubation, antibody-DNA complexes were bound to Protein G Dynabeads and thoroughly washed, DNA was recovered with Chelex-100, the bound fraction was suspended in 0.1 ml 10% Chelex-100 (Bio-Rad), vortexed, boiled for 10 min, and cooled to room temperature. This sample was added to 4 μl of 20 mg/ml Proteinase K followed by incubation at 55°C for 30 min while shaking. Beads were boiled for another 10 min. Sample was centrifuged and supernatant collected. Beads were suspended with 100 μl 2× TE to the beads, vortexed, centrifuged, and supernatants pooled.
For LAMS-HTGTS, linear amplification-mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) libraries were prepared from genomic DNA as previously described (Hu et al., 2016; Yin, Liu, Liu, & Hu, 2019; Yin, Liu, Liu, Wu, et al., 2019).
For DRIP-seq, libraries were prepared as described in (Ginno et al., 2012; Sanz et al., 2016)

treatment_protocol:
CD43- resting B cells were isolated and cultured in B cell media (BCM, RPMI-1640 supplemented with 10% fetal calf serum, 1% L-glutamine, 50 IU/ml penicillin/streptomycin, 1% sodium pyruvate, 53 μM 2-mercaptoethanol, 10 mM HEPES).
B cells were stimulated with LPS, α-RP105 and interleukin 4 (IL-4) for IgG1, LPS/α-RP105/TGF-B for IgG2b and LPS/α-RP105/TGF-B/CD40L for IgA class switch recombination.

value: Spleen

value: primary B cells

value: setx-/-


title: SPECTRUM-OV-052_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-051_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: 2h_inf_donor_J

value: MDM


title: Fig3D 2x35Sp ribozyme A form rep1

value: wild type


title: SPECTRUM-OV-052_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig3D 2x35Sp A form rep2


title: Mutant_soft palate

city: Alhambra

first: Eva

last: Janeckova

address: 2250 Alcazar street

institute: USC, CCMB

library_source: transcriptomic single cell

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 3.1.0.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: Soft palate

extract_protocol:
Soft palate tissue (dissected from the posterior third of the palatal region) from E14.5 control and Osr2-Cre;Alk5fl/fl embryos was digested and dissociated into single-cell suspension with TrypLE Express enzyme (12605010, Thermo Fisher Scientific) at 37°C with shaking at 600 rpm for 15 min using a Thermomixer (2231000269, Thermo Fisher Scientific). Single-cell suspension was loaded into the 10X Chromium system and prepared for single-cell library construction using the 10X Genomics Chromium single-cell 3’ v2 reagent kit (PN-120267, 10X Genomics) according to the manufacturer’s protocol. Sequencing was performed on Novaseq 6000 (Illumina). Library quality control, sequence alignment, and read counts were analyzed using Cell Ranger 4.0.0. Two control samples were combined using the function cellranger aggr so that the combined control sample had comparable cell numbers to the sample from Osr2-Cre;Alk5fl/fl.
cDNA libraries were prepared for sequencing using standard 10X Genomics protocols

tag: genotype/variation

value: Soft palate


title: Fig3C pUB10 C form rep2

tag: strain


title: SPECTRUM-OV-051_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: Control_soft palate2

value: control


title: 2h_inf_donor_H


title: LAMS HTGTS-seq rnaseh2b-/- cut biol rep 2

description: digested to enrich for translocation


title: 4h_inf_donor_D2


title: SPECTRUM-OV-051_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig3Cand3D GFP control


title: Control_soft palate1


title: SPECTRUM-OV-051_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: LAMS HTGTS-seq rnaseh2b-/- setx-/- cut biol rep 2

description: digested to enrich for translocation

value: rnaseh2b-/- setx-/-


title: 4h_inf_donor_B2


title: SPECTRUM-OV-050_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig3C pUB10 C form 30 bp spacer rep2


title: SPECTRUM-OV-050_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: LAMS HTGTS-seq WT cut biol rep 1

description: digested to enrich for translocation

value: WT


title: 4h_inf_donor_B1

value: Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Group B Streptococcus, Yersinia pseudotuberculosis, Shigella flexneri and Salmonella enterica


title: Fig3C pUB10 C form 30 bp spacer rep1


title: Fig3Cand3D CmYLCVp A form rep2


title: SPECTRUM-OV-050_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_donor_J


title: 4h_inf_donor_D1


title: 4h_inf_donor_C2


title: Fig3D 2x35Sp A form rep1


title: 4h_inf_donor_H


title: LAMS HTGTS-seq WT cut biol rep 2

description: digested to enrich for translocation


title: LAMS HTGTS-seq rnaseh2b-/- cut biol rep 1

description: digested to enrich for translocation


title: SPECTRUM-OV-050_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_with_GBS_donor_A

value: GBS


title: SPECTRUM-OV-050_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-051_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-049_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_donor_C1


title: Fig3C CmYLCVp A form 30 bp spacer rep2

value: mysophyll protoplast


title: Fig3C pUB10 C form rep1

value: 3-4 weeks


title: SPECTRUM-OV-049_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: LAMS HTGTS-seq setx-/- cut biol rep 1

description: digested to enrich for translocation


title: SPECTRUM-OV-050_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: 4h_inf_donor_A


title: Fig3C CmYLCVp A form 30 bp spacer rep1


title: MM-17-85-1

city: Brno

first: Jana

last: Gregorova

address: Kamenice 5

country: Czech Republic

institute: Masaryk University

data_processing:
Adaptor trimming, alignment and read count performed using Chimira tool (http://wwwdev.ebi.ac.uk/enright-dev/chimira/)
Supplementary_files_format_and_content: counts

source_name: Bone marrow plasma cells

growth_protocol: The cells were stored at -80°C

extract_protocol:
The miRNA was isolated using miRNeasy Mini Kit (Qiagen)
Libraries were prepared according to Trilink instruktions accompanying the CleanTag Small RNA Library Prep Kit.

tag: disease

value: Extramedullary disease


title: MM-17-83-1

value: Multiple myeloma


title: SPECTRUM-OV-050_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: MM-16-94-1


title: LAMS HTGTS-seq rnaseh2b-/- setx-/-  biol rep 2

tag: treatment


title: Fig3C CmYLCVp C form rep2


title: Fig3C CmYLCVp C form rep1


title: LAMS HTGTS-seq rnaseh2b-/-  biol rep 2


title: MM-16-9-1


title: LAMS HTGTS-seq rnaseh2b-/- setx-/- cut biol rep 1

description: digested to enrich for translocation


title: Fig3C CmYLCVp C form 30 bp spacer rep2


title: SPECTRUM-OV-045_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: LAMS HTGTS-seq setx-/-  biol rep 2


title: SPECTRUM-OV-049_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: LAMS HTGTS-seq WT  biol rep 2


title: LAMS HTGTS-seq rnaseh2b-/-  biol rep 1


title: Fig3C CmYLCVp C form 30 bp spacer rep1


title: Fig3C 2x35Sp C form rep2


title: MM-16-126-1


title: WT BMDM LPS-treated rep3

city: Seoul

first: Soo Young

last: Lee

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

data_processing:
Illumina bcl2fastq  v2.20.0.422 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.18
mapped to mm10 whole genome using TopHat v2.0.13 and calculate abundance using cuffdiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow

growth_protocol: Murine bone marrow-derived macrophages were generated by flushing out the bone marrow cells in the femurs and tibias of 8-10-week-old C57BL/6 male mice, suspending them in DMEM (Hyclone) supplemented with 20% FBS (Hyclone), 100 units ml-1 penicillin (Hyclone) and 100 μg/ml streptomycin (Hyclone), and culturing them at 37°C, 5% CO2 for 1 d. Non-adherent cells were then further cultured with 10 ng/ml recombinant human macrophage colony-stimulating factor (R&D Systems) for 7 d

extract_protocol:
Total RNA was extracted from cells with Monarch Total RNA Miniprep Kit (New England Biolabs, Cat#T2010S) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing according to Illumina's protocols using the Truseq Stranded mRNA Prep Kit.

treatment_protocol: Cells were seeded in 12-well plates and then treated with 100 ng/ml LPS (Sigma-Aldrich) for 4 h

value: Bone marrow-derived macrophages (BMDMs)

value: LPS-treated


title: LAMS HTGTS-seq setx-/-  biol rep 1

value: Spleen


title: Fig3B PDS3gR10 pUB10 B form


title: SPECTRUM-OV-045_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: MM-16-104-1


title: WT BMDM LPS-treated rep2


title: LAMS HTGTS-seq WT  biol rep 1

value: primary B cells


title: MM-16-92-1


title: SPECTRUM-OV-045_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-042_S1_CD45P_RIGHT_DIAPHRAGM

description:
matrix.h5
GEO_cells.tsv


title: MM-11-182-1


title: SPECTRUM-OV-049_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig3B PDS3gR10 U6 promoter


title: Fig3C 2x35Sp C form rep1


title: MM-17-58-1


title: Fig3C 2x35Sp C form 30 bp spacer rep2


title: MM-17-48-1


title: SPECTRUM-OV-045_S1_CD45P_PELVIC_IMPLANT

description:
matrix.h5
GEO_cells.tsv

source_name: Other


title: Fig3C 2x35Sp C form 30 bp spacer rep1


title: LAMS HTGTS-seq rnaseh2b-/- setx-/-  biol rep 1


title: SPECTRUM-OV-045_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: MM-16-10-1


title: MM-16-96-1


title: Fig3B PDS3gR10 pUB10 C form


title: Fig3B PDS3gR10 CmYLCVp C form


title: WT BMDM untreated rep1

value: untreated


title: SPECTRUM-OV-045_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig3B PDS3gR10 pUB10 A form


title: Fig3B PDS3gR10 CmYLCVp B form


title: WT BMDM LPS-treated rep1


title: SPECTRUM-OV-042_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: MM-11-160-1


title: Fig3B PDS3gR10 CmYLCVp A form


title: Fig3B PDS3gR10 control


title: WT BMDM untreated rep2


title: MM-15-136-1


title: M-B09136-JOBU


title: SPECTRUM-OV-042_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Fig3B PDS3gR10 2x35Sp C form

source_name: Arabidopsis mesophyll protoplast


title: SPECTRUM-OV-042_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: Pim1-KO BMDM untreated rep3


title: Fig3B PDS3gR10 2x35Sp B form


title: SPECTRUM-OV-042_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: WT BMDM untreated rep3


title: M-012071


title: SPECTRUM-OV-042_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: M-B12084-LP


title: Pim1-KO BMDM LPS-treated rep3


title: Fig2C fwa protoplast FWAgR6 rep2

value: FWA


title: M-B16054-JMO


title: M-B06004-FRKR


title: Pim1-KO BMDM LPS-treated rep2


title: SPECTRUM-OV-041_S1_CD45P_RIGHT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: M-B11030-SD


title: 144_RNAseq_shKDM1A_IL4_4

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

description: diff_shKDM1A_KD_IL4_RNA_seq_raw_tags.output.txt

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.

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

value: Macrophage

value: BALB/c

value: IL4 6h

value: No antibody

tag: chip antibody vendor

value: No

tag: chip antibody cat.


title: Pim1-KO BMDM LPS-treated rep1


title: SPECTRUM-OV-042_S1_CD45N_RIGHT_DIAPHRAGM

description:
matrix.h5
GEO_cells.tsv


title: M-B15025-VC


title: M-B11151-JB


title: Fig3B PDS3gR10 2x35Sp A form

tag: tissue

tag: developmental stage

value: wild type


title: Pim1-KO BMDM untreated rep2


title: 142_RNAseq_shKDM1A_IL4_2


title: SPECTRUM-OV-042_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: 143_RNAseq_shKDM1A_IL4_3


title: Fig2C fwa protoplast FWAgR6 rep1

tag: background genotype

tag: target locus


title: Pim1-KO BMDM untreated rep1

tag: cell type


title: SPECTRUM-OV-041_S1_CD45N_RIGHT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv

tag: sort


title: SPECTRUM-OV-041_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: MM-11-76-1


title: SPECTRUM-OV-041_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig2C fwa protoplast FWAgR4 rep2


title: 141_RNAseq_shKDM1A_IL4_1

tag: chip antibody


title: Fig2C fwa protoplast FWAgR5 rep2


title: SPECTRUM-OV-041_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: MM-10-248-1


title: SPECTRUM-OV-041_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: 139_RNAseq_shKDM1A_3

value: Control


title: SPECTRUM-OV-037_S1_CD45P_LUQ_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: MM-11-133-1


title: Fig2C fwa protoplast FWAgR5 rep1

value: mysophyll protoplast


title: MM-16-125-1


title: Fig2C fwa protoplast FWAgR4, gR5, gR6 control

value: 3-4 weeks


title: 140_RNAseq_shKDM1A_4


title: Fig2C fwa protoplast FWAgR4 rep1


title: MM-11-55-1


title: MM-11-93-1


title: SPECTRUM-OV-037_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: 136_RNAseq_shGFP_4


title: Fig2C fwa protoplast FWAgR1 control


title: Fig2C fwa protoplast FWAgR1 rep2


title: 138_RNAseq_shKDM1A_2


title: Fig2C WT protoplast FWAgR6 rep1


title: Fig2C fwa protoplast FWAgR1 rep1


title: MM-12-129-1


title: SPECTRUM-OV-037_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-037_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig2C WT protoplast FWAgR5 rep2


title: MM-17-94-1


title: 137_RNAseq_shKDM1A_1


title: 132_RNAseq_shGFP_IL4_4


title: SPECTRUM-OV-036_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: MM-16-90-1


title: Fig2C WT protoplast FWAgR5 rep1


title: SPECTRUM-OV-037_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Fig2C WT protoplast FWAgR6 rep2


title: SPECTRUM-OV-037_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: MM-11-89-1


title: 135_RNAseq_shGFP_3


title: SPECTRUM-OV-036_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: MM-16-62-1


title: 134_RNAseq_shGFP_2


title: MM-16-140-1


title: Fig2C WT protoplast FWAgR4 rep2


title: 133_RNAseq_shGFP_1


title: MM-16-93-1


title: MM-16-13-1


title: Fig2C WT protoplast FWAgR1 rep2


title: Fig2C WT protoplast FWAgR4, gR5, gR6 control


title: SPECTRUM-OV-036_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-036_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: MM-16-30-1


title: 130_RNAseq_shGFP_IL4_2


title: MM-12-210-1


title: Fig2C WT protoplast FWAgR1 rep1


title: Fig2C WT protoplast FWAgR4 rep1


title: 129_RNAseq_shGFP_IL4_1


title: MM-15-127-1


title: 131_RNAseq_shGFP_IL4_3


title: 110_cut_and_tag_shKDM1A_KDM1A

description: library strategy: Cut&Tag

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.
Supplementary_files_format_and_content: ChIP-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
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.
Supplementary_files_format_and_content: ATAC-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
4C-seq raw files (fastq, single-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window. As the 4C-seq program only provides the heatmaps, only the list of the 4C primers which was used to amplified the signals is provided.
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.
Supplementary_files_format_and_content: RNA-seq: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.
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.
Supplementary_files_format_and_content: CUT&TAG: Bedgraph files contain the genomic coordinates and p-value of each peak. The differential expression files were further provided.

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.
4C-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 2×105 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.
4C-Seq: Fresh cells were crosslinked with 2% formaldehyde for 10 min at room temperature. Cells were counted and aliquoted with 10x7 cells per tube. For each 4C sample, 1 ml lysis buffer was applied for 10 min. Nuclei were spined down and discarded the supernatant. The nuclei were treated with the first digestion enzyme (Dpn II) overnight. The next day, the cell nuclei were heat-inactivated at 65C for 20 min and then treated with the first ligation enzyme overnight at room temperature. The genomic DNA was extracted and followed with the second digestion enzyme (Bfa I) overnight. Then heat-inactivated the enzyme and applied with then second the ligation enzyme overnight. The genomic DNA was purified again by phenol-chloroform extraction.
4C-Seq: PCR purified DNA (by baits) 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.
RNA-Seq: 2×105 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: 2×105 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 .
4C-Seq: RAW264.7 cells were treated  with or without LPS (100ng/ml) or IL4 (20ng/ml) treatment for indicated time.
RNA-Seq: BMDM cells were treated  with or without IL4 (20ng/ml) treatment for 6h.
Cut&Tag: No treatment

value: Abcam


title: SPECTRUM-OV-036_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: Fig2B FWAgR8 RNP edited protoplast


title: SPECTRUM-OV-036_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: 111_cut_and_tag_shKDM1A_MED1_rp1

description: library strategy: Cut&Tag

value: Bethyl


title: 112_cut_and_tag_shKDM1A_MED1_rp2

description: library strategy: Cut&Tag


title: Fig2C WT protoplast FWAgR1 control


title: SPECTRUM-OV-031_S1_CD45P_INFRARENAL_LYMPH_NODE

description:
matrix.h5
GEO_cells.tsv


title: MM-15-100-1

value: Multiple myeloma


title: Fig2B FWAgR9 RNP edited protoplast


title: Fig2B FWAgR7 RNP edited protoplast


title: 109_cut_and_tag_shKDM1A_H3K27ac_rp2

description: library strategy: Cut&Tag


title: MM-15-31-1


title: SPECTRUM-OV-031_S1_CD45P_LEFT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-031_S1_CD45N_INFRARENAL_LYMPH_NODE

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-036_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: MM-14-6-1


title: MM-14-57-1


title: SPECTRUM-OV-031_S1_CD45N_LEFT_FALLOPIAN_TUBE

description:
matrix.h5
GEO_cells.tsv


title: 105_cut_and_tag_shKDM1A_H3K4me3_rp2

description: library strategy: Cut&Tag


title: 107_cut_and_tag_shKDM1A_H3K9me3_rp2

description: library strategy: Cut&Tag


title: 106_cut_and_tag_shKDM1A_H3K9me3_rp1

description: library strategy: Cut&Tag


title: SPECTRUM-OV-036_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: MM-12-163-1


title: SPECTRUM-OV-026_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Fig2B FWAgR7, gR8, gR9 control


title: sci-Plex D28 D78 D185 (snRNA-seq)

city: Seattle

first: Amy

middle: Moreda

last: Tresenrider

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
cds_joint_annotated_220712.RDS
Note, d28_d78_d185_sci_unfiltered_gene_metadata.csv and d28_individuals_unfiltered_gene_metadata.csv are the same.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Brotman Baty sci-RNA-seq demultiplexing and processing pipelines (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci).   The output of the pipeline was further analyzed using Monocle3
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:
D28: 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.  D78 + D185: 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.
The library was prepared by the original sci-RNA-seq protocol (Cao et al., 2017). A reverse transcription reaction with barcoded RT primers captured 3'-polyAdenylated transcripts. Using FACs, nuclei were sorted into wells of 96-well plates where second strand synthesis was followed by tagmentation of dsDNA. PCR was performed with barcoded primers and the library was size-selected. The unique combination of barcodes in the RT and PCR steps enable the reconstruction of individual cells in silico.
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

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

value: WA09 (H9) hESC with NRL-GFP

tag: fraction

value: nuclear polyA RNA


title: SPECTRUM-OV-026_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: MM-13-77-1


title: SPECTRUM-OV-026_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: 103_cut_and_tag_shKDM1A_GPS2_rp2

description: library strategy: Cut&Tag

value: Home made


title: Fig2B FWAgR5 RNP edited protoplast

value: FWA


title: 104_cut_and_tag_shKDM1A_H3K4me3_rp1

description: library strategy: Cut&Tag

value: Macrophage


title: 108_cut_and_tag_shKDM1A_H3K27ac_rp1

description: library strategy: Cut&Tag

value: BALB/c


title: RNAiSvb rep3

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

institute: Centre de Biologie Intégrative de Toulouse

data_processing:
Quality of sequencing was measured with fastQC (v0.11.5)
Sequenced reads were mapped on Drosophila genome (r6.13 Flybase) with STAR (v 2.5.2b default parameters)
Reads were counted with HTseq-count (v 0.6.0, parameter -t gene -r pos - i gene_symbol)
Statistical analysis were performed with edgeR using the negative binomial generalized log-linear model to the read counts ( gmLRT), the TMM normalization and decideTest were used to determine the differentially expressed genes.
Clustering analysis was performed on the matrix of the reads count average centrered and reduced for each condition previously filtered for the gene expression (difference of read > 50 between condition. n = 3556 gene
Two steps of clustering were done. The hierarchical ascendant clustering was performed with R function hclust() with the Spearman distance and the Ward.D2 option.
The k-means clustering was done with R function kmeans() with default options and k = 5. The kmeans clustering was repeated 15 times ( 5 times with predefined centroid and 10 with random centroids). The predefined centroids are genes of differents cluster defined by the hierarchical clustering.
Different k-means clusters obtained by each repetition were compared with cluster_similarity (Clusteval v 0.1). Clustering is similar if the score eaqual 1.
Assembly: dm6
Supplementary files format and content: bigwig file of each condition Smooth (bin:200) for representation
Supplementary files format and content: Matrix table with normalized counts, logFC, Pvalue, LogCPM, status for expressed genes

organism: Drosophila melanogaster

source_name: Intestinal Stem Cell

growth_protocol: esg-Gal4, UAS-GFP; tubGal80TS/SM66B flies were crossed to the following strains: Canton-S (BL#64349), UAS-SvbRNAi (VDRC# 41584), UAS-SvbACT::GFP (al Hayek et al., 2021), UAS-Svb3Kmut::GFP (al Hayek et al., 2021). Adult progeny (only virgin females) was aged 3 days at room temperature, then transferred at 29°C for 6 days prior to midgut dissection.

extract_protocol:
RNA were purified from each cell sample using MasterPure RNA purification kit (Epicentre), following manufacturer’s recommendation. Sorted cells were incubated at 65°C with rocking for 15 minutes. Samples were put on ice then total nucleic acid were precipitated. Contaminating DNA was removed using DNase, then nucleic acids were precipitated again. RNAs were finally resuspended in 10uL TE and 1uL RiboGuard (RNases inhibitor) and stored at -20°C.
Construction of RNA banks and sequencing was made at the Montpellier GenomiX Platform (MGX). RNA banks were obtained using the Ovation SoLo RNAseq System kit (Nugen). Bank validation was done with the quantification of the complementary DNA with the Standard Sensitivity NGS kit on Fragment Analyzer and with qPCR (ROCHE Light Cycler 480). 100nt single-reads sequencing was performed on NovaSeq 6000 (Illumina) with NovaSeq Reagent Kits (100cycles).

treatment_protocol:
Batches of >20 virgin females are CO2-anaethesized and put on ice. From then, all solutions are used cold and samples kept on ice whenever possible. Their midgut are dissected in 1XPBS and transferred to a clean PBS dish. Malpighian tubules and hindgut are removed and only the posterior part of the midgut is kept (R3, R4, R5). PBS was replaced by PBS1X-EDTA 1mM. Posterior midguts were transferred on a glass slide in a droplet of PBS, and shrinked into pieces using a razorblade. Samples were transferred into a fresh tube and spun 3- 5minutes at 1000rpm 4°C to pellet the tissue and remove all supernatant except 50μL. 200uL TrypLE 10X (8X final with 0.2mM EDTA) was added for enzymatic digestion. Then the guts were incubated at 37°C and rocked vigorously for 10 minutes. Digestions were stopped with 750μL SSM (Serum Supplemented Medium = S2 Cell culture medium). Trituration was made by pipetting up and down using low binding, flame-rounded narrow tips (5 times with narrow tip; 2-3 times with very narrow tip).
Strain the cell solution (70μM nylon cell strainer, pre-wet with SSM) into a falcon tube. The tube and the strain were rinsed thrice with 1mL PBS-EDTA. The quality of the dissociation and the health of the cells in solution can be checked under a fluorescent macroscope. Samples were spun at 700rcf, 4°c, for >10 minutes and supernatant carefully removed except 100/200μL. 200μL PBS + 3μL clean NGS were added to obtain final samples for FACS. For each cell sample a tube was prepared with 300μL Tissue and Cell Lysis solution + 1μg Proteinase K [50μg/μL]. Cells are sorted in this buffer, vortexed and placed on ice just after sorting. RNA extraction was started less than 1 hour after sorting

value: GAL4/GAL80TS system allows spacial and temporal control of UAS induction. UASs were activated in ISCs for 6 days before midgut dissection

value: Posterior midgut (R3 to R5)

tag: age

value: 9 days (6 days of induction)

tag: Sex

value: female

value: Intestinal Stem Cell

value: 3 days old female flies were transfered to 29°C for 6 days, to induce UASs expression.


title: Fig2B FWAgR4, gR5, gR6 control

value: mysophyll protoplast

value: 3-4 weeks

value: wild type


title: 102_cut_and_tag_shKDM1A_GPS2_rp1

description: library strategy: Cut&Tag

value: Control

value: No


title: Fig2B FWAgR3 control


title: Fig2B FWAgR4 RNP edited protoplast


title: SPECTRUM-OV-026_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: RNAiSvb rep2

tag: genotype


title: SPECTRUM-OV-026_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: 100_cut_and_tag_shGFP_MED1_rp1

description: library strategy: Cut&Tag

value: Bethyl


title: Fig2B FWAgR6 RNP edited protoplast


title: 101_cut_and_tag_shGFP_MED1_rp2

description: library strategy: Cut&Tag


title: SvbRep rep2


title: SvbRep rep3


title: Fig2B FWAgR3 RNP edited protoplast


title: Fig2B FWAgR2 control


title: RNAiSvb rep1


title: 99_cut_and_tag_shGFP_KDM1A

description: library strategy: Cut&Tag

value: Abcam


title: SPECTRUM-OV-026_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: SvbRep rep1


title: 98_cut_and_tag_shGFP_H3K27ac_rp2

description: library strategy: Cut&Tag


title: Fig2B FWAgR2 RNP edited protoplast


title: SPECTRUM-OV-026_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: 97_cut_and_tag_shGFP_H3K27ac_rp1

description: library strategy: Cut&Tag


title: Fig2B FWAgR1 control


title: ISC Ctrl rep 3

value: esg-Gal4, UAS-GFP/+; tubGal80TS/+


title: SvbAct rep 1


title: Fig2B FWAgR1 RNP edited protoplast

value: FWA


title: SvbAct rep 3


title: SvbAct rep 2


title: 96_cut_and_tag_shGFP_H3K9me3_rp2

description: library strategy: Cut&Tag

value: Macrophage


title: SPECTRUM-OV-025_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-025_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Fig2B FWAgR10 RNP edited protoplast


title: 94_cut_and_tag_shGFP_H3K4me3_rp2

description: library strategy: Cut&Tag

value: BALB/c


title: 95_cut_and_tag_shGFP_H3K9me3_rp1

description: library strategy: Cut&Tag


title: ISC Ctrl rep 1

value: GAL4/GAL80TS system allows spacial and temporal control of UAS induction. UASs were activated in ISCs for 6 days before midgut dissection


title: SPECTRUM-OV-025_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-025_S1_CD45N_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-024_S1_CD45P_LEFT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: Table S1 andSupFig1B WT plant control amplified for PDS3gR10 region

source_name: Arabidopsis leaf tissue

value: leaf tissue


title: SPECTRUM-OV-026_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: ISC Ctrl rep 2

value: Posterior midgut (R3 to R5)

value: 9 days (6 days of induction)


title: 93_cut_and_tag_shGFP_H3K4me3_rp1

description: library strategy: Cut&Tag


title: Table S1 Version1 PDS3gR10 T1plant33leaf d

value: 6 weeks


title: SPECTRUM-OV-025_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: roca7

city: ANN ARBOR

first: Hernan

last: Roca

state: MI

address: 1011 N. University Ave.

department: Periodontics and Oral Medicine

institute: University of Michigan

data_processing:
Samples were sequenced on Illumina NavaSeq6000 with the following configuration: Read 1 - 150 cycles; i7 index read - 8 cycles; Read 2 - 150 cycles.
Samples were aligned to Mouse genome mm10 using CellRanger v3.0.0
Poor quality cells were removed using CellRanger software v3.0.0 and Seurat package v3.1.
Genome_build: Mouse genome mm10
Supplementary_files_format_and_content: CellRanger output files including table deliminated barcode, features, and matrix files

source_name: Primary Macrophages

extract_protocol:
Apoptotic RM1 cells were labeled with CellTrace™ CFSE (ThermoFisher Scientific, C34554), and then co-cultured with macrophages for 16–18 h. Efferocytic and non-efferocytic macrophages were collected and incubated in fluorescence-activated cell sorter (FACS) staining buffer (phosphate buffered saline-1X, 0.2% bovine serum albumin). F4/80 antibody and isotype control were added and incubated for 1 h at 4 °C. F4/80+ only (non-efferocytic macrophages) and F4/80+CFSE+ (efferocytic macrophages) were sorted using a BD FACSAriaTM III (BD biosciences, San Jose, CA, USA)
The single cell scRNA-seq libraries were prepared at the University of Michigan Advanced Genomics Core using the 10X Genomics Chromium Next GEM Single Cell 3′ Kit v3.1 (part number 1000268) following the manufacturer’s protocol.  Cell suspensions were diluted to target a recovery of 10,000 cells per sample.  The libraries were run on an Agilent TapeStation 4200 (part number G2991BA) for library quality control before sequencing.  Libraries were sequenced at a depth of 50,000 reads/cell on a NovaSeq6000 with the following run configuration: Read 1 - 150 cycles; i7 index read - 8 cycles; Read 2 - 150 cycles.

tag: efferocytotic status

value: efferocytic

tag: experiment

value: Experiment 2


title: 92_cut_and_tag_shGFP_GPS2_rp2

description: library strategy: Cut&Tag

tag: strain

value: Home made


title: Table S1 Version1 PDS3gR10 T1plant33flower a

source_name: Arabidopsis floral tissue

value: floral tissue

value: wild type


title: roca5

value: Experiment 1


title: SPECTRUM-OV-024_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: Table S1 Version1 PDS3gR10 T1plant33leaf c


title: Fig2B FWAgR10 control

value: mysophyll protoplast

value: 3-4 weeks


title: Table S1 Version1 PDS3gR10 T1plant33leaf b


title: 91_cut_and_tag_shGFP_GPS2_rp1

description: library strategy: Cut&Tag

tag: treatment

value: Control

value: No


title: SPECTRUM-OV-024_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv


title: Table S1 Version1 PDS3gR10 T1plant33leaf a


title: D40 Tumor CD103-CD69- replicate 2

city: Melbourne

first: Franco

last: Caramia

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Adaptor trimming was performed and reads were aligned to the mm10 reference genome using HISAT2.
Aligned reads were quantified using HTSeq
Counts were normalized using RUVIII in R
Assembly: mm10
Supplementary files format and content: comma-delimited text files include normalized counts values for each Sample

source_name: BREAST, D40 Tumor CD103-CD69-

extract_protocol:
FACS purified CD8+ T cell subsets were processed for RNA using the RNeasy mini kit (Qiagen) as per the manufacturer's instructions. RNA TapeStation (Agilent, USA) analysis was performed as per the manufacturer's instructions to assess the quantity and quality of RNA material isolated from TNBC tumors
10ng total RNA was used for library preparation according to manufacturer’s instructions (QuantSeq 3' mRNA-Seq FWD, Lexogen)

tag: cell line

value: tumor infiltrating T cells

tag: time

value: mammary tumor

tag: facs purified cd8+ t cell subset

value: Immune Checkpoint Blockade


title: SPECTRUM-OV-024_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: roca6

value: Non-efferocytic


title: SPECTRUM-OV-024_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: D40 Tumor CD103-CD69- replicate 1

tag: tissue


title: SPECTRUM-OV-024_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: D40 Tumor CD103+CD69+ replicate 3

source_name: BREAST, D40 Tumor CD103+CD69+


title: SPECTRUM-OV-022_S1_CD45P_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: D40 Tumor CD103-CD69+ replicate 2

source_name: BREAST, D40 Tumor CD103-CD69+


title: Vegetative nuclei, Mature pollen grain, Rep3

city: Lisbon

first: Jörg

middle: Dieter

last: Becker

address: ITQB NOVA Avenida da República

country: Portugal

institute: ITQB

data_processing:
3D-RNA-seq platform
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore
Trimmed sequence reads were then used an input for transcript quantification using Salmon
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include TPM values for each biological replicate of sperm cells and vegetative nuclei

source_name: Vegetative nuclei

growth_protocol: Seeds of a transgenic marker line harbouring MGH3p::MGH3-GFP and ACT11p::H2B-mRFP  were sown on soil in short-day conditions (8-h light at 21–23 °C) for 8 weeks and then transferred to long-day conditions (16-h light) to induce flowering. Flowers were collected, pollen cracked and FACS sorting of sperm cells and vegetative nucleus from mature pollen grain (MPG) was performed.

extract_protocol:
FACS based purification of sperm cells and vegetative nuclei
Smart-seq2 protocol was used to prepare RNA-seq libraries from sorted cells.

value: Vegetative nuclei

value: WT


title: roca4


title: Vegetative nuclei, Mature pollen grain, Rep2


title: SPECTRUM-OV-024_S1_CD45N_LEFT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

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

source_name: UQ

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: D40 Tumor CD103+CD69+ replicate 2


title: D40 Tumor CD103-CD69+ replicate 3


title: CRE-Negative Areg-flox/flox FLU 2

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 910C

department: Microbiology & Immunology

institute: Columbia University Irving Medical Center

data_processing:
Fastq files were ran through fastqc to check for sequencing quality. QC was visualized using MultiQC (Ewels et al Bioinformatics 2016)
Kallisto alignment (Bray et al, Nature Biotech. 2016) was used to generate an index of the CHR Gencode mouse transcriptome (gencode.vM21.annotation.gff3)
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Gencode GRCm38 primary assembly genome sequence
Genome_build: Differential expression files include log2 fold changes generated by DESeq2 for each indicated comparison (with all samples from a given group identified utilized in the differential expression test). These files are listed as .csv files. Counts for each gene is provided with the DESeq2 analysis.
Supplementary_files_format_and_content: CSV file of differential expression of FLU/PBS performed by DeSeq and count data per gene per sample.

source_name: Lung type II alveolar epithelial cells

growth_protocol: Fresh type II alveolar epithelial cells were isolated from lungs following enzymatic digestion, negatively enriched using magnetic biotinylated beads for depletion of CD45+, CD31+, and Ter119+ cells, then sorted by FACs.

extract_protocol:
Cells were pelleted and flash frozen. RNA extraction performed using Qiagen kit by core facility at Columbia University core of molecular pathology.
Library preparation and RNA sequencing performed by Columbia University Genome Center using standard poly A enrichment.
40 million reads paired-end Novaseq

treatment_protocol: Mice were infected with 400TCID50 PR8/H1N1; lungs were harvested at day 7 post infection.

value: Lung type II alveolar epithelial cells

value: Areg-flox/flox

value: H1N1/PR8 at day 7 post infection


title: SPECTRUM-OV-024_S1_CD45N_INFRACOLIC_OMENTUM

first: Florian

last: Uhlitz

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-022_S1_CD45P_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: CRE-Negative Areg-flox/flox FLU 3


title: CRE-Negative Areg-flox/flox PBS 2

value: Mock PBS control isolated at day 7 post treatment


title: SPECTRUM-OV-022_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Sperm cells, Mature pollen Grain, Rep3

source_name: Sperm cells

value: Sperm cells


title: Vegetative nuclei, Mature pollen grain, Rep1


title: D40 Tumor CD103-CD69+ replicate 1


title: CRE-Negative Areg-flox/flox FLU 1


title: D40 Tumor CD103+CD69+ replicate 1


title: SPECTRUM-OV-022_S1_CD45N_RIGHT_ADNEXA

description:
matrix.h5
GEO_cells.tsv


title: CRE-Negative Areg-flox/flox PBS 3


title: Week4 Tumor CD103-CD69- replicate 3

source_name: BREAST, Week4 Tumor CD103-CD69-


title: Sperm cells, Mature pollen Grain, Rep1


title: Sperm cells, Mature pollen Grain, Rep2


title: Week1 Tumor CD103-CD69- replicate 1

source_name: BREAST, Week1 Tumor CD103-CD69-


title: Myo-Areg-4

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Genome_build: Gencode GRCm38 primary assembly genome sequence
Supplementary_files_format_and_content: CSV file of count data per gene per sample

source_name: Mouse lung

growth_protocol: Fresh mesenchymal cells were isolated from lungs by enzymatic digestion.

extract_protocol:
RNA from adherent cells was extracted in Trizol
Poly-A pull-down to enrich mRNAs from total RNA samples then proceed with library construction using Illumina TruSeq chemistry.

treatment_protocol: Cells were plated overnight followed by in vitro stimulation for 4 hours.

value: Lung mesenchymal cells

value: 200ng/mL AREG


title: Week2 Tumor CD103-CD69- replicate 3

source_name: BREAST, Week2 Tumor CD103-CD69-


title: CRE-Negative Areg-flox/flox PBS 1


title: Myo-Egf-6

value: 50ng/mL EGF


title: SPECTRUM-OV-022_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: SPECTRUM-OV-022_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: Myo-Areg-3


title: SPECTRUM-OV-022_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Week6 Tumor CD103-CD69- replicate 2

source_name: BREAST, Week6 Tumor CD103-CD69-


title: SPECTRUM-OV-014_S1_CD45P_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: Myo-Egf-5


title: Mouse - isolated LSEC - wildtype - Biological replicate 2

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from isolated liver sinusoidal endothelial cells of wildtype mice, replicate 2.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: liver sinusoidal endothelial cells isolated from wildtype mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Using the Qiagen RNeasy Mini Kit RNA was extracted from retina samples according to the manufacturer's instructions.

treatment_protocol: Livers of WT (C57BL/6J) and Lyve-1-KO (B6.129S1-Lyve1tm1Lhua/J (JAX stock #006221)) were perfused with a 0.05 % collagenase containing amino acid/ saccharide calcium-deprived medium (C2674, Sigma Aldrich, St. Louis, MO, USA) via the portal vein. Mice were sacrificed and livers were excised. Livers were minced mechanically and digested at 38 °C in a collagenase/Gey’s balanced salt solution (G9779, Sigma-Aldrich, St. Louis, MO, USA). Afterwards livers were filtered through a 250 µm mesh. A gradient was applied by 35% Nycodenz (1002424, Axis-Shield, Alere Technologies, Oslo, Norway) and cells were separated. Utilizing anti-CD146 MicroBeads (ME-9F1, 130-092-007, Miltenyi Biotech, Bergisch Gladbach, Germany) LSECs were isolated by magnetic-activated cell sorting according to the manufacturers’ instructions. For additional analysis, LSECs were pooled from three mice.

value: WT Kontr

value: liver sinusoidal endothelial cells


title: SPECTRUM-OV-014_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Week4 Tumor CD103-CD69- replicate 2


title: SPECTRUM-OV-022_S1_CD45N_LEFT_ADNEXA

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: Mouse - isolated LSEC - wildtype - Biological replicate 3

description: Gene expression data from isolated liver sinusoidal endothelial cells of wildtype mice, replicate 3.


title: Week1 Tumor CD103-CD69- replicate 2


title: Col14-Egf-6


title: SPECTRUM-OV-014_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Col14-Egf-5


title: SPECTRUM-OV-014_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-014_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: Breg-2

city: Beijing

first: Mingming

last: Shao

state: State...

address: 8 Gongren Tiyuchang Nanlu

institute: Beijing Chao-Yang Hospital

description:
immune cell
Breg cells

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: pleural effusion

extract_protocol:
1 × 10^6 naïve B cells and Bregs were isolated by FACS Aria II from MPE. A total amount of 3 μg RNA per sample was purified from total RNA using poly-T oligo-attached magnetic beads. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

value: pleural effusion

value: B cell

tag: cell subtype

value: Breg


title: Week6 Tumor CD103-CD69+ replicate 3

source_name: BREAST, Week6 Tumor CD103-CD69+

value: tumor infiltrating T cells

value: mammary tumor


title: Myo-NT-2

city: New York

value: untreated


title: Week6 Tumor CD103+CD69+ replicate 3

source_name: BREAST, Week6 Tumor CD103+CD69+


title: Mouse - isolated LSEC - Lyve-1-KO - Biological replicate 3

description: Gene expression data from isolated liver sinusoidal endothelial cells of mice with deficiency of Lyve-1, replicate 3.

source_name: liver sinusoidal endothelial cells isolated from mice with deficiency of Lyve-1

value: LYVE


title: Col14-NT-2


title: Week2 Tumor CD103-CD69- replicate 1


title: Myo-NT-1


title: Week2 Tumor CD103-CD69- replicate 2


title: EndoC-BH1 cells siRNA SRRM3 replicate 3

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: EndoC-BH1 cells

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

tag: sirna

value: siRNA SRRM3


title: Cntrl Spleen T CM replicate 1

source_name: SPLEEN, Cntrl Spleen T CM

tag: cell type

value: Cntrl

value: Spleen

value: CM


title: Col14-NT-1


title: Naïve B-2

description:
immune cell
Naïve B cells

value: Naive


title: Week2 Tumor CD103+CD69+ replicate 4

source_name: BREAST, Week2 Tumor CD103+CD69+


title: Breg-1

description:
immune cell
Breg cells


title: Mouse - isolated LSEC - wildtype - Biological replicate 1

description: Gene expression data from isolated liver sinusoidal endothelial cells of wildtype mice, replicate 1.


title: Naïve B-3

description:
immune cell
Naïve B cells


title: SPECTRUM-OV-014_S1_CD45N_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv

tag: sort


title: Mouse - isolated LSEC - Lyve-1-KO - Biological replicate 1

description: Gene expression data from isolated liver sinusoidal endothelial cells of mice with deficiency of Lyve-1, replicate 1.


title: Col14-Areg-4

value: Lung mesenchymal cells


title: Week4 Tumor CD103-CD69- replicate 1

source_name: BREAST, Week4 Tumor CD103-CD69-


title: Breg-3

description:
immune cell
Breg cells


title: Cntrl Spleen T EM replicate 2

source_name: SPLEEN, Cntrl Spleen T EM

value: EM


title: Col13-Egf-1

source_name: Mouse lung

value: 50ng/mL EGF


title: SPECTRUM-OV-014_S1_CD45N_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

source_name: UQ


title: Week6 Tumor CD103-CD69- replicate 1


title: SPECTRUM-OV-014_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: EndoC-BH1 cells siRNA control replicate 3

description: polyA-selected RNA

value: siRNA control


title: Col13-Egf-2


title: SPECTRUM-OV-014_S1_CD45N_BOWEL

description:
matrix.h5
GEO_cells.tsv


title: Week6 Tumor CD103+CD69+ replicate 2


title: Col13-Areg-2

value: 200ng/mL AREG


title: EndoC-BH1 cells siRNA control replicate 2

description: polyA-selected RNA


title: Naïve B-1

description:
immune cell
Naïve B cells

value: pleural effusion


title: EndoC-BH1 cells siRNA SRRM3 replicate 1

description: polyA-selected RNA


title: EndoC-BH1 cells siRNA control replicate 1

description: polyA-selected RNA


title: EndoC-BH1 cells siRNA SRRM3 replicate 2

description: polyA-selected RNA


title: Week2 Tumor CD103-CD69+ replicate 3

source_name: BREAST, Week2 Tumor CD103-CD69+


title: Week6 Tumor CD103-CD69+ replicate 2


title: Col13-NT-2


title: Week4 Tumor CD103-CD69+ replicate 1

source_name: BREAST, Week4 Tumor CD103-CD69+


title: SPECTRUM-OV-014_S1_CD45N_ASCITES

description:
matrix.h5
GEO_cells.tsv

source_name: Ascites


title: SPECTRUM-OV-009_S1_CD45P_LEFT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: Col13-NT-1


title: Col13-Areg-1


title: SPECTRUM-OV-009_S1_CD45P_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv

source_name: Peritoneum


title: Cntrl Spleen T Naive replicate 2

source_name: SPLEEN, Cntrl Spleen T Naive


title: Areg-flox CD4-cre mesenchyme

data_processing:
Raw fastq files were aligned and processed to count matrices using CellRanger v2.1.1
Supplementary_files_format_and_content: File type = tsv, mtx; Content = barcodes, count matrix, gene names

source_name: Lung mesenchymal cells

growth_protocol: Areg-flox and CD4cre Areg-flox mice were infected with PR8/H1N1. Mesenchymal cells were extracted from mouse lung by enzymatic digestion and enriched by negative depletion of CD45+, Epcam+, Ter119+, and CD31+.

extract_protocol:
cells were directly given to Columbia University Genome center for 10X bead emulsification.
Library preparation and RNA sequencing performed by Columbia University Genome Center using standard poly A enrichment.
10X sc-Seq/MiSeq

treatment_protocol: Mice were infected with 500TCID50 PR8/H1N1 influenza; lungs were harvested at day 8 post infection.

value: Enriched lung mesenchymal cells from influenza-infected mice

value: CD4-cre Areg-flox/flox

value: H1N1/PR8 influenza at day 8 post infection


title: SPECTRUM-OV-009_S1_CD45P_LEFT_OVARY

description:
matrix.h5
GEO_cells.tsv

source_name: Adnexa


title: SPECTRUM-OV-009_S1_CD45P_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv


title: SPECTRUM-OV-009_S1_CD45P_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: Week2 Tumor CD103+CD69+ replicate 3

value: tumor infiltrating T cells

value: mammary tumor


title: SPECTRUM-OV-009_S1_CD45P_INFRACOLIC_OMENTUM

description:
matrix.h5
GEO_cells.tsv

source_name: Omentum


title: HeLa cells with SRRM3 transgene, high dox induced

description: polyA-selected RNA

source_name: HeLa cells

value: HeLa

tag: transgene

value: SRRM3 transgene, high dox induced


title: Areg-flox wildtype control mesenchyme

value: Areg-flox/flox


title: Week1 Tumor CD103-CD69+ replicate 3

source_name: BREAST, Week1 Tumor CD103-CD69+


title: Mouse - isolated LSEC - Lyve-1-KO - Biological replicate 2

description: Gene expression data from isolated liver sinusoidal endothelial cells of mice with deficiency of Lyve-1, replicate 2.

source_name: liver sinusoidal endothelial cells isolated from mice with deficiency of Lyve-1

value: LYVE

value: liver sinusoidal endothelial cells


title: HeLa cells overexpressing GFP

description: polyA-selected RNA

value: Overexpressing GFP


title: Week1 Tumor CD103+CD69+ replicate 3

source_name: BREAST, Week1 Tumor CD103+CD69+


title: Cntrl Spleen T EM replicate 1

value: Cntrl

value: Spleen


title: SPECTRUM-OV-009_S1_CD45P_ASCITES

description:
matrix.h5
GEO_cells.tsv


title: HeLa cells with SRRM3 transgene, mid dox induced

description: polyA-selected RNA

value: SRRM3 transgene, mid dox induced


title: Cntrl Spleen T CM replicate 2

source_name: SPLEEN, Cntrl Spleen T CM

value: CM


title: SPECTRUM-OV-009_S1_CD45P_BOWEL

description:
matrix.h5
GEO_cells.tsv

source_name: Bowel


title: APL patient 2 RNA-seq

city: London

first: Cameron

last: Osborne

address: Guy's Hospital Campus

department: Medical and Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Reads were trimmed of adapters and low-quality reads using Trimmomatic (Bolger et al., 2014) and aligned to the hg19 genome using STAR 2 pass aligner
Gene counts were generated using Feature Counts from the Rsubread R package (Liao 2019 NAR) and normalized using the voom normalization approach for differential analysis
Differential analysis comparing uninduced and induced U937-PR9 cells was performed using limma
Genome_build: hg19
Supplementary_files_format_and_content: Log2_Counts_Per_Million_All_RNA-seq.csv: contains the noralised log2 counts per million reads for each dataset, data is normalised by library size
Supplementary_files_format_and_content: Control_vs_Induced_RNA-seq_Limma_DEG.txt contains the 2,314 differentially expressed genes after PML-RARA induction in the U937-PR9 cells

source_name: PBMC

growth_protocol: U937-PR9 cells were cultured in RPMI 1640 (Thermo Fisher, A10491), supplemented with 10% fetal bovine serum (Thermo Fisher, 10082147) and incubated at 37°C, 5% CO2.

extract_protocol:
RNA was extracted from U937-PR9 cells using Trizol reagent (Life Technologies).
Libraries were prepared using the Illumina SureSelect Strand-Specific RNA Library Prep kit following the manufacturer’s instructions
sequenced using an Illumina HiSeq 2500 instrument for paired-end sequencing.

treatment_protocol: For the zinc induction of U937-PR9 cells, ZnSO4 (Sigma, Z0251) was dissolved in sterile water as a stock solution at 100 mM. ZnSO4 was added directly to the culture medium at a final concentration of 100 μM and incubated at 37°C for 5 hours, as described previously (Martens et al., 2010). For the non-induced U937-PR9 cells, sterile water was added instead of ZnSO4 and incubated under the same conditions.

value: Blast cells


title: IgG control 2

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
The low-quality reads and adaptor were trimmed by using Trim Galore 0.6.4 (https://github.com/FelixKrueger/TrimGalore).
The trimmed reads were mapped against fly genome dm6 by bowtie2 2.3.5.1 with the additional argument "-q --local" .
Samtools 1.6 were used to sort, filter unique reads, and convert file format to bam files.
Peak calling was performed with MACS2 2.2.6 using the additional parameter "-B --SPMR -f BAMPE -g dm" .
Peaks were annotated with HOMER 4.11.
Supplementary files format and content: dwg_vs_control_summits.bed
Supplementary files format and content: dwg_vs_input_summits.bed

extract_protocol:
DNA was fragmented and extrated using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol
ChIP-seq libraries were prepared using the  KAPA HyperPlus Library Preparation Kit

tag: antibody

value: IgG


title: IP flag-dwg1 1


title: IP flag-dwg1 2


title: SPECTRUM-OV-009_S1_CD45N_RIGHT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

growth_protocol: Primary samples.


title: U937-PR9 Induced rep2 RNA-seq

value: myeloid cell line


title: Week6 Tumor CD103-CD69+ replicate 1

source_name: BREAST, Week6 Tumor CD103-CD69+


title: U937-PR9 Induced rep1 RNA-seq


title: SPECTRUM-OV-009_S1_CD45N_RIGHT_OVARY

description:
matrix.h5
GEO_cells.tsv


title: input dwg1 2


title: IgG control 1


title: Col14-Areg-3

source_name: Mouse lung

value: Lung mesenchymal cells

value: 200ng/mL AREG


title: input dwg1 1


title: U937-PR9 Control rep2 RNA-seq


title: SPECTRUM-OV-009_S1_CD45N_LEFT_UPPER_QUADRANT

description:
matrix.h5
GEO_cells.tsv

source_name: UQ


title: Week6 Tumor CD103+CD69+ replicate 1

source_name: BREAST, Week6 Tumor CD103+CD69+

value: tumor infiltrating T cells


title: SPECTRUM-OV-009_S1_CD45N_PELVIC_PERITONEUM

description:
matrix.h5
GEO_cells.tsv


title: U937-PR9 Control rep1 RNA-seq


title: Cntrl Spleen T Naive replicate 1

value: Naive