title: MH3, Sham for CACPR

city: Los Angeles

middle: William

last: Nelson

address: 1333 San Pablo St.

institute: University of Southern California

description: 10x Genomics

data_processing:
Fastq files for “CACPR” and “Sham for CACPR”  were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 6.0.1 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Fastq files for “IRI” and “Sham for IRI” were downloaded from SRP226225 and then aligned to a reference genome using Cellranger v. 7.2.0 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0.4
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.4.0
Assembly: mm10-2020-A
Supplementary files format and content: Raw and filtered feature-barcode matrices from each replicate
Supplementary files format and content: Integrated seurat objects containing multiple replicates

molecule: nuclear RNA

source_name: Whole Kidney

extract_protocol:
Kidney nuclei were extracted using standard protocol by Singulomics.
Single nucleus RNA-seq for "CACPR" and "Sham for CACPR" samples were performed using the Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics) by Singluomics targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. ( https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry )
snRNAseq

tag: Sex

value: Male

tag: genotype

value: WT

value: Whole Kidney

value: All Kidney Cells

value: Sham

tag: age


title: PolII ChIP-seq of Mmyco strain (IP), rep2

status: Public on Feb 14 2025

type: SRA

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
For standard ChIP-seq, bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. For calibrated Scc1 ChIP-seq, bowtie2 was used in two rounds of alignments, first on C. glabrata (CBS138) and then on the appropriate S. cerevisiae genome reference, allowing the generation of IP and input (WCE) alignments that exclusively mapped on S. cerevisiae (and vice-versa for C. glabrata).
Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded. PCR duplicates were removed using samtools. When available, the input was similarly processed.
Fragment coverage was normalized by library depth (CPM) and converted into a genomic track (bigwig) using deepTools. Input-normalized fragment coverage was also generated, when possible, using bamCompare from deepTools with “--scaleFactorsMethod readCount”.
For calibrated Scc1 ChIP-seq, CPM-normalized fragment coverages were also multiplied by the ORi factor for calibration (WCEglabrata x IPcerevisiae / WCEcerevisiae x IPglabrata, in which WCEglabrata and IPglabrata correspond to the number of paired reads that mapped uniquely on C. glabrata genome and same for S. cerevisiae reads).
MACS2 2.2.7.1 was used to call peaks using the input alignment files as control.
Assembly: 10.5281/zenodo.7198985
Supplementary files format and content: Bigwig files for ChIP-seq coverage (IP, IP/Input and calibrated) are provided. Peaks are provided as .narrowPeak files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells of either S. cerevisiae or Candida glabrata were grown exponentially to OD600 = 0.5. 15 OD600 units of S. cerevisiae cells were mixed with 3 OD600 units of C. glabrata cells to a total volume of 45 mL for Scc1 calibration only.

extract_protocol:
Cells were fixed using 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS. The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transferred in 2mL tubes containing glass beads (ozyme, P000913-LYSK0-A.0) before mechanical cells lysis. The soluble fraction was isolated by centrifugation at 2,000 rpm for 3min then transferred to sonication tubes (Covaris milliTUBE 1ml, 520135) and samples were sonicated to produce sheared chromatin with a size range of 200-1,000bp using a Covaris sonicator. After sonication the samples were centrifuged at 13,200 rpm at 4°C for 20min and the supernatant was transferred into 700µL of ChIP lysis buffer. 80µL (27µl of each sample) of the supernatant was removed (termed ‘whole cell extract [WCE] sample’) and store at -80°C. 5ug of antibody was added to the remaining supernatant which is then incubated overnight at 4°C (wheel cold room). 50µL of protein G Dynabeads or protein A Dynabeads was then added and incubated at 4°C for 2h. Beads were washed 2 times with ChIP lysis buffer, 3 times with high salt ChIP lysis buffer (50mMHEPES-KOH, pH 8.0; 500 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate;1 mM PMSF), 2 times with ChIP wash buffer (10 mM Tris-HCl, pH 8.0; 0.25MLiCl; 0.5% NP-40; 0.5% sodium deoxycholate; 1mM EDTA;1 mMPMSF) and 1 time with TE pH7.5. The immunoprecipitated chromatin was then eluted by incubation in 120µL TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) for 15min at 65°C and the supernatant is collected termed ‘IP sample’. The WCE samples were mixed with 40µL of TES3 buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 3% SDS). ALL (IP and WCE) samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified by a phenol/Chloroform extraction.
The triplicate IP samples were mixed in 1 tube and libraries for IP and WCE samples were prepared using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.

tag: background

tag: strain

tag: Stage

value: Asy

tag: tag

value: PolII

tag: step

value: IP

tag: hash


title: PolII ChIP-seq of Mmyco strain (input), rep1

value: WCE


title: MH1, CACPR

first: Jonathan

state: CA

department: Medicine

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue

tag: cell type

tag: treatment

value: CACPR


title: DMSO_R3_d5

city: Boulder

first: Taylor

middle: K

last: Jones

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

description:
RNA-seq from OV90 cells
rnaseq_ercc_normalized_counts.txt

library_source: transcriptomic

data_processing:
Mapping of PRO-seq data was performed using the NascentFlow Pipeline (DOI 10.17605/OSF.IO/NDHJ2)
Assembly: hg38
Supplementary files format and content: NOT PROVIDED

molecule: total RNA

organism: Homo sapiens

source_name: wild type OV90 cells

growth_protocol: Roughly 7 million early-passage wild-type OV90 cells were grown in MCDB 105 media 1:1 with Medium 199 and supplemented with 15% FBS and 1% Pen-strep per ATCC guidelines.

extract_protocol:
RNA-seq: Cells were then harvested by washing with cold D-PBS, scraped in D-PBS into 15mL conical tubes, and centrifuged at 1000rpm for 5min 4C. RNA was extracted with TRIzol according to the manufacturer’s instructions. DNaseI digestion was then performed with the RNeasy kit (Qiagen) using the on-column protocol (Rimel et al., 2020). RNA was eluted in 50µL RNase-free water and samples analyzed by Qubit and TapeStation. PRO-seq: As previously described in (Levandowski, C. B.; Jones, T.; Gruca, M.; Ramamoorthy, S.; Dowell, R. D.; Taatjes, D. J, 2021), after treatment the cells were washed 3x with ice cold PBS, and then treated with 10 ml (per 15 cm plate) ice-cold lysis buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol, 1 mM DTT, 1x Protease Inhibitors (1mM Benzamidine (Sigma B6506-100G), 1mM Sodium Metabisulfite (Sigma 255556-100G), 0.25mM Phenylmethylsulfonyl Fluoride (American Bioanalytical AB01620), and 4U/mL SUPERase-In). Cells were centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1.5 mL lysis buffer to a homogenous mixture by pipetting 20-30X before adding another 8.5 mL lysis buffer. Suspension was centrifuged with a fixed-angle rotor at 1000xg for 15 min at 4◦C. Supernatant was removed and pellet was resuspended in 1 mL of lysis buffer and transferred to a 1.7 mL pre-lubricated tube (Costar cat. No. 3207). Suspensions were then pelleted in a microcentrifuge at 1000xg for 5 min at 4◦C. Next, supernatant was removed and pellets were resuspended in 500 μL of freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 4U/ml SUPERase-In). Nuclei were centrifuged 2000xg for 2 min at 4◦C. Pellets were resuspended in 100 μL freezing buffer. To determine concentration, nuclei were counted from 1 μL of suspension and freezing buffer was added to generate 100 μL aliquots of 10x106 nuclei. Aliquots were flash frozen in liquid nitrogen and stored at −80◦C.
RNA-seq: Samples were concentrated, 300-400ng/µL, and of high quality, RIN values >8.6. For deep mRNA sequencing to asses splicing alterations, poly(A) selection was performed with the KAPA mRNA HyperPrep Kit with 1µg of RNA containing 1:100 diluted ERCC RNA spike-in mix (Invitrogen Thermo Fisher). KAPA mRNA HyperPrep Kit, NovaSEQ6000, using a paired-end 150- bp cycle (2x150). PRO-seq: Nuclear run-on experiments were performed as described previously (Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., et al. (2016). Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols, 11(8), 1455–1476. with the following modifications: the final concentration of non-biotinylated CTP was raised from 0.25 μM to 25 μM, a clean-up and size selection was performed using 1X AMPure XP beads (1:1 ratio) (Beckman) prior to test PCR and final PCR amplification, and the final library clean-up and size selection was accomplished using 1X AMPure XP beads (1:1 ratio) (Beckman).

treatment_protocol: RNA-seq: Cells were then treated in T-75 flasks with one of 3 CDK7 inhibitors or the equivalent DMSO for 30min at 37C, heat-shocked for 30min at 42C, and recovered for 1hr at 37C. RNA-seq experiments with SY5609 also were completed with a no heat-shock condition or were heat-shocked continuously for 2hrs (Xu et al., 2021; Cardiello et al., 2018). PRO-seq: Cells were then treated in T-75 flasks with SY5609 or the equivalent DMSO for 30min at 37C, heat-shocked for 0min, 20min or 45min at 42C with no heat-shock recovery.

tag: cell line

value: Wild-type OV90 cells

value: ovarian cancer

value: 30min pretreatment with DMSO at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C

tag: time


title: PolII ChIP-seq of Mmyco strain (IP), rep1


title: H2A ChIP-seq of Mmyco strain (IP), rep1


title: DMSO_R1_mb

source_name: CDK7 analog sensitive OV90 cells

value: CDK7 analog sensitive OV90 cells


title: DMSO_R2_d5


title: H2A ChIP-seq of Mmyco strain (IP), rep2

value: CXNJIS


title: H3 ChIP-seq of Mmyco strain (input), rep2


title: H3 ChIP-seq of Mmyco strain (IP), rep2


title: SY5102_R2

value: 30min pretreatment with SY5102 at 37C followed by a 42C heat shock for 30min with a 60min recovery at 37C


title: Sir3 ChIP-seq of Mmyco strain (input)


title: Calibrated Scc1-PK ChIP-seq of BY (input), rep2

source_name: BY

value: BY


title: H3 ChIP-seq of Mmyco strain (IP), rep1

value: KDTEGO


title: DMSO_R1_d5


title: 6_023_01

city: Stanford

first: Zhiyuan

last: Yao

state: CA California

address: 1291 Welch Rd. Room S136

institute: Stanford University

data_processing:
CellRanger v3.1.0 (10x Genomics) was used to process scRNA-seq. To generate a gene expression matrix for each sample, we mapped their reads to a combined reference of GRCh38 genome and DENV genome and recorded the number of UMIs for each gene in each cell. We marked cells with high quality based on the following quality criteria: less than 15% mitochondrial reads, more than 400 expressed genes, less than 30000 detected transcripts and more than 1000 detected transcripts. We further excluded genes that were expressed in less than three cells. The data after pre-process and quality control was log-normalized before downsteam analysis. The original gene counts for each cell were normalized by total UMI counts, multiplied by 1000,000 (cpm) and then log transformed by log2(cpm+1).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell in each sample, stored in loom format.

source_name: PBMC

extract_protocol:
PBMCs were isolated using SepMate tubes (Stemcell Technologies) according to the manufacturer’s instructions. Briefly, whole blood was diluted 1:1 with phosphate-buffered saline (PBS) and added to a SepMate tube, which contained 15 ml of Ficoll. Tubes were then centrifuged for 10 minutes at 1,200g, after which the PBMC layer was poured off into a fresh tube and washed with PBS. Tubes were then centrifuged at 250 x g for 10 minutes and resuspended in freezing media. Cryovials containing PBMCs were then placed in a CoolCell at -80 º C for 24 hours prior to being transferred to liquid nitrogen for storage.
The master mix containing 10000~14000 cells per sample were prepared followed 10X protocol. To captured DENV RNA, additional 30nM of customized DENV captured oligos ()were added into the master mix before loading to the ChromiumTM Controller for partitioning single cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). The Next GEM Single Cell 5’ reagent kit was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (10x Genomics) following the detailed protocol provided by 10x Genomics. Libraries quality were checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Sequencing was performed in paired-end mode with a S1 and S4 flow cell (2 X 50 cycles) using NovaSeq 6000 sequencer (Illumina)

tag: clinical condition

value: dengue

value: blood


title: SY5102_R1


title: 6_001_01


title: Calibrated Scc1-PK ChIP-seq of BY (input), rep1


title: PolII ChIP-seq of BY (input), rep2


title: PolII ChIP-seq of BY (IP), rep2


title: PolII ChIP-seq of BY (input), rep1

value: CIJXLY


title: PolII ChIP-seq of BY (IP), rep1


title: 5_130_01


title: 5_154_01


title: Calibrated Scc1-PK ChIP-seq of BY (IP), rep1


title: 6_029_01


title: 5_010_01


title: Calibrated Scc1-PK ChIP-seq of BY (IP), rep2


title: H3 ChIP-seq of Mmyco strain (input), rep1


title: 1_019_01


title: RNA_sh2_2

city: Chongqing

first: Qinlv

last: Wei

state: Chongqing

address: Chongqing

country: China

institute: Children’s Hospital of Chongqing Medical University

description:
Library name: hnRNPL-sh2-2
The raw data are being open accessed in SRA with accession number PRJNA988254

data_processing:
Raw reads were trimmed using cutadapt version 1.18. Clean reads were aligned to the UCSC hg38 genome using TopHat v2.1.1. only uniquely mapping reads were used.
Assembly: hg38
Supplementary files format and content: htseq

molecule: polyA RNA

source_name: Ovarian cancer

growth_protocol: OVCAR3 cells were cultured in RPMI1640 medium (GIBCO) containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
PCR amplification was performed by addition of 25 mM i5 index primer, 25 mM i7 index primer (He Lab, Peking University), and the reaction was set up by incubation at 98°C for 2 min, 10-15 cycles of amplification (98°C for 20 s, 65°C for 30 s, 72°C for 1 min), and final 72°C extension for 5 min. After PCR amplification, the library was purified with XP beads once.

treatment_protocol: All cells were cultured in a cell incubator at 37°C and 5% CO2. OVCAR3 cells were transfected with Versatile DNA/siRNA transfection reagent following the manufacturer’s instructions.

value: Ovarian cancer

value: Human Ovarian fibroblasts

value: shhnRNPL

value: knockdown of hnRNPL


title: RNA_sh1_1

description:
Library name: hnRNPL-sh1-1
The raw data are being open accessed in SRA with accession number PRJNA988254


title: RNA_control_1

description:
Library name: hnRNPL-shNC-1
The raw data are being open accessed in SRA with accession number PRJNA988254

value: shNC


title: RNA_control_2

description:
Library name: hnRNPL-shNC-2
The raw data are being open accessed in SRA with accession number PRJNA988254


title: 1_113_01


title: RP_WT_Biological_Rep 2

city: New York

first: Yajas

last: Shah

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
Transcript abundance was quantified by mapping sequencing reads to a custom human transcriptome reference (GENCODE v42, hg38) that included EGFP and was performed using simpleaf/alevin-fry (12).
Assembly: hg38
Supplementary files format and content: scRNA transcript abundance matrices

source_name: RP Cell Culture

extract_protocol: Single-cell capture, reverse transcription, cell lysis, and library preparation were carried out by the WCM Epigenomics Core Facility using Chromium Single Cell 3’ v3 kits according to the manufacturer’s protocol (10x Genomics, USA). Single cell suspenions of RUES2-dervied RPM and RPM (T58A) day 50 cultures were prepared by incubating wells in 0.05% Trypsin/0.02% EDTA for 10-15 min. Digestions were then quenched with excess 0.1% BSA/PBS buffer and passed through 40μm mesh strainer. EGFP+ singlets were sorted at the WCM Flow Cytometry Core Facility on a BD Influx or Sony MA900 cell sorter. Each RUES2-dervied RPM and RPM(T58A) day 50 culture pools were isolated from 3 wells of a 12-well plate across two biological replicates, targeting ∼50,000 viable, EGFP+ viable cells per replicate. Cell counts were then adjusted to 6000-9000 cells/50uL in PBS by Trypan Blue exclusion to achieve an estimated capture of 4000-5000 cells

value: RP Cell Culture

value: RUES2 RP

value: 2D Culture


title: RNA_sh2_1

description:
Library name: hnRNPL-sh2-1
The raw data are being open accessed in SRA with accession number PRJNA988254


title: 5_193_01


title: RP_WT_Biological_Rep 1


title: RPM_T_WT

data_processing:
Single-cell capture, reverse transcription, cell lysis, and library preparation were carried out by the WCM Epigenomics Core Facility using Chromium Single Cell 3’ v3 kits according to the manufacturer’s protocol (10x Genomics, USA). Single cell suspenions of RUES2-dervied RPM and RPM (T58A) day 50 cultures were prepared by incubating wells in 0.05% Trypsin/0.02% EDTA for 10-15 min. Digestions were then quenched with excess 0.1% BSA/PBS buffer and passed through 40μm mesh strainer. EGFP+ singlets were sorted at the WCM Flow Cytometry Core Facility on a BD Influx or Sony MA900 cell sorter. Each RUES2-dervied RPM and RPM(T58A) day 50 culture pools were isolated from 3 wells of a 12-well plate across two biological replicates, targeting ∼50,000 viable, EGFP+ viable cells per replicate. Cell counts were then adjusted to 6000-9000 cells/50uL in PBS by Trypan Blue exclusion to achieve an estimated capture of 4000-5000 cells. Sequencing was performed by the WCM Genomics Resources Core Facility on a HiSeq 2500 (Illumina, paired-end protocol with 26 base pairs for read 1 and 98 bases for read 2). Single cell RNA sequencing from RP cultures were obtained from previous experiments (5). Transcript abundance was quantified by mapping sequencing reads to a custom human transcriptome reference (GENCODE v42, hg38) that included EGFP and was performed using simpleaf/alevin-fry (12).
Assembly: hg38
Supplementary files format and content: scRNA count matrices

source_name: RPM WT MYC Xenograft

extract_protocol:
Single-cell capture, reverse transcription, cell lysis, and library preparation were carried out by the WCM Epigenomics Core Facility using Chromium Single Cell 3’ v3 kits according to the manufacturer’s protocol (10x Genomics, USA). Single cell suspenions of RUES2-dervied RPM and RPM (T58A) day 50 cultures were prepared by incubating wells in 0.05% Trypsin/0.02% EDTA for 10-15 min. Digestions were then quenched with excess 0.1% BSA/PBS buffer and passed through 40μm mesh strainer. EGFP+ singlets were sorted at the WCM Flow Cytometry Core Facility on a BD Influx or Sony MA900 cell sorter. Each RUES2-dervied RPM and RPM(T58A) day 50 culture pools were isolated from 3 wells of a 12-well plate across two biological replicates, targeting ∼50,000 viable, EGFP+ viable cells per replicate. Cell counts were then adjusted to 6000-9000 cells/50uL in PBS by Trypan Blue exclusion to achieve an estimated capture of 4000-5000 cells. Sequencing was performed by the WCM Genomics Resources Core Facility on a HiSeq 2500 (Illumina, paired-end protocol with 26 base pairs for read 1 and 98 bases for read 2). Single cell RNA sequencing from RP cultures were obtained from previous experiments (5). Transcript abundance was quantified by mapping sequencing reads to a custom human transcriptome reference (GENCODE v42, hg38) that included EGFP and was performed using simpleaf/alevin-fry (12).
10x v3

value: RPM WT MYC Xenograft

value: RUES2 RPM WT

value: Tumor xenograft


title: RPM_T_T58A

source_name: RPM T58A MYC Xenograft

value: RPM T58A MYC Xenograft

value: RUES2 RPM T58A


title: 5_044_01


title: RPM_2D_WT

source_name: RPM WT MYC Cell Culture

value: RPM WT MYC Cell Culture


title: RPM_2D_T58A

source_name: RPM T58A MYC Cell Culture

value: RPM T58A MYC Cell Culture


title: Salt_2

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

description: Library name: Salt_2

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
High-quality reads of each sample were aligned to the reference genome of Lumnitzera littorea via hisat2 program
Gene counts were obtained using featureCounts.
Assembly: reference genome of Lumnitzera littorea is published by Xie et al. in 2022, and it is publicly available at DDBJ/ENA/GenBank under the accessions JAMXBB000000000 (L. littorea) of BioProject PRJNA849397 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA849397) and  National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn/) under accession numbers GWHBCKN00000000 (https://ngdc.cncb.ac.cn/gwh/Assembly/20694/show)
Supplementary files format and content: One csv file containing raw count values for each sample

organism: Lumnitzera littorea

source_name: leaf

growth_protocol: Mature seeds of Lumnitzera littorea were picked in Tielu Bay, Sanya, Hainan, China, and cultivated in the ecological garden of Hainan Normal University under natural conditions for one year.

extract_protocol:
Total RNAs was extracted from the leaves of each plant using GeneJET Plant RNA Purification Kit
Illumina sequencing libraries were prepared following manufacturer’s instruction

treatment_protocol: These seedlings were then assigned into two groups, where one group was treated with fresh water as control (CK), while the other was treated with saline water at 400 mM for three days.

value: leaf

value: 400mM NaCl for 3d


title: 5_041_01

value: blood


title: Salt_3

description: Library name: Salt_3


title: Salt_1

description: Library name: Salt_1


title: 5_030_01


title: CK_2

description: Library name: CK_2

value: CK


title: CK_3

description: Library name: CK_3


title: RNA_sh1_2

description:
Library name: hnRNPL-sh1-2
The raw data are being open accessed in SRA with accession number PRJNA988254

value: Ovarian cancer

value: Human Ovarian fibroblasts

value: shhnRNPL


title: 1_140_01


title: CK_1

description: Library name: CK_1


title: Resistant 12H cross 5 rep 5

city: Fort Collins

first: Todd

last: Gaines

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

description:
JHM69_Res_12_5_Resistant_12_
cross 5 rep 5

data_processing:
Raw reads were pre-processed by removal of library adapter sequences, removal of low quality reads, and assessing the quality control using fastp.
Read alignment of the 72 libraries to the available male genome of Palmer amaranth (v1.1, id55760) was performed using Hisat2.2.1.
Most of the reads (>77%) aligned concordantly once, while >7% aligned concordantly more than one time and about 14% of reads aligned not concordantly.
Mapped reads were assigned using featureCounts.
The alignment of the RNA-sequencing experiment was used to analyzed differentially expressed genes (DEGs) using DEseq2 (v1.20.0)
Assembly: Palmer amaranth (v1.1, id55760)
Supplementary files format and content: comma-separated values files, which contains DEseq2 normalized counts for each sample

organism: Amaranthus palmeri

source_name: meristem youngest leaf

growth_protocol: Palmer amaranth seed was sown on 0.7% agar medium (Sigma-Aldrich), placed in a refrigerator at 4 °C for seven d and then germinated on a germination bench at room temperature with 16/8h day/night cycle. Germinated seedlings were transplanted into commercial potting soil in 5x5 cm inserts and maintained in the greenhouse at 24±2°C temperatures and 15/9 h day/night photoperiods supplemented with metal-halide lamps (400 µmol m-2 s-1). Plants were watered daily. A pseudo-F2 generation was generated by first spraying parental NER individuals at 7-10 cm height with a field rate of 91 a.i. ha-1 tembotrione (Laudis, Bayer CropScience) and 1% v/v methylated seed oil (MSO). Surviving NER were transplanted into 22.5 cm diameter pots and individually crossed with another NES individual using pollination bags. Five crosses with NERmale  NESfemale and five crosses with NERfemale  NESmale were performed and grown to seed. The resulting F1 generations were grown out and sprayed again under the same conditions described above. Two F1 individuals from each parental cross that survived the application were crossed with each other. Seeds from the resulting Pseudo-F2 generation were subsequently used for the RNA-Seq experiment. About 150 seedlings from each Pseudo-F2 cross were transplanted into 4x4 cm inserts each and maintained in a growth chamber at 25/22°C day/night temperatures, 70% relative humidity, and 16h photoperiod with 700 μmol m-2 s-1 provided by incandescent and fluorescent bulbs. At 4-5 cm height and 4-5 leaf stage, the first fully expanded leaf from the apical meristem of each plant was cut and immediately frozen at -80°C for timepoint 0. The plants were then sprayed at 77 g a.i. ha-1 (85% of the field rate) with 1% v/v MSO as described above to ensure resistant plants would be able to survive despite removing leaves for testing. Six HAT the second expanded leaf and twelve HAT the third expanded leaf were cut and immediately frozen at -80 °C, respectively. Visual damage and survival data were recorded after treatment for 21 d to phenotype resistant and susceptible individuals. From each pseudo-F2 cross only the six visually most resistant and the six visually most susceptible individuals were used for RNA-Sequencing.

extract_protocol:
Total RNA was extracted from frozen ground tissue using the Direct-zol™ RNA MiniPrep Plus (Zymo Research) which includes DNAse treatment. Yield and purity were measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity (RIN) was measured on an Agilent 2200 Bio TapeStation system (Agilent Technologies) using Agilent High Sensitivity RNA ScreenTape.
RNASeq library preparation was performed with the TruSeq stranded mRNA library prep kit (Illumina) preparing for 150 nucleotide paired-end sequencing.
The 72 libraries were run on an Illumina HiSeq 4000 platform on a total of 16 lanes (2 flow cells) with seven libraries per lane, yielding 5.2 billion paired-end reads.

treatment_protocol: tembotrione 77 g a.i. ha-1

value: meristem youngest leaf

value: Resistant

tag: time point


title: 1_075_01


title: Resistant 12H cross 5 rep 6

description:
JHM72_Res_12_6_Resistant_12_
cross 5 rep 6


title: Resistant 6H cross 5 rep 6

description:
JHM71_Res_6_6_Resistant_6_
cross 5 rep 6


title: 1_144_01


title: 1_002_01


title: 3_074_01

value: Healthy


title: Resistant 0H cross 5 rep 5

description:
JHM67_Res_0_5_Resistant_0_
cross 5 rep 5


title: Resistant 12H cross 5 rep 4

description:
JHM66_Res_12_4_Resistant_12_
cross 5 rep 4


title: Resistant 0H cross 5 rep 6

description:
JHM70_Res_0_6_Resistant_0_
cross 5 rep 6


title: Resistant 6H cross 5 rep 4

description:
JHM65_Res_6_4_Resistant_6_
cross 5 rep 4


title: Resistant 6H cross 5 rep 5

description:
JHM68_Res_6_5_Resistant_6_
cross 5 rep 5


title: 3_037_01


title: Resistant 0H cross 5 rep 3

description:
JHM61_Res_0_3_Resistant_0_
cross 5 rep 3


title: Resistant 12H cross 5 rep 2

description:
JHM60_Res_12_2_Resistant_12_
cross 5 rep 2


title: Resistant 12H cross 5 rep 3

description:
JHM63_Res_12_3_Resistant_12_
cross 5 rep 3


title: 3_012_01


title: Resistant 0H cross 5 rep 4

description:
JHM64_Res_0_4_Resistant_0_
cross 5 rep 4


title: 6_028_01

value: DWS


title: Resistant 6H cross 5 rep 1

description:
JHM56_Res_6_1_Resistant_6_
cross 5 rep 1


title: 6_025_01


title: 3_047_01


title: 6_020_01


title: Resistant 6H cross 5 rep 3

description:
JHM62_Res_6_3_Resistant_6_
cross 5 rep 3


title: Susceptible 12H cross 5 rep 6

description:
JHM54_Susc_12_6_Susceptible_12_
cross 5 rep 6

value: Susceptible


title: Resistant 0H cross 5 rep 1

description:
JHM55_Res_0_1_Resistant_0_
cross 5 rep 1


title: Resistant 6H cross 5 rep 2

description:
JHM59_Res_6_2_Resistant_6_
cross 5 rep 2


title: Susceptible 6H cross 5 rep 6

description:
JHM53_Susc_6_6_Susceptible_6_
cross 5 rep 6


title: Resistant 0H cross 5 rep 2

description:
JHM58_Res_0_2_Resistant_0_
cross 5 rep 2


title: Resistant 12H cross 5 rep 1

description:
JHM57_Res_12_1_Resistant_12_
cross 5 rep 1


title: 5_089_01


title: Susceptible 0H cross 5 rep 5

description:
JHM49_Susc_0_5_Susceptible_0_
cross 5 rep 5


title: delta tsdA delta shdrR cells grown on methanol and thiosulfate (biol rep 2)

city: Bonn

first: Christiane

last: Dahl

address: Meckenheimer Allee 168

department: Institut für Mikrobiologie & Biotechnologie

country: Germany

description: Library name: Sample 4

data_processing:
RNAseq Pipeline v2.0
Raw sequencing data are preprocessed to generate clean data for downstream analysis. In this step, quality of raw sequencing ischecked and filtered to retain only high quality bases by performing adapter trimming, quality filtering and per-read qualitypruning.
Quality is interpreted as the probability of an incorrect base call or, equivalently, the base call accuracy. The quality score islogarithmically based, so a quality score of 10 reflects a base call accuracy of 90%, but a quality score of 20 reflects a base callaccuracy of 99% and a quality score of 30 reflects a base call accuracy of 99.9%. These probability values are the results from thebase calling algorithm and depend on how much signal was captured for the base incorporation.
Sequencing reads representing reads with quality score at least Q30 is above 90% is of very good quality. For a reasonably goodsample source material, according to Illumina specifications, one could expect >75% reads with at least Q30 Phred quality.
Raw sequencing data was processed using fastp software to remove poor quality bases (below Phred Quality 20) using thesliding window approach where  if the average quality of the bases drops below Q20, those bases are removed from the reads. After quality trimming, program checks for presence of any adapters in the reads and removes from the reads. Further, shorterreads which are <30bp length are also removed to retain only high quality sequencing reads for each sample in the analysis. Incase of paired-end reads, both the sequencing reads which pass the QC criteria are considered for downstream analysis.
Assembly: High quality sequence reads were aligned to the reference genome using STAR (Spliced Transcripts Alignment to a Reference) along with the known gene models.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes significant fold changes for each gene
Supplementary files format and content: tab-delimited text file includes fold changes for each gene

organism: Hyphomicrobium denitrificans

source_name: bacterial cell

growth_protocol:
methanol and thiosulfate
H. denitrificans strains ΔtsdA ΔsoxR and ΔtsdA ΔshdrR were cultured in 50 ml minimal medium containing 24.4 mM methanol in 200 ml Erlenmeyer flasks at 30°C with shaking at 200 rpm to early log phase.

extract_protocol:
From the frozen pellets, the RNA was purified with the FastGene RNA Premium Kit (NIPPON Genetics EUROPE, Düren, Germany) according to the manufacturer’s instructions. A modification was introduced regarding the cell lysis step. After addition of the lysis buffer that contained 1% (v/v) 2-mercaptoethanol, cells were disrupted by bead beating (Bead Ruptor 12 Bead Mill Homogenizer, Omni International, Kennesaw, GA, USA) for three cycles of 30 s at maximum speed and incubation on ice for 1 min. RNA quality was checked on 1% agarose gels and its concentration was measured using NanoPhotometer NP80 (IMPLEN, Munich, Germany).
The RNA was shipped on dry ice to Eurofins Genomics GmbH (Ebersberg, Germany). The subsequent analysis pipeline included rRNA depletion, library preparation (mRNA fragmentation, strand specific cDNA synthesis), Illumina paired end sequencing (2 x 150 bp, minimum 10 MB reads)), and bioinformatic analysis (mapping against the reference genome, identification and quantification of transcripts, pairwise comparison of expression levels and determination of significant fold differences) and was conducted by the company.
Strand-specific cDNA library. RNA-seq Technology: Genome Sequencer Illumina NovaSeq. Sequence mode: NovaSeq 6000 S4 PE150 XP

treatment_protocol: Cells from 20 ml culture were harvested and flash frozen in liquid N2 and stored at -70°C.

value: bacterial cell

value: delta tsdA delta shdrR

value: growth in batch culture


title: Cardiomyocytes5, histidine 100nM and doxorubicin 1μM, 72h

city: Beijing

first: Hongxuan

last: Xu

address: No.8 Xishiku Street

department: Cardiology

institute: Peking university first hospital

description: Library name: CMDH5

data_processing:
Low-quality regions at both ends of the sequences were trimmed using Trimmomatic, with a quality threshold set at 30. Adapter sequences were removed. Sequences containing ambiguous bases (N) were eliminated. Sequences shorter than 60 bp were discarded.
Assembly: mRatBN7.2
Supplementary files format and content: text file includes raw counts and fpkm for each sample

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocytes

extract_protocol:
RNA was harbested using Dynabeads Oligo (dT)25-61002 (ThermoFisher).
Fragmentation buffer was added to break the mRNA into short segments. Using the mRNA as a template, first-strand cDNA was synthesized with random hexamer primers. Following this, a buffer, dNTPs, DNA polymerase I, and RNase H were added to synthesize double-stranded cDNA, which was then purified using AMPure XP beads.  The purified double-stranded cDNA underwent end repair, A-tailing, and ligation of sequencing adapters, followed by size selection using AMPure XP beads. PCR amplification was then performed, and the PCR products were purified with AMPure XP beads to obtain the final library. Once the library construction was complete, preliminary quantification was conducted using a Qubit 2.0, and the library was diluted to 1.5 ng/µL. The insert size of the library was assessed using an Agilent 2100. After confirming that the insert size met expectations, accurate quantification of the library’s effective concentration was performed using Q-PCR (with effective concentration > 2 nM) to ensure library quality.

value: Neonatal rat cardiomyocytes


title: delta tsdA delta shdrR cells grown on methanol and thiosulfate (biol rep 1)

description: Library name: Sample 3


title: M exposed to Clas-positive psyllids_time60_ replicate 3

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

data_processing:
Adapter removal and quality trimming of raw reads was done with cutadapt.
Clean reads were analysed using FastQC.
Clean read pairs longer than 20 nt were mapped to the reference genomes (for Citrus and Bergera) or de novo transcriptome (for Bergera) using STAR.
Differential expression analysis was performed with DESeq2.
Assembly: Citrus sinensis SWO.v3.0 genome + Liberibacter_asiaticus NZ_CP019958 genome, Murraya paniculata genome + Liberibacter_asiaticus NZ_CP019958 genome (Murraya_paniculata_final.chr.fasta), and Bergera transcriptome + Liberibacter_asiaticus NZ_CP019958 genome (Bergera_ST_Streptophyta.fasta) combined genomes.
Supplementary files format and content: Tab-delimited text files including count of reads for each gene in each sample.

organism: Murraya paniculata

source_name: young flush

growth_protocol: C. × sinensis ‘Valencia’ plants, and M. paniculata and B. koenigii seedlings were pruned at 15-25 cm to promote new flushes. A V2 flush was selected, and the remaining ones were eliminated.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Two µg of total RNA per sample were used for library generation using the TruSeq stranded total RNA Library Kit plus Ribo-Zero and NEBNext kits for ribosomal RNA depletion.
The Illumina NovaSeq6000 was used on a paired-end sequencing of 150pb. All procedures were performed according to Illumina’s protocols.

treatment_protocol: Five 15-20 days-old CLas-positive or negative adult psyllids were confined to a single flush per plant for 48 h.

value: young flush

value: Clas-positive psyllid


title: Susceptible 12H cross 5 rep 4

description:
JHM48_Susc_12_4_Susceptible_12_
cross 5 rep 4


title: Susceptible 12H cross 5 rep 5

description:
JHM51_Susc_12_5_Susceptible_12_
cross 5 rep 5


title: Cardiomyocytes4, histidine 100nM and doxorubicin 1μM, 72h

description: Library name: CMDH4


title: Susceptible 0H cross 5 rep 6

description:
JHM52_Susc_0_6_Susceptible_0_
cross 5 rep 6


title: M exposed to Clas-negative psyllids_time60_ replicate 2

value: Clas-negative psyllid


title: M exposed to Clas-positive psyllids_time60_ replicate 2


title: delta tsdA delta soxR cells grown on methanol (biol. rep 2)

description: Library name: Sample 2

growth_protocol:
methanol
H. denitrificans strains ΔtsdA ΔsoxR and ΔtsdA ΔshdrR were cultured in 50 ml minimal medium containing 24.4 mM methanol in 200 ml Erlenmeyer flasks at 30°C with shaking at 200 rpm to early log phase.

value: delta tsdA delta soxR


title: M exposed to Clas-positive psyllids_time60_ replicate 1


title: delta tsdA delta soxR cells grown on methanol (biol rep 1)

description: Library name: Sample 1


title: M exposed to Clas-negative psyllids_time60_ replicate 1


title: Susceptible 6H cross 5 rep 4

description:
JHM47_Susc_6_4_Susceptible_6_
cross 5 rep 4


title: M exposed to Clas-negative psyllids_time60_ replicate 3


title: Mouse EAE Brain Myeloid C3 Positive

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Raw fastq files were processed with cellranger (v7.0.1) with "Include introns" set to true
Assembly: Reference used for cellranger was a custom reference built using Ensembl GRCm39.104 transcriptome with the sequence for tdTomato added (gene called "TDT")
Supplementary files format and content: Cellranger generated raw and filtered feature barcode matrices in HDF5 format

source_name: Brain

growth_protocol: Mice were maintained in temperature-controlled animal facility at Johns Hopkins University School of Medicine with 12 h/12 h light/dark cycles and fed 18% autoclaved feed and water ad libitum

extract_protocol:
Mice were euthanized with isoflurane followed by perfusion with chilled HBSS containing 10μM triptolide, 27.1μg/mL anisomycin, and 5μg/mL actinomycin D. Brains were extracted, chopped into small pieces, then digested with 20U/mL Papain and 100U/mL DNAse I in digestion buffer (EBSS with 22.5mM D(+)-glucose, 26mM NaHCO3, 0.5mM EDTA, 1mM L-cysteine,10μM triptolide, 27.1μg/mL anisomycin, and 5μg/mL actinomycin D at pH 7.4) under slow rotation at 37c for 60 minutes with manual trituration steps every 15 minutes. After filtering, myelin debris was removed with debris removal solution (Miltenyi Biotec) following manufacturer's recommended protocol. Cells from 4 animals (3 female, 1 male) were pooled and stained for viability (L/D Violet),CD45 (anti-CD45 APC-Fire750), and CD11b (PerCP-Cy5.5) then two populations were sorted: viable;CD45+;CD11b+;C3-tdTomato- and viable;CD45+;CD11b+;C3-tdTomato+. Following sorting, cells were washed, counted, and loaded onto 2 seperate lanes (Pos cells in 1 lane, Neg cells in the other) of a 10X Chromium Chip G then partitioned into GEMs on a Chromium Controller following manufacturer's recommended protocol.)
Libraries were constructed and sequenced using 10X 3' 3.1 chemistry according to manufacturer's recommendations

treatment_protocol: Mice were immunized with MOG35-55 emulsion (150μl of emulsion containing 150μg MOG35-55 peptide, 600μg Mtb) subcutaneously. On day of immunization and 2 days later, mice were also injected with 250ng pertussis toxin intraperitoneally. Mice were monitored for onset of EAE symptoms (all mice reached score greater than 2.5 - significant hind limb weakness) until 16 days post-immunizaiton.

value: Brain

value: 3 female, 1 male

value: C3-tdTomato Reporter

value: MOG35-55 EAE


title: Susceptible 0H cross 5 rep 4

description:
JHM46_Susc_0_4_Susceptible_0_
cross 5 rep 4

value: meristem youngest leaf


title: Cardiomyocytes3, histidine 100nM and doxorubicin 1μM, 72h

description: Library name: CMDH3


title: Cardiomyocytes2, histidine 100nM and doxorubicin 1μM, 72h

description: Library name: CMDH2


title: M exposed to Clas-positive psyllids_time30_ replicate 3


title: Susceptible 6H cross 5 rep 5

description:
JHM50_Susc_6_5_Susceptible_6_
cross 5 rep 5


title: M exposed to Clas-positive psyllids_time30_ replicate 2


title: Cardiomyocytes1, histidine 100nM and doxorubicin 1μM, 72h

description: Library name: CMDH1


title: Susceptible 12H cross 5 rep 3

description:
JHM45_Susc_12_3_Susceptible_12_
cross 5 rep 3


title: Susceptible 6H cross 5 rep 3

description:
JHM44_Susc_6_3_Susceptible_6_
cross 5 rep 3


title: M exposed to Clas-positive psyllids_time30_ replicate 1


title: Mouse EAE Brain Myeloid C3 Negative


title: Cardiomyocytes5, doxorubicin 1μM, 72h

description: Library name: CMD5


title: Mixed C3 Positive Myeloid, Rep 3

data_processing:
Raw sequencing data of the 1 multiplexed library was processed with cellranger multi (v7.1.0) using Chromium Mouse Transcriptome Probe Set v1.0.1 and demultiplexed into per sample feature barcode matrices along with unassigned reads (provided as supplementary file unassigned_alignments.bam)
Assembly: mm10-2020-A
Supplementary files format and content: cellranger generated filtered and raw feature barcode matrices in HDF5 format
Library strategy: RNA Templated Ligation (RTL)

source_name: Brain+Spinal Cord

extract_protocol:
Mice were euthanized with isoflurane followed by perfusion with chilled HBSS containing 27.1μg/mL anisomycin and 5μg/mL actinomycin D. Brains and spinal cords were extracted, chopped into small pieces, then digested with 20U/mL Papain and 100U/mL DNAse I in digestion buffer (EBSS with 22.5mM D(+)-glucose, 26mM NaHCO3, 0.5mM EDTA, 1mM L-cysteine,10μM triptolide, 27.1μg/mL anisomycin, and 5μg/mL actinomycin D at pH 7.4) under slow rotation at 37c for 30 minutes with manual trituration steps every 10 minutes. After filtering, myelin was removed with myelin removal beads (Miltenyi Biotec) following manufacturer's recommended protocol. Cells from 2 animals (2 female, 2 male, or 1 male and 1 female) were pooled and stained for viability (L/D Violet),CD45 (anti-CD45 APC-Fire750), CD11b (anti-CD11b BV510), and ACSA2 (anti-ACSA2 APC) then three populations were FACS sorted from each pooled sample: viable;CD45-;ACSA2+;C3-tdTomato+ and C3-tdTomato-, viable;CD45+;CD11b+;C3-tdTomato- and viable;CD45+;CD11b+;C3-tdTomato+. Following sorting, cells were washed and fixed with 4% formaldehyde overnight at 4c, then quenched and stored at -80c. Cells were later thawed and labeled with barcoded probes (10X Genomics Chromium Fixed RNA Profiling) then washed, pooled, and partitioned into GEMs in a single lane of a Chromium Next Gem Chip Q using a Chromium X controller.
The single multiplexed library containing 9 samples was generated following manufacturer's (10X Genomics Chromium Fixed RNA Profiling using Multiplexed Samples) guidelines

treatment_protocol: Mice were immunized with MOG35-55 emulsion (150μl of emulsion containing 150μg MOG35-55 peptide, 600μg Mtb) subcutaneously. On day of immunization and 2 days later, mice were also injected with 250ng pertussis toxin intraperitoneally. Mice were monitored for onset of EAE symptoms (all mice reached score greater than 1.5 - complete tail tone loss and some hind limb weakness) until 16 days post-immunization.

value: Brain+Spinal Cord

tag: pooled animals

value: 1 female + 1 male

tag: barcode


title: Unassigned_Alignments

description:
Alignments not assigned to any samples
This sample's raw file (unassigned_alignments.bam) is essential in case anyone wants to reproduce our analyses from scratch.

value: Mix of 3 biological replicates

value: Mix of 3 sorted cell types

tag: genotype


title: M exposed to Clas-negative psyllids_time30_ replicate 3


title: Mixed Astrocytes, Rep 3

value: CD45-;ACSA2+;C3+ and C3-


title: Male C3 Positive Myeloid, Rep 2

value: 2 male


title: Cardiomyocytes4, doxorubicin 1μM, 72h

description: Library name: CMD4


title: Mixed C3 Negative Myeloid, Rep 3


title: Susceptible 12H cross 5 rep 2

description:
JHM42_Susc_12_2_Susceptible_12_
cross 5 rep 2

value: Susceptible


title: M exposed to Clas-negative psyllids_time30_ replicate 2


title: Cardiomyocytes3, doxorubicin 1μM, 72h

description: Library name: CMD3

value: Neonatal rat cardiomyocytes


title: Susceptible 6H cross 5 rep 2

description:
JHM41_Susc_6_2_Susceptible_6_
cross 5 rep 2


title: M exposed to Clas-positive psyllids_time20_ replicate 3

value: young flush


title: Cardiomyocytes4, histidine 100nM, 72h

description: Library name: CMH4


title: Susceptible 12H cross 5 rep 1

description:
JHM39_Susc_12_1_Susceptible_12_
cross 5 rep 1


title: M exposed to Clas-positive psyllids_time20_ replicate 1

value: Clas-positive psyllid


title: Susceptible 0H cross 5 rep 2

description:
JHM40_Susc_0_2_Susceptible_0_
cross 5 rep 2


title: M exposed to Clas-negative psyllids_time20_ replicate 3

value: Clas-negative psyllid


title: Cardiomyocytes2, doxorubicin 1μM, 72h

description: Library name: CMD2


title: Male Astrocytes, Rep 2


title: M exposed to Clas-negative psyllids_time20_ replicate 2


title: Cardiomyocytes1, doxorubicin 1μM, 72h

description: Library name: CMD1


title: Susceptible 0H cross 5 rep 1

description:
JHM37_Susc_0_1_Susceptible_0_
cross 5 rep 1


title: Cardiomyocytes3, histidine 100nM, 72h

description: Library name: CMH3


title: M exposed to Clas-negative psyllids_time30_ replicate 1


title: Cardiomyocytes5, histidine 100nM, 72h

description: Library name: CMH5


title: Susceptible 6H cross 5 rep 1

description:
JHM38_Susc_6_1_Susceptible_6_
cross 5 rep 1


title: Susceptible 0H cross 5 rep 3

description:
JHM43_Susc_0_3_Susceptible_0_
cross 5 rep 3


title: Female C3 Positive Myeloid, Rep 1

value: 2 female


title: Male C3 Negative Myeloid, Rep 2


title: Cardiomyocytes2, histidine 100nM, 72h

description: Library name: CMH2


title: M exposed to Clas-positive psyllids_time20_ replicate 2


title: Resistant 12H cross 4 rep 6

description:
JHM36_Res_12_6_Resistant_12_
cross 4 rep 6

value: Resistant


title: Female C3 Negative Myeloid, Rep 1


title: M exposed to Clas-negative psyllids_time20_ replicate 1


title: Cardiomyocytes1, histidine 100nM, 72h

description: Library name: CMH1


title: Mouse Peak EAE C3 WT Optic Nerve ATAC, Rep 2

library_source: genomic single cell

data_processing:
Raw sequencing files were processed with cellranger arc (v2.0.2) to generate joint single cell gene expression and chromatin accesibility fragment matrices
Assembly: mm10 2020-A-2.0.0
Supplementary files format and content: Cellranger generated raw and filtered feature barcode matrices in HDF5 format
Supplementary files format and content: Cellranger generated tab-separated fragments files and associated tabix index

source_name: Optic Nerve

extract_protocol:
Mice were euthanized with isoflurane overdose then eyes were enucleated and optic nerves detached and flash frozen in liquid nitrogen then stored in liquid nitrogen. Later, optic nerves were retrieved and pooled across mice (n = 5 mice, 10 optic nerves per biological replicate) then lysed and nuclei isolated with 10X Chromium Nuclei Isolation Kit. Following debris removal, nuclei underwent transposition for 1 hour at 37c then were loaded onto Chromium Next Gem Chip J and partitioned into GEMs on Chromium Controller.
Both ATAC and Gene Expression libraries were generated according to 10X Multi-Ome recommendations
snMulti-ome-seq (paired snRNA-seq and snATAC-seq)

treatment_protocol: Mice were immunized with MOG35-55 emulsion (150μl of emulsion containing 150μg MOG35-55 peptide, 600μg Mtb) subcutaneously. On day of immunization and 2 days later, mice were also injected with 250ng pertussis toxin intraperitoneally. Mice were monitored for onset of EAE symptoms (all mice reached score greater than 1.0 - complete tail tone loss) until 16 days post-immunizaiton.

value: Optic Nerve

tag: tissue source

value: 2 female, 3 male

value: nuclei

value: Complement C3 Wildtype

value: MOG 35-55 EAE


title: Resistant 0H cross 4 rep 6

description:
JHM34_Res_0_6_Resistant_0_
cross 4 rep 6

value: meristem youngest leaf


title: Multiome, K562, DMSO treated, Replicate 2, GEX

city: San Francisco

first: Scot

middle: M

last: Federman

address: 499 Illinois St

department: Biochemistry

institute: UCSF

description: Library name: K562_DMSO_RNA_2

data_processing:
Demultiplexed FASTQs were processed using Cellranger-Arc
Assembly: hg38
Supplementary files format and content: Tab separated values files and CellRanger matrix files

extract_protocol:
Adherent cells (iPSCs) were dissociated into single cell suspension using accutase and then counted using the automated cell counter Countess. Suspension cells (K562) were directly counted using countess. Appropriate number of cells were used for nuclear extraction and tagmentation following the 10x Multiome protocol. The nuclei were then encapsulated in Gel-bead in Emulsion (GEMs) using the 10X chromium controller and Chromium Next GEM Single Cell Multiome ATAC Kit A.
RNA and ATAC libraries were constructed according to 10X instructions. For generating guide RNA libraries during the GEM Generation and step, a duplex splint oligo was spiked into the barcoding reaction mix to allow reverse transcription of gRNAs and ligation onto the capture oligo of 10X multiome gel beads. The resulting cDNA from captured guide RNAs is amplified to make an Illumina-compatible sequencing library containing P5 and P7 adaptors as well as sample indexes.

value: Myeloid

value: CRISPRi + DMSO treatment

tag: library type

value: mRNA


title: Cardiomyocytes4, PBS, 72h

description: Library name: CMC4


title: Female Astrocytes, Rep 1

value: Brain+Spinal Cord

value: CD45-;ACSA2+;C3+ and C3-

value: C3-tdTomato Reporter


title: Mouse Peak EAE C3 KO Optic Nerve ATAC, Rep 2

value: Complement C3 Knockout


title: Multiome, K562, Dasatinib treated, Replicate 2, GEX

description: Library name: K562_Dasatinib_RNA_2

value: CRISPRi + dasatnib treatment


title: Cardiomyocytes5, PBS, 72h

description: Library name: CMC5

value: Neonatal rat cardiomyocytes


title: Mouse Peak EAE C3 KO Optic Nerve ATAC, Rep 1


title: K562, DMSO treated, Replicate 2, guideRNA library

description: Library name: K562_DMSO_guideRNA_2

library_source: other

molecule: other

value: CRISPR guideRNA


title: Mouse Peak EAE C3 WT Optic Nerve ATAC, Rep 1


title: K562, DMSO treated, Replicate 1, guideRNA library

description: Library name: K562_DMSO_guideRNA_1


title: Cardiomyocytes1, PBS, 72h

description: Library name: CMC1


title: Multiome, K562, Dasatinib treated, Replicate 1, GEX

description: Library name: K562_Dasatinib_RNA_1


title: Resistant 0H cross 4 rep 4

description:
JHM28_Res_0_4_Resistant_0_
cross 4 rep 4

value: Resistant


title: Resistant 12H cross 4 rep 5

description:
JHM33_Res_12_5_Resistant_12_
cross 4 rep 5


title: Cardiomyocytes3, PBS, 72h

description: Library name: CMC3


title: Resistant 0H cross 4 rep 5

description:
JHM31_Res_0_5_Resistant_0_
cross 4 rep 5


title: Mouse Peak EAE C3 WT Optic Nerve GEX, Rep 1

value: Optic Nerve


title: Resistant 6H cross 4 rep 4

description:
JHM29_Res_6_4_Resistant_6_
cross 4 rep 4


title: Mouse Peak EAE C3 KO Optic Nerve GEX, Rep 2

value: 2 female, 3 male


title: Resistant 6H cross 4 rep 5

description:
JHM32_Res_6_5_Resistant_6_
cross 4 rep 5


title: Resistant 12H cross 4 rep 3

description:
JHM27_Res_12_3_Resistant_12_
cross 4 rep 3


title: K562, Dasatinib treated, Replicate 2, guideRNA library

description: Library name: K562_Dasatinib_guideRNA_2


title: MycCapWTB

type: RNA

city: Tucson

first: Amber

last: Clements

state: AZ

address: 1515 N Campbell Ave

institute: University of Arizona

description: MyC-Cap cells co-injected with macrophages expressing WT PIM expression

hyb_protocol: NanoString hybridization protocol

scan_protocol: NanoString nCounter

data_processing: Samples were analyzed using nanostring nSolver software

source_name: Cell culture

growth_protocol: Macrophages were co-injected with MyC-Cap cells in FVB mice. After 2 wks of growth, tumors were harvested, fixed, and paraffin embedded

extract_protocol: Total RNA was isolated from paraffin embedded tumor tissue using deparaffinization solution and the RNeasy FFPE

tag: pim macrophage expression

value: Macrophages with WT PIM expression


title: K562, Dasatinib treated, Replicate 1, guideRNA library

description: Library name: K562_Dasatinib_guideRNA_1


title: S19 and S20, Fracture gap, sample 19/20, External fixation compliant, isotype control, scRNAseq

city: Dresden

first: Annemarie

last: Lang

address: Fetscherstrasse 74

institute: TU Dresden

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fracture gap

extract_protocol:
The osteotomized left femur was carefully dissected and the bone pieces within the two middle pins were transferred into a petridish with PBS. Cells were flushed from the bone pieces. For control samples - the contralateral femur was dissected and the bone marrow was flushed using PBS. Isolated cells were passed through a CellStrainer and underwent Red Blood Cell Lysis (Miltenyi Biotech - 130-094-183). Cells were washed and resuspended in PBS/0.1% BSA before performing Dead Cell Reomval (according to manufacturer's instructions - Miltenyi Biotech 130-090-101). Cells were washed and resuspended in PBS/0.04% BSA and transferred on ice to the Core Facility.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Samples were processed with Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with Dual Index Kit TT Set A

value: Mixed

value: Fracture gap

tag: strain

tag: Sex

value: female

tag: age

value: 14-16 weeks old


title: Multiome, K562, DMSO treated, Replicate 2, scATACseq

description: Library name: K562_DMSO_ATAC_2

value: Myeloid

value: CRISPRi + DMSO treatment

value: ATAC


title: MycCapWTC


title: MycCapTKOC

description: MyC-Cap cells co-injected with PIM triple KO macrophages

value: Macrophages with PIM Triple KO


title: Mouse Peak EAE C3 KO Optic Nerve GEX, Rep 1

value: nuclei

value: MOG 35-55 EAE


title: S15 and S16, Fracture gap, sample 15/16, External fixation compliant, isotype control, scRNAseq

description: 10x Genomics


title: Resistant 6H cross 4 rep 3

description:
JHM26_Res_6_3_Resistant_6_
cross 4 rep 3

value: meristem youngest leaf


title: Multiome, K562, DMSO treated, Replicate 1, GEX

description: Library name: K562_DMSO_RNA_1

value: mRNA


title: MycCapTKOB


title: Cardiomyocytes2, PBS, 72h

description: Library name: CMC2

value: Neonatal rat cardiomyocytes


title: Resistant 0H cross 4 rep 3

description:
JHM25_Res_0_3_Resistant_0_
cross 4 rep 3

value: Resistant


title: S17 and S18, Fracture gap, sample 17/18, External fixation compliant, isotype control, scRNAseq

description: 10x Genomics


title: Multiome, K562, DMSO treated, Replicate 1, scATACseq

description: Library name: K562_DMSO_ATAC_1


title: Resistant 0H cross 4 rep 2

description:
JHM22_Res_0_2_Resistant_0_
cross 4 rep 2


title: MycCapTKOA


title: Resistant 12H cross 4 rep 2

description:
JHM24_Res_12_2_Resistant_12_
cross 4 rep 2


title: Multiome, K562, Dasatinib treated, Replicate 2, scATACseq

description: Library name: K562_Dasatinib_ATAC_2

value: CRISPRi + dasatnib treatment


title: S13 and S14, Fracture gap, sample 13/14, External fixation compliant, isotype control, scRNAseq

description: 10x Genomics


title: MycCapWTA


title: Resistant 6H cross 4 rep 2

description:
JHM23_Res_6_2_Resistant_6_
cross 4 rep 2


title: Multiome, K562, Dasatinib treated, Replicate 1, scATACseq

description: Library name: K562_Dasatinib_ATAC_1


title: S11 Fracture gap, sample 11, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics


title: S11 Contralateral bone marrow, sample 11, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics

source_name: Contralateral bone marrow

value: Contralateral bone marrow


title: MycCapPIM1A

description: MyC-Cap cells co-injected with PIM1 KO Macrophages

value: Macrophages with PIM1 KO


title: Resistant 6H cross 4 rep 1

description:
JHM20_Res_6_1_Resistant_6_
cross 4 rep 1


title: Resistant 0H cross 4 rep 1

description:
JHM19_Res_0_1_Resistant_0_
cross 4 rep 1


title: Resistant 12H cross 4 rep 1

description:
JHM21_Res_12_1_Resistant_12_
cross 4 rep 1


title: iPSC, GEX

description: Library name: iPSC_GEX

source_name: iPSC

value: iPSC

value: Pluripotent stem cell

value: CRISPRa overexpression


title: iPSC, guideRNA

description: Library name: iPSC_guideRNA

value: CRISPR guideRNA


title: MycCapPIM1C


title: MycCapC

description: MyC-Cap cells

value: No macrophages


title: Susceptible 12H cross 4 rep 6

description:
JHM18_Susc_12_6_Susceptible_12_
cross 4 rep 6

value: Susceptible


title: S7 and S8, Fracture gap, sample 7/8, External fixation compliant, isotype control, scRNAseq

description: 10x Genomics

value: Mixed

value: Fracture gap

value: female

value: 14-16 weeks old


title: Susceptible 6H cross 4 rep 6

description:
JHM17_Susc_6_6_Susceptible_6_
cross 4 rep 6

value: meristem youngest leaf


title: S12 Fracture gap, sample 12, External fixation rigid, Cd71 antibody, scRNAseq

description: 10x Genomics


title: MycCapB

description: MyC-Cap cells


title: MycCapPIM1B


title: S9 and S10, Fracture gap, sample 9/10, External fixation compliant, Cd71 antibody, scRNAseq

description: 10x Genomics


title: scRNAseq HTO 10x Lane 1

city: Bethesda

first: Eduard

last: Ansaldo

address: 4 Memorial Drive

department: LHIM

institute: NIH/NIAID

description: 10x Genomics lane, 14 Samples (see HTO_features.csv) hashtagged and pooled. GEX library lane 3

data_processing:
Sequencing data was demultiplexed using the bcl-convert tool from llumina and processed using the Cell Ranger (57) (v.7.1.0) (10X Genomics Pleasanton, CA) cellranger multi-function, which was run with the default 'Include-introns=True' option. After running cellranger multi 11230 cells were captured.
Downstream analyses were performed with Seurat v.4.4.0 (Hao2021) with the parameters described below. CreateSeuratObject was run with min.cells=3. Low quality cells were filtered with the following thresholds for gene counts, UMI counts, and percentage mitochondria:  500 < nFeature_RNA < 6000, nCount_RNA < 30000, percent.mt <7, with 6009 cells remaining. The RNA count data was normalized with the LogNormalize method, while the HTO count data was normalized with the CLR method. HTO count data were used to demultiplex mice and to identify doublets (63) with the HTODemux function with the parameter positive.quantile = 0.99. 2400 cells were classified as singlets and used for downstream analyses. FindVariableFeatures (nFeatures=2000) was run, data was scaled with ScaleData,  RunPCA was run (npcs=100) and the top 35 dimensions were used to run FindNeighbors, FindClusters (with a range of resolutions and a final chosen resolution of 0.25), and RunUMAP.The resulting clusters were manually annotated using cell type specific markers. Contaminating clusters comprised of immune, endothelial, and fibroblast cells were removed, while clusters of interest comprised of basal cells, epithelial cells, and putative stem cells were retained. On this subset of cells FindVariableFeatures (nFeatures=2000) was run, data was scaled with ScaleData, RunPCA was run (npcs=100) and the top 28 dimensions were used to run FindNeighbors, FindClusters (with a range of resolutions and a final chosen resolution of 0.6), and RunUMAP. The resulting clusters were manually annotated using cell type specific markers.
Assembly: mm10
Supplementary files format and content: The sample_filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi command. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The scRNAsq_MEC_clusterpaper.rds file contains the final Seurat object, product of the analysis described in the processing step section.

source_name: Mammary Gland

extract_protocol:
For mammary epithelial and myoepithelial scRNA-seq, thymic IELp (CD1d-tetramer–CD4–CD8α–TCRβ+CD5+CD122+H-2Kb+PD-1+) were adoptively transferred (+IELp) or not (-IELp) into pregnant Rag2-/-c-/- /- at day 10.5 of gestation. Mammary epithelial cells and myoepithelial cells (CD45-CD31-EPCAM+) from Rag2-/-c-/- mice with or without IELp and WT were sorted 8 days post-transfer (G18.5) from samples labeled with TotalSeqC hashtags antibodies (Biolegend) with a Sony MA900 sorter
Sorted cells were pooled together and 45,000 cells were loaded to a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets (1 lanes). The gene expression (GEX) and hashtag oligo (HTO) sequencing libraries were prepared using a Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions and sequenced on an Illumina Nextseq2000 platform (NextSeq 1000/2000 P3 reagents (200 cycles))

value: Mammary Gland

value: Epithelial Cells

value: WT

value: Pregnancy


title: scRNAseq GEX 10x Lane 1

description: 10x Genomics lane, 14 Samples (see HTO_features.csv) hashtagged and pooled. GEX library lane 2


title: MycCapA

description: MyC-Cap cells


title: iPSC, scATACseq

description: Library name: iPSC_ATAC

value: ATAC


title: S6 Fracture gap, sample 6, External fixation rigid, Cd71 antibody, scRNAseq

description: 10x Genomics


title: S5 Contralateral bone marrow, sample 5, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics

value: Contralateral bone marrow


title: S5 Fracture gap, sample 5, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics


title: Susceptible 0H cross 4 rep 6

description:
JHM16_Susc_0_6_Susceptible_0_
cross 4 rep 6


title: Susceptible 12H cross 4 rep 5

description:
JHM15_Susc_12_5_Susceptible_12_
cross 4 rep 5


title: S1 Fracture gap, sample 1, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics


title: Susceptible 6H cross 4 rep 5

description:
JHM14_Susc_6_5_Susceptible_6_
cross 4 rep 5


title: scRNAseq VDJ 10x Lane 6

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 6

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger (57) v7.1.0 (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 114629 estimated number of cells, 21832 mean reads per cell (from eight GEX libraries), 543 Median hashtag UMIs per Cell (across eight HTO libraries), 66544 cells with a productive V-J spanning TRA and TRB pair (from eight VDJ libraries).
In the downstream analysis of the expression data, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 4.4.1 (58) using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established minimum thresholds for gene (nCount_RNA > 1000) and UMI counts (nFeature_RNA > 300), and a maximum threshold for percentage mitochondrial content (percent.mt < 6) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize function) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into the individual mice within nulliparous/pregnant/lactation groups and removing any doublets, HTODemux was run with a positive quantile = 0.99. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA  function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 60. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 60 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.25, resulting in 16 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.25 resolution) were further annotated using cell type-specific markers.
TCR repertoire sequencing data were analyzed with the scRepertoire package v2.0.0 (59) in R v4.4.1. Starting with the filtered contig annotations output table from 'cellranger aggr', the createHTOContigList, combineTCR, and combineExpression functions were used for combining the TCR data from each sample and for integration of the combined TCR data with the Seurat object. We utilized the amino acid sequence of the paired CDR3 regions of the alpha and beta chains as the clonotype definition. T cell repertoire diversity was estimated using the D50 metric, which was calculated in R as the fraction of clonotypes, ordered by abundance, which account for 50 percent of total TCR sequences (defined as paired aminoacid CDR3 sequences). Clonotype size was defined at the level of each biological replicate (Rare: between 0% and 0.01%, Small: between 0.01% and 0.1%, Medium: between 0.1% and 1%, Large: between 1% and 10%, Hyperexpanded: between 10% and 100%). Cells with a putative iNKT TCR were defined as containing a TRAV11-TRAJ18 alpha chain V gene usage, while cells with a putative MAIT TCR were defined as containing a TRAV1-TRAJ33 alpha chain V gene usage. TCR overlap between clusters or between mice was defined at the level of the CDR3 amino acid region for the combined alpha and beta chains, and visualized using the package circlize (PMID: 24930139).
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The scRNAseq_Tcells.rds file contains the final Seurat object, product of the analysis described in the processing step section.
Library strategy: scTCR-seq

extract_protocol:
Mammary T cells from nulliparous,  pregnant (G18.5), and lactating (L5) mice were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter.
Sorted cells were pooled and 42000 cells per lane (total of 8 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX),  hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents (100 cycles)).

value: T cells


title: S2 Fracture gap, sample 2, External fixation rigid, Cd71 antibody, scRNAseq

description: 10x Genomics


title: Susceptible 0H cross 4 rep 5

description:
JHM13_Susc_0_5_Susceptible_0_
cross 4 rep 5


title: scRNAseq VDJ 10x Lane 7

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 7


title: scRNAseq VDJ 10x Lane 8

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 8


title: Susceptible 6H cross 4 rep 4

description:
JHM11_Susc_6_4_Susceptible_6_
cross 4 rep 4


title: Resistant 12H cross 4 rep 4

description:
JHM30_Res_12_4_Resistant_12_
cross 4 rep 4

value: Resistant


title: cancer-associated fibroblast _donor 11

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Illumina protocol.

scan_protocol: Illumina protocol.

data_processing:
The data was analyzed with the minfi R package and normalized using ssNoob. CpG sites on XY chromosomes, non-CG probes, and SNP associated CpGs were removed. In addition, the detection P of the remaining CpGs were evaluated using SeSAMe package and CpG sites with detection P > 0.05 were removed.
20240203_unmeth_WW.csv and 20240203_meth_WW.csv (Unmethylated and methylated signal intensities, and Detection P-Values as detected by the pOOBAH method from the Sesame package).

label: Cy3, Cy5

source_name: Liver tumor

label_protocol: Illumina protocol.

growth_protocol: Tissue biopsies from liver tumors and adjacent healthy tissues were received from the Clinic for General, Visceral, and Transplantation Surgery at RWTH Aachen after written consent and following the guidelines of the Ethic Committee for the Use of Human Subjects at the University of Aachen (Permit number: EK 206/09). HCC = hepatocellular carcinoma , CRLM = colorectal carcinoma liver metastasis, ALM = anal cancer liver metastasis.

extract_protocol: Genomic DNA was isolated using the NucleoSpin Tissue Kit (Macherey-Nagel) and quantified on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). 1.2 µg of DNA were bisulfite converted.

treatment_protocol: Tissue pieces were minced into small pieces, washed with PBS and incubated at 37°C in collagenase IV (1 mg/ml) containing medium (KnockOut DMEM from Gibco) overnight. After filtering through a strainer, the cells were cultured in DMEM medium containing 10% human platelet lysate, Penicillin-Streptomycin (100 U/ml), and L-Glutamine (2 mM). Cells were expanded at 37°C and 5% CO2 for 2-3 passages upon reaching confluence. CAFs and NAFs were successfully isolated from 11 patients (5 HCC, 5 CRLM and 1 ALM; mean age 62.6 ± 12.8 sd; 8 male and 3 female).

tag: individual

value: donor 11

value: Liver tumor

value: CAF

tag: gender

value: male

tag: cancer type

value: HCC

tag: initial sample id


title: Mouse Peak EAE C3 WT Optic Nerve GEX, Rep 2

tag: tissue

value: Optic Nerve

value: 2 female, 3 male

tag: cell type

value: nuclei

value: Complement C3 Wildtype

tag: treatment

value: MOG 35-55 EAE


title: Susceptible 12H cross 4 rep 4

description:
JHM12_Susc_12_4_Susceptible_12_
cross 4 rep 4

value: meristem youngest leaf

value: Susceptible

tag: time point


title: bESC_E_BL_p9_VTNN

city: Davis

first: Anna

middle: Carolina

last: Denicol

address: 450 BIOLETTI WAY, MEYER HALL

department: Animal Science

institute: University of California Davis

description:
Library name: Sample 9
PE150

data_processing:
Trimmomatic was used to trim adaptors with the following settings: SLIDINGWINDOW:4:15 MINLEAN: 36 LEADING:3 TRAILING:3.
Assembly: Alignment was performed using star/2.7.10a (default settings) and Bos taurus reference genome UCD2.0 NCBI.
Supplementary files format and content: Raw counts table was prepared using FeatureCounts (subread/1.6.2), using -p -O -g gene_id arguments. Raw data was processed removing low counts and normalization with edgeR, TMM function.

organism: Bos taurus

source_name: Embryonic stem cell

growth_protocol: Bovine ESCs were derived from early (eBL) or full (BL) blastocyst-staged embryos and maintained in NBFR medium on mouse embryonic fibroblast feeders (Samples 1-4) or feeder-free on vitronectin-N (Samples 6-9). MEF (Sample 5) were grown according to manufacturer protocols (Gibco, A34180).

extract_protocol:
RNA was isolated using the Purelink Mini Kit (12183018A, Invitrogen) with DNAse treatment (12185010, Invitrogen).
Library preparation was performed using 1000 ng input with the KAPA mRNA Hyper Prep kit (Batch 1) or NEBNext Ultra II kit (Batch 2).

value: Embryonic stem cell

tag: cell line

value: E

value: Bovine ESC

value: NBFR, p32, VTN-N

tag: batch


title: S1 Contralateral bone marrow, sample 1, External fixation rigid, Isotype control, scRNAseq

description: 10x Genomics

value: Mixed

value: Contralateral bone marrow

value: female

value: 14-16 weeks old


title: bESC_C_BL_p9_VTNN

description:
Library name: Sample 8
PE150

value: C

value: NBFR, p23, VTN-N


title: scRNAseq VDJ 10x Lane 4

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 4

value: Mammary Gland

value: T cells

tag: genotype

value: WT

value: Pregnancy


title: scRNAseq VDJ 10x Lane 5

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 5


title: Resistant 6H cross 4 rep 6

description:
JHM35_Res_6_6_Resistant_6_
cross 4 rep 6

value: Resistant


title: Susceptible 0H cross 4 rep 4

description:
JHM10_Susc_0_4_Susceptible_0_
cross 4 rep 4

value: meristem youngest leaf


title: scRNAseq VDJ 10x Lane 3

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 3


title: bESC_D_eBL_p9_VTNN

description:
Library name: Sample 7
PE150

value: D

value: NBFR, p24, VTN-N


title: Susceptible 12H cross 4 rep 3

description:
JHM9_Susc_12_3_Susceptible_12_
cross 4 rep 3

value: Susceptible


title: scRNAseq VDJ 10x Lane 2

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 2


title: Susceptible 12H cross 4 rep 2

description:
JHM6_Susc_12_2_Susceptible_12_
cross 4 rep 2


title: LPC-7-3

city: Changsha

first: Panpan

last: Liu

state: China

address: Xiangya road

institute: Xiangya hospital

data_processing:
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2.
The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05.
The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LPC-7_mouse skin lesions

extract_protocol:
RNA was extracted from cells using TRIpure Reagent (Bioteke Cat. RP1001) according to manufacturer’s instructions.
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform. High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2. The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05. The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.

treatment_protocol: Intradermal administration of 10 μl LPC (10mM) or 10 μl normal saline (Vehicle) once per day for 6 consecutive days during the application of IMQ in mice (BALB/c) ear.

value: BALB/c

value: 8 weeks

value: LPC-treated

value: skin


title: scRNAseq HTO 10x Lane 8

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger (57) v7.1.0 (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. The TCR data was processed with Cell Ranger v7.1.0 using a VDJ reference based on the IGMT database: The IGMT reference was generated with Cell Ranger v7.1.0 using the 'fetch-imgt' and 'cellranger mkvdjref' functions. Processing of the expression data was performed with the 'cellranger multi' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 114629 estimated number of cells, 21832 mean reads per cell (from eight GEX libraries), 543 Median hashtag UMIs per Cell (across eight HTO libraries), 66544 cells with a productive V-J spanning TRA and TRB pair (from eight VDJ libraries).
In the downstream analysis of the expression data, the Cell Ranger aggregation output (filtered_feature_bc_matrix directory) was loaded into Seurat version 4.4.1 (58) using the CreateSeuratObject function with min.cells=3. For filtering out low-quality cells, we established minimum thresholds for gene (nCount_RNA > 1000) and UMI counts (nFeature_RNA > 300), and a maximum threshold for percentage mitochondrial content (percent.mt < 6) based on visual inspection of the corresponding metric distributions across all cells. Log-normalization (LogNormalize function) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing cells into the individual mice within nulliparous/pregnant/lactation groups and removing any doublets, HTODemux was run with a positive quantile = 0.99. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA  function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 60. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 60 dimensions and a range of resolutions to determine the optimal resolution that captures biological diversity in the dataset, which was determined to be 0.25, resulting in 16 clusters. The clusters identified by the FindClusters function of Seurat (default Louvain clustering setting and 0.25 resolution) were further annotated using cell type-specific markers.
TCR repertoire sequencing data were analyzed with the scRepertoire package v2.0.0 (59) in R v4.4.1. Starting with the filtered contig annotations output table from 'cellranger aggr', the createHTOContigList, combineTCR, and combineExpression functions were used for combining the TCR data from each sample and for integration of the combined TCR data with the Seurat object. We utilized the amino acid sequence of the paired CDR3 regions of the alpha and beta chains as the clonotype definition. T cell repertoire diversity was estimated using the D50 metric, which was calculated in R as the fraction of clonotypes, ordered by abundance, which account for 50 percent of total TCR sequences (defined as paired aminoacid CDR3 sequences). Clonotype size was defined at the level of each biological replicate (Rare: between 0% and 0.01%, Small: between 0.01% and 0.1%, Medium: between 0.1% and 1%, Large: between 1% and 10%, Hyperexpanded: between 10% and 100%). Cells with a putative iNKT TCR were defined as containing a TRAV11-TRAJ18 alpha chain V gene usage, while cells with a putative MAIT TCR were defined as containing a TRAV1-TRAJ33 alpha chain V gene usage. TCR overlap between clusters or between mice was defined at the level of the CDR3 amino acid region for the combined alpha and beta chains, and visualized using the package circlize (PMID: 24930139).
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The filtered_contig_annotations.csv file contains the gene and HTO expression output of the cellranger (10x Genomics) multi and aggr commands. Please see the supplementary files for the HTO - sample correspondence and aggregation parameters.
Supplementary files format and content: The scRNAseq_Tcells.rds file contains the final Seurat object, product of the analysis described in the processing step section.


title: LPC-7-2


title: Susceptible 6H cross 4 rep 3

description:
JHM8_Susc_6_3_Susceptible_6_
cross 4 rep 3


title: bESC_A_eBL_p9_VTNN

description:
Library name: Sample 6
PE150

value: Embryonic stem cell

value: A

value: Bovine ESC


title: scRNAseq HTO 10x Lane 6


title: Susceptible 6H cross 4 rep 2

description:
JHM5_Susc_6_2_Susceptible_6_
cross 4 rep 2


title: LPC-7-4


title: Susceptible 0H cross 4 rep 2

description:
JHM4_Susc_0_2_Susceptible_0_
cross 4 rep 2


title: scRNAseq HTO 10x Lane 5


title: cancer-associated fibroblasts_donor 6

value: donor 6

value: Liver tumor

value: CAF

value: male

value: HCC


title: normal tissue-associated fibroblasts_donor 10

value: donor 10

value: NAF


title: IMQ-7-3

source_name: IMQ-7_mouse skin lesions

value: IMQ


title: IMQ-7-2


title: Susceptible 6H cross 4 rep 1

description:
JHM2_Susc_6_1_Susceptible_6_
cross 4 rep 1

value: meristem youngest leaf


title: scRNAseq HTO 10x Lane 3

value: Mammary Gland

value: T cells

value: WT

value: Pregnancy


title: scRNAseq HTO 10x Lane 2


title: normal tissue-associated fibroblasts_donor 9

value: donor 9

value: female


title: cancer-associated fibroblasts_donor 10


title: cancer-associated fibroblasts_donor 8

value: donor 8

value: CRLM


title: cancer-associated fibroblasts_donor 7

value: donor 7


title: C exposed to Clas-positive psyllids_time60_ replicate 3

description:
C.Las.60.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

organism: Citrus sinensis

tag: cultivar

value: Valencia

value: young flush

value: Clas-positive psyllid


title: scRNAseq HTO 10x Lane 1

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 1


title: Susceptible 0H  cross 4 rep 1

description:
JHM1_Susc_0_1_Susceptible_0_"
cross 4 rep 1

value: Susceptible


title: Susceptible 0H cross 4 rep 3

description:
JHM7_Susc_0_3_Susceptible_0_
cross 4 rep 3


title: Susceptible 12H cross 4 rep 1

description:
JHM3_Susc_12_1_Susceptible_12_
cross 4 rep 1


title: C exposed to Clas-positive psyllids_time60_ replicate 2

description:
C.Las.60.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: IMQ-7-1

value: BALB/c

value: 8 weeks

value: skin


title: cancer-associated fibroblasts_donor 5

value: donor 5

value: Liver tumor

value: CAF

value: ALM


title: LPC-4-4

source_name: LPC-4_mouse skin lesions

value: LPC-treated


title: RNA-seq of XVIfMmycot1 strain +thiolutin, rep2

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

institute: Institut Pasteur

data_processing:
Bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for forward-strand, reverse-strand and unstranded coverage are provided.

extract_protocol:
RNA was extracted using MN Nucleospin RNA kit and following manufacturer instructions.
Directional mRNA library (rRNA removal) was prepared by the Biomics platform of Institut Pasteur, Paris and Paired-end sequencing (PE150) was performed by Novogene.

tag: background

tag: Stage

value: Asy

tag: hash


title: scRNAseq GEX 10x Lane 8

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 8

value: Mammary Gland

value: T cells

tag: strain

value: WT

value: Pregnancy


title: cancer-associated fibroblasts_donor 3

value: donor 3

value: male

value: CRLM


title: normal tissue-associated fibroblasts_donor 6

value: donor 6

value: NAF

value: HCC


title: LPC-4-3

value: BALB/c

tag: age

value: 8 weeks

value: skin


title: scRNAseq VDJ 10x Lane 1


title: scRNAseq GEX 10x Lane 7

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 7


title: RNA-seq of XVIfMmycot1 strain +thiolutin, rep1


title: C exposed to Clas-negative psyllids_time60_ replicate 3

description:
C.h.60.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

value: young flush

value: Clas-negative psyllid


title: normal tissue-associated fibroblasts_donor 5

tag: individual

value: donor 5

value: Liver tumor

value: female

value: ALM


title: RNA-seq of XVIfMmycot1 strain +DMSO, rep2

value: Asy


title: normal tissue-associated fibroblasts_donor 2

value: donor 2

tag: gender


title: LPC-4-2

value: LPC-treated


title: C exposed to Clas-negative psyllids_time60_ replicate 2

description:
C.h.60.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: normal tissue-associated fibroblasts_donor 3

value: donor 3

value: male

tag: cancer type

value: CRLM


title: normal tissue-associated fibroblasts_donor 1

value: donor 1

value: NAF

value: HCC

tag: initial sample id


title: normal tissue-associated fibroblasts_donor 4

value: donor 4

tag: tissue


title: IMQ-4-4

source_name: IMQ-4_mouse skin lesions

value: BALB/c

value: 8 weeks

value: IMQ

value: skin


title: RNA-seq of XVIfMmycot2' strain, rep2


title: C exposed to Clas-negative psyllids_time60_ replicate 1

description:
C.h.60.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

value: young flush

value: Clas-negative psyllid


title: cancer-associated fibroblasts_donor 4

value: Liver tumor

tag: cell type

value: CAF

value: female


title: scRNAseq GEX 10x Lane 4

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 4

value: Mammary Gland

value: T cells

value: WT

tag: treatment

value: Pregnancy


title: scRNAseq HTO 10x Lane 7


title: C exposed to Clas-positive psyllids_time30_ replicate 3

description:
C.Las.30.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-positive psyllid

tag: time point


title: cancer-associated fibroblasts_donor 2

value: donor 2

value: male

value: CRLM


title: C exposed to Clas-positive psyllids_time30_ replicate 2

description:
C.Las.30.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: scRNAseq GEX 10x Lane 5

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 5

tag: cell line


title: RNA-seq of XVIfMmycot2' strain, rep1

value: Asy


title: IMQ-4-3

value: BALB/c

value: 8 weeks

value: IMQ


title: IMQ-4-2

value: skin


title: LPC-7-1

value: LPC-treated


title: scRNAseq GEX 10x Lane 2

description: 10x Genomics lane, 15 Samples (4 nulliparous mice, 5 Pregnant nice, 5 Lactating mice) hashtagged and pooled. GEX library lane 2


title: RNA-seq of XVIfMmycot2 strain, rep2


title: scRNAseq HTO 10x Lane 4


title: C exposed to Clas-positive psyllids_time30_ replicate 1

description:
C.Las.30.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

value: young flush


title: cancer-associated fibroblasts_donor 1

value: donor 1

value: Liver tumor

value: CAF

value: HCC


title: RNA-seq of XVIfMmycot2 strain, rep1


title: scRNAseq GEX 10x Lane 1

value: Mammary Gland

value: T cells

value: WT

value: Pregnancy


title: IMQ-4-1


title: LPC-3

data_processing:
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2.
The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05.
The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: T cells

treatment_protocol: Mouse naïve CD4+ T cells were activated in vitro for 3 days with CD3/CD28 antibodies under Th1-polarizing conditions in the presence of vehicle control or LPC (20 μM).

value: spleen

value: 3 weeks

tag: agent


title: cancer-associated fibroblasts _donor7

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: Salmon -quant mode
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

extract_protocol:
Tissue pieces were minced into small pieces, washed with PBS and incubated at 37°C in collagenase IV (1 mg/ml) containing medium (KnockOut DMEM from Gibco) overnight. After filtering through a strainer, the cells were cultured in DMEM medium containing 10% human platelet lysate, Penicillin-Streptomycin (100 U/ml), and L-Glutamine (2 mM). Cells were expanded at 37°C and 5% CO2 for 2-3 passages upon reaching confluence. CAFs and NAFs were successfully isolated from patients.
Total RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel). For library preparation the TruSeq Stranded mRNA kit (Illumina) was selected and sequenced on a NextSeq 500 (Illumina) using the NextSeq 500/550 High Output Kit v2.5 (150 cycles). Sequencing was performed at IZKF-associated Genomics Facility of the RWTH University.

value: CRLM

tag: initial sample_id

value: male


title: cancer-associated fibroblasts _donor6


title: C exposed to Clas-negative psyllids_time30_ replicate 1

description:
C.h.30.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

tag: cultivar

value: Clas-negative psyllid


title: 0-3

value: vehicle


title: IMQ-7-4

value: BALB/c

value: 8 weeks

value: IMQ

value: skin


title: cancer-associated fibroblasts_donor 9

value: donor 9

value: Liver tumor

value: female


title: C exposed to Clas-negative psyllids_time30_ replicate 2

description:
C.h.30.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Valencia

value: young flush


title: RNA-seq of Mpneumo strain (rrp6-/-), rep1

tag: background

value: XVIfMpneumo

value: Asy


title: 0-2

value: spleen


title: RNA-seq of Mpneumo strain (rrp6-/-), rep2

tag: Stage

value: HGZGCS


title: normal tissue-associated fibroblasts_donor5

value: NAF

value: ALM


title: C exposed to Clas-positive psyllids_time60_ replicate 1

description:
C.Las.60.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)

value: Clas-positive psyllid


title: C exposed to Clas-positive psyllids_time20_ replicate 3

description:
C.Las.20.3
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: normal tissue-associated fibroblasts_donor 8

value: donor 8

value: male

value: CRLM


title: C exposed to Clas-positive psyllids_time20_ replicate 2

description:
C.Las.20.2
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: normal tissue-associated fibroblasts_donor6

value: HCC


title: RNA-seq of Mpneumo strain (upf1-/-)

tag: hash


title: cancer-associated fibroblasts _donor5

value: CAF


title: 0-1

tag: strain

value: 3 weeks

value: vehicle


title: C exposed to Clas-positive psyllids_time20_ replicate 1

description:
C.Las.20.1
Citrus x sinensis 'Valencia’ grafted on Citrus x limonia Osbeck (‘Rangpur’ lime)


title: MNase-seq of yeast + P. vitis YAC strain, 60min

data_processing:
Bowtie2 was used to align paired-end MNase-seq data on the appropriate genome reference. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded.
PCR duplicates were removed using samtools and fragments smaller than 130 or longer than 200 bp were manually removed.
Fragment coverage was normalized by library depth (CPM) and converted into stranded or unstranded genomic tracks (bigwig) using deepTools.
Assembly: https://doi.org/10.5281/zenodo.7198984
Supplementary files format and content: Bigwig files for Mnase-seq coverage (fragments ranging from 130 to 200bp) are provided.

growth_protocol: Five 1.5ml Tubes were prepared with 1.5 x 10^8 asynchronous yeast cells: cells were centrifuged, pelleted, washed in 1x PBS and frozen at -80C.

extract_protocol:
Cell pellets were thawed on ice and resuspended in 1mL 1xPBS supplemented with 27ul 37% formaldehyde. Cells were fixed for 20min at room temperature on rotation. 200ul of 2.5M Glycine was added for a further 5 min incubation. Cells were centrifuged at 2500g, 4C for 5 min. Pellets were gently washed with cold 1xPBS before resuspension in 500ul of lysis solution (Sorbitol 1M, EDTA 10mM, Zymo100T 250ug) and incubation at 37C with gently shaking for 30min/45min or until complete spheroplasting.
Cells were gently washed with cold 1xPBS and resuspended in 50ul 1X Nuclease Digest buffer plus an increasing amount of Mnase (NEB, M0247S) enzyme starting with 0.2ul. Digestion was performed at 22C in a shaker set at 1250rpm for 15min. 5ul of 0.5M EGTA and 3ul of 20% SDS were added for incubation at 22C in a shaker set at 1250rpm for 5 min. 65ul of TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) was added and samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified using Zymo Research DNA Clean and Concentrator™-5 Kit. Mnase digestion was verified on a Bioanalyzer System using HS DNA kit. DNA was purified using 1.2x volume of AmpureXP beads and librairies prepared with Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.