title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#14 , Mouse#8 , Left ear [L2002814_LoWT8L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#14 , Mouse#8 , Left ear [L2002814_LoWT8L]


title: scHH_Trinity_Uninfected_1

status: Public on Mar 20 2026

type: SRA

city: Durham

first: Angela

middle: G

last: Jones

state: NC

address: 0048B CARL, Box 3053 DUMC

department: MGM

country: USA

institute: Duke Unversity

description:
Library name: DCK-sc39
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing results were processed using the 10X Genomics CellRanger v7.0.1 pipeline. Ambient RNA was removed with CellBender v.0.3.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Comma-separated Seurat metadata
Supplementary files format and content: Tab-separated pseudo bulk expression data

molecule: polyA RNA

organism: Homo sapiens

source_name: LCL

extract_protocol:
Cell samples were counted and checked for viability on a Guava EasyCyte HT system by 7-AAD staining before they were diluted to 1 million cells/mL with an intended capture of 25,000 cells/sample.
10x Chromium Single Cell 3’ platform version 3.1

tag: cell type

value: LCL

tag: treatment

value: mock infection


title: scHH_Trinity_Uninfected_3

description:
Library name: DCK-sc41
10X Genomics


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#11 , Mouse#7 , Left ear [L2002777_LoWT7L]

city: Magdeburg

first: Yan

last: Fu

state: Saxony-Anhalt

address: Haus 26, Institut für Molekulare und Klinische Immunologie, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44

country: Germany

institute: Otto-von-Guericke-Universität Magdeburg

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#11 , Mouse#7 , Left ear [L2002777_LoWT7L]

library_source: transcriptomic

data_processing:
Raw fastq files were processed with Cutadapt (v3.7) to remove poly-A tails and adapter sequences introduced during library construction (SMART-seq: AAGCAGTGGTATCAACGCAGAGT & Nextera XT: CTGTCTCTTATACACATCT).
The first 15 bases of each read, bases with Qscore < 20 and reads left with less than 25 bases after trimming were also discarded.
Reads were mapped to a reference genome using STAR with default parameters.
The used reference genome has been built by combining the mouse (GRCm38) and Leishmania major (ASM272v2) genomes as well as spike-ins (ERCC92) and the Kikume Green-Red transcript sequences.
The raw count matrix was generated from the mapping results with featureCounts (Subread, v1.6.3)
Assembly: GRCm38,  ASM272v2, ERCC92
Supplementary files format and content: Tab-separated matrix files

molecule: total RNA

organism: Mus musculus

source_name: ear tissue

extract_protocol:
Ears of mice were separated in two sheets (ventral and dorsal) using forceps and enzymatically digested in RPMI 1640 medium containing 1 mg/ml collagenase and 50 ng/ml DNase for 60 min at 600 rpm and 37°C and passed through a 70 μm cell strainer. Cells were centrifuged at 4°C with 300 g for 10 min. Cells were washed with PBS and FACS buffer before surface staining of cells was done by using surface marker specific antibodies (PEcy7-CD45.2, PerCPcy5.5-CD45.1, APC-CD11c, APC-cy7-Ly6c, and BV510-CCR2). Samples were blocked with Fc-block using anti-CD16/32 antibody (1:25 in FACS buffer) for 15 min on ice before the antibody staining. Antibodies were applied with a final concentration of 1:200. Leishmania major infections were analyzed with a FACS ARIA III flow cytometer/sorter.
50-100 cells per cell subpopulation per sample were sorted into an individual well from a 96-well plate (Costar) filled with 4.65 µl of Buffer RLT Plus (Qiagen), 0.25 µl of SUPERase-In RNase-Inhibitor (Invitrogen). Sorted cells were immediately frozen and stored at -80 °C. Sequencing libraries were prepared using Smart-seq2 protocol as previous described with minor modifications: Following cDNA amplification, ACTB expression was measured in each cDNA library by qPCR. All cDNA libraries were diluted aiming to an equivalent ct value for ACTB (average = 21.11, SD = 1.05) and were subsequently used as input for a tagmentation-based protocol (Nextera XT, Illumina) using one quarter of the recommended volumes, 10 min for tagmentation at 55°C20. The indexed libraries were quantified using Qubit dsDNA Hs Assay (Life Technologies) and fragment size of libraries was analysed using QIAxcel DNA high resolution Kit (Qiagen) and bioanalyser (Agilent). Libraries were normalized to 2 nM and pooled. Particularly, 87 libraries were sequenced for HiSeq 2500 (Illumina).

value: monocytes

tag: tissue

value: ear tissue

tag: strain

value: wt

tag: age

value: 22 weeks old


title: HASMCs, ad-Vector2+PBS

city: Nanjing

first: Hailong

last: Cao

state: Jiangsu

address: 87 Dingjiaqiao

department: Department of Cardiac Surgery

country: China

institute: Zhongda hospital

description:
Library name: Sample 2
Column name in genes_fpkm_expression.xlsx: FPKM.B_3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited file include FPKM values for each Samples

source_name: primary cells

growth_protocol: Human aortic smooth muscle cells (HASMCs, 6110, ScienCell) purchased from ScienCell Research Laboratories were cultured in Smooth Muscle Cell Medium (SMCM, 1101, ScienCell).

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen),2μg of RNA was used for construction of sequencing library. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Total RNA was extracted and quantified, requiring a RIN > 7.0. mRNA was purified from 5 µg of total RNA using oligo(d)T beads and fragmented thermally. First-strand cDNA was synthesized using SuperScript™ II Reverse Transcriptase, followed by second-strand synthesis incorporating dUTP. Indexed adapters were ligated to the A-tailed fragments, and size selection was performed. U-labeled second strands were digested using heat-labile UDG enzyme, and the library was amplified via PCR. The final libraries (average insert size 300 ± 50 bp) were subjected to 2 × 150 bp paired-end sequencing on an Illumina Novaseq™ 6000.

treatment_protocol: HASMCs were serum-starved in DMEM without FBS for 12 h, followed by stimulation with PDGF-BB (MedChemExpress, Cat# HY-P7055) at the indicated concentration (20 ng/mL) for 24 h.

value: aorta

value: smooth muscle cell

tag: genotype

value: WT

tag: batch


title: Fungal hyphae cells, D-3

city: kunming

first: xuemei

last: li

state: yunnan

address: South Road of Dongwai Ring, University Town, Chenggong District, Kunming City

institute: yunnan university

description: Library name: Sample 9

data_processing:
The data from high-throughput sequencing were analyzed using the Metware Cloud, a free online platform for data analysis.
Assembly: GCF_000225545.1
Supplementary files format and content: xlsx file includes fpkm value for each sample

organism: Orbilia oligospora

source_name: Fungal

growth_protocol: The wild-type and  mutant strains were cultured on tryptone yeast glucose agar (TYGA) medium at 28°C for 5 days.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

value: Fungal

tag: cell line

value: Fungal hyphae cells

value: Vps1 knockdown

value: Aerial hyphae differentiation

value: Day 5


title: scHH_Trinity_Uninfected_4

description:
Library name: DCK-sc42
10X Genomics


title: Fungal hyphae cells, D-2

description: Library name: Sample 8


title: SAT47

city: Los Angeles

first: Asha

last: Kar

state: CA

address: 695 Charles E. Young Drive South

department: Human Genetics

institute: University of California Los Angeles

description: Library name: SAT47

data_processing:
Sequencing reads were aligned to the GRCh38 human genome reference with GENCODE v42 gene annotations using STARSolo in STARv2.7.10b.
Assembly: hg38
Supplementary files format and content: Matrix market format for gene counts
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names)

source_name: subcutaneous adipose tissue

extract_protocol:
Frozen tissue was minced on dry ice and transferred into ice-cold lysis buffer containing 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl₂. After a 10-minute incubation, the lysate was gently homogenized using a Dounce homogenizer and passed through a 70-μm MACS SmartStrainer (Miltenyi Biotec #130-098-462) to remove debris. Nuclei were collected by centrifugation at 500 × g for 5 minutes at 4 °C and washed in 1 mL of resuspension buffer composed of 1× PBS, 1.0% BSA, and 0.2 U/μL RNase inhibitor. The nuclei suspension was then filtered through a 40-μm Flowmi cell strainer (Sigma-Aldrich #BAH136800040) and centrifuged again at 500 × g for 5 minutes at 4 °C.
The libraries were prepared using the 10x Chromium Single Cell 3’ Reagent Kit v3.1.

value: subcutaneous adipose tissue

tag: Sex

value: male

tag: ethnicity

value: Mexican


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#7 , Mouse#5 , Right ear [L2002753_LoWT5R]

department: Institut für Molekulare und Klinische Immunologie

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#7 , Mouse#5 , Right ear [L2002753_LoWT5R]


title: HASMCs, ad-Vector3+PDGF-BB

description:
Library name: Sample 6
Column name in genes_fpkm_expression.xlsx: FPKM.D_3


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#11 , Mouse#7 , Right ear [L2002784_LoKO7R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#11 , Mouse#7 , Right ear [L2002784_LoKO7R]


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#2 , Mouse#2 , Left ear [L2002734_LoWT2L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#2 , Mouse#2 , Left ear [L2002734_LoWT2L]


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#10 , Mouse#6 , Right ear [L2002813_LoWT6R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#10 , Mouse#6 , Right ear [L2002813_LoWT6R]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#9 , Mouse#6 , Right ear [L2002809_LoKO6R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#9 , Mouse#6 , Right ear [L2002809_LoKO6R]


title: SAT49

description: Library name: SAT49

value: female


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#13 , Mouse#8 , Left ear [L2002793_LoWT8L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#13 , Mouse#8 , Left ear [L2002793_LoWT8L]


title: SAT44

description: Library name: SAT44


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#6 , Mouse#5 , Left ear [L2002745_LoKO5L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#6 , Mouse#5 , Left ear [L2002745_LoKO5L]


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#8 , Mouse#6 , Left ear [L2002761_LoWT6L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#8 , Mouse#6 , Left ear [L2002761_LoWT6L]


title: HER2+ breast cancer primary tumor T537 (scRNA-seq)

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
Library name: T537
10x Genomics

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using cellranger v7.0.1.
Assembly: hg19
Supplementary files format and content: h5 matrix files

source_name: HER2+ breast tumor

extract_protocol:
Tumor pieces were chopped and digested for 2h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium. Immediately before library preparation, dead cells and debris was removed using percoll purification (50%/40%/20% layers).
About 10,000 single cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were generated using Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics).

value: HER2+ breast tumor


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#4 , Mouse#2 , Right ear [L2002812_LoWT2R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#4 , Mouse#2 , Right ear [L2002812_LoWT2R]

value: monocytes


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#1 , Mouse#1 , Right ear [L2002730_LoWT1R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#1 , Mouse#1 , Right ear [L2002730_LoWT1R]

value: ear tissue


title: scHH_Trinity_Uninfected_2

description:
Library name: DCK-sc40
10X Genomics

value: LCL

value: mock infection


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#6 , Mouse#5 , Left ear [L2002746_LoWT5L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#6 , Mouse#5 , Left ear [L2002746_LoWT5L]

value: wt

value: 22 weeks old


title: HER2+ breast cancer primary tumor T565 (scRNA-seq)

description:
Library name: T565
10x Genomics


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#3 , Mouse#2 , Right ear [L2002737_LoKO2R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#3 , Mouse#2 , Right ear [L2002737_LoKO2R]


title: Fungal hyphae cells, AO-2

description: Library name: Sample 2

value: WT


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#1 , Mouse#1 , Right ear [L2002729_LoKO1R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#1 , Mouse#1 , Right ear [L2002729_LoKO1R]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#14 , Mouse#8 , Right ear [L2002800_LoKO8R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#14 , Mouse#8 , Right ear [L2002800_LoKO8R]


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#9 , Mouse#5 , Left ear [L2002748_H1WT5L]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#9 , Mouse#5 , Left ear [L2002748_H1WT5L]


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#7 , Mouse#8 , Left ear [L2002795_H1WT8L]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#7 , Mouse#8 , Left ear [L2002795_H1WT8L]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#13 , Mouse#8 , Left ear [L2002792_LoKO8L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#13 , Mouse#8 , Left ear [L2002792_LoKO8L]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#12 , Mouse#7 , Right ear [L2002810_LoKO7R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#12 , Mouse#7 , Right ear [L2002810_LoKO7R]


title: Fungal hyphae cells, D-1

description: Library name: Sample 7

value: Fungal


title: SAT48

description: Library name: SAT48


title: AGO-99b_BR1

city: Ankara

first: Efe

last: Dalli

address: Dogol Street

country: Turkey

institute: Ankara University

description: Library name: Tes388

data_processing:
Quality control of raw paired-end reads was performed using FastQC (v0.11.9).
Adaptor sequences and low-quality bases were removed using Cutadapt (v3.5).
Cleaned reads were aligned to the GRCh38 reference genome using STAR (v2.7.11b) in two-pass mode with Ensembl gene annotations.
Sorted BAM files were generated and gene-level read counts were obtained using STAR's quant mode.
Differential gene expression analysis was performed using the DESeq2 framework via PyDESeq2 package (v0.4.11) in Python.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

source_name: MDA-MB-231 cell culture

extract_protocol:
RNA was isolated using Qiazol (Qiagen) from the Ago2-immunoprecipitated and flow-through fractions according to the manufacturer’s instructions.
RNA libraries were prepared using the MGIEasy RNA Library Prep Set through double-stranded cDNA synthesis, magnetic bead-based purification, adaptor ligation, and PCR amplification.

value: MDA-MB-231 cell culture

value: Breast cancer cells


title: SAT38

description: Library name: SAT38


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#4 , Mouse#6 , Right ear [L2002771_H1WT6R]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#4 , Mouse#6 , Right ear [L2002771_H1WT6R]


title: Fungal hyphae cells, M-1

description: Library name: Sample 4

value: Fungal hyphae cells

value: Mdv1 knockdown

value: Aerial hyphae differentiation


title: SAT46

description: Library name: SAT46

value: subcutaneous adipose tissue


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#2 , Mouse#5 , Right ear [L2002755_H1WT5R]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#2 , Mouse#5 , Right ear [L2002755_H1WT5R]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#7 , Mouse#6 , Left ear [L2002760_LoKO6L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#7 , Mouse#6 , Left ear [L2002760_LoKO6L]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#10 , Mouse#7 , Left ear [L2002776_LoKO7L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#10 , Mouse#7 , Left ear [L2002776_LoKO7L]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#8 , Mouse#6 , Right ear [L2002768_LoKO6R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#8 , Mouse#6 , Right ear [L2002768_LoKO6R]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#15 , Mouse#8 , Right ear [L2002811_LoKO8R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#15 , Mouse#8 , Right ear [L2002811_LoKO8R]


title: Fungal hyphae cells, M-3

description: Library name: Sample 6

value: Day 5


title: SAT43

description: Library name: SAT43

value: female

value: Mexican


title: Fungal hyphae cells, M-2

description: Library name: Sample 5


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#5 , Mouse#3 , Left ear [L2002741_LoKO3L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#5 , Mouse#3 , Left ear [L2002741_LoKO3L]

value: monocytes


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#4 , Mouse#2 , Right ear [L2002808_LoKO2R]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#4 , Mouse#2 , Right ear [L2002808_LoKO2R]

value: ear tissue


title: SAT45

description: Library name: SAT45


title: SAT40

description: Library name: SAT40


title: Fungal hyphae cells, AO-1

description: Library name: Sample 1


title: SAT41

description: Library name: SAT41

value: male


title: Fungal hyphae cells, AO-3

description: Library name: Sample 3


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#8 , Mouse#8 , Right ear [L2002803_H1WT8R]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#8 , Mouse#8 , Right ear [L2002803_H1WT8R]


title: Low-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#2 , Mouse#2 , Left ear [L2002733_LoKO2L]

description:
SmartSeq2
Low-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#2 , Mouse#2 , Left ear [L2002733_LoKO2L]


title: SAT42

description: Library name: SAT42


title: AGO-99b_BR2

description: Library name: Tes389


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#5 , Mouse#7 , Left ear [L2002779_H1WT7L]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#5 , Mouse#7 , Left ear [L2002779_H1WT7L]


title: SAT36

description: Library name: SAT36


title: SAT33

description: Library name: SAT33


title: SAT37

description: Library name: SAT37


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#2 , Mouse#5 , Left ear [L2002747_H1KO5L]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#2 , Mouse#5 , Left ear [L2002747_H1KO5L]


title: SAT32

description: Library name: SAT32


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#5 , Mouse#6 , Left ear [L2002762_H1KO6L]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#5 , Mouse#6 , Left ear [L2002762_H1KO6L]


title: SAT35

description: Library name: SAT35


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#6 , Mouse#7 , Right ear [L2002787_H1WT7R]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#6 , Mouse#7 , Right ear [L2002787_H1WT7R]


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#3 , Mouse#6 , Left ear [L2002763_H1WT6L]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#3 , Mouse#6 , Left ear [L2002763_H1WT6L]


title: mack1_p77_s_1

city: Medford

first: Michael

last: Saad

state: MA

address: 200 College Ave

institute: Tufts University

description: Library name: p77_s1

data_processing:
Data processing, including normalization, perfromed with DESeq2. The data normalization method was the median of ratios method.
Assembly: Raw FASTQ files were quality controlled using FastQC. Reads were aligned to the Scomber scombrus reference genome (GCF_963691925.1) using STAR. Transcript abundance was quantified using Salmon (v1.10.1 or similar) with a decoy-aware transcriptome index.
Supplementary files format and content: csv file for raw_counts
Supplementary files format and content: csv file for normalized_counts

organism: Scomber scombrus

growth_protocol: For routine cell culture, mackerel muscle cell lines were cultured in Mack growth medium (GM), consisting of comprised of Leibovitz’s L-15 Medium (ThermoFisher Scientific #11415064) with 20% fetal bovine serum (FBS; ThermoFisher Scientific #26140079), 1 ng/mL recombinant human fibroblast growth factor (FGF2; 154 a.a., PeproTech #100-18B, Cranbury, NJ, USA), 20 mM HEPES pH 7.4 (Sigma Aldrich #H4034, St. Louis, MO, USA), and 1% Antibiotic–Antimycotic (anti-anti; ThermoFisher Scientific #1540062).

extract_protocol:
RNA was extracted from mack cells using the RNEasy Mini kit (Qiagen #74104, Hilden, Germany) according to the manufacturer's directions. RNA was extracted for three experimental replicates for each Mack1 condition and four experimental replicates for each Mack2 condition. RNA samples were sent on dry ice to Genewiz for library preparation and RNA sequencing.
RNA samples were quantified using the Agilent 2100 Bioanalyzer. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by second strand cDNA synthesis. The library was prepared using a non-directional (non-strand-specific) protocol. Final libraries were quantified by QPCR and sequenced on an Illumina NovaSeq X Plus platform (PE150).

treatment_protocol:
For muscle differentiation via serum starvation, mackerel cells were grown to confluence followed by cessation of feeding.
For muscle differentiation via serum reduction, mackerel cells were grown to confluence followed by regular feeding of L-15 with 2.5% FBS, 20 mM HEPES pH 7.4, and 1% antibiotic-antimycotic.
For lipid loading, mackerel cells were grown to confluence followed by regular feeding with adipogenic medium consisting of growth medium with 10 μg/mL insulin (Sigma Aldrich #I0516), 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma Aldrich #I5879), 0.25 μM dexamethasone (Sigma Aldrich #D4902), and 10 μL/mL lipid mixture (Sigma Aldrich #L5146).

value: Muscle stem cell

value: muscle differentiation (serum starvation)


title: SAT39

description: Library name: SAT39


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#10 , Mouse#8 , Right ear [L2002802_H1KO8R]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#10 , Mouse#8 , Right ear [L2002802_H1KO8R]

value: 22 weeks old


title: Uninfected-single cell#72 , Mouse#1_Right ear [3_H2]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz

extract_protocol:
Ears of mice were separated in two sheets (ventral and dorsal) using forceps and enzymatically digested in RPMI 1640 medium containing 1 mg/ml collagenase and 50 ng/ml DNase for 60 min at 600 rpm and 37°C and passed through a 70 μm cell strainer. Cells were centrifuged at 4°C with 300 g for 10 min. Mouse CD45 MicroBeads (Miltenyi Biotec) were used to isolate leukocytes prior to cell surface staining according to manufacturer’s instructions. Afterwards, cells were washed with PBS and FACS buffer before surface staining of cells was done by using surface marker specific antibodies (APC-CD11c and APC-cy7-Ly6c). Samples were blocked with Fc-block using anti-CD16/32 antibody (1:25 in FACS buffer) for 15 min on ice before the antibody staining. Antibodies were applied with a final concentration of 1:200. mKikume G&R Leishmania major infections were analyzed with a FACS ARIA III flow cytometer/sorter. Specifically, mKikumeGreen refers to high-proliferating L. major infected monocytes, while mKikumeRed refers to low-proliferating L. major infected monocytes.
Single cells were sorted into different wells from a 96-well plate (Costar) filled with 4.65 µl of Buffer RLT Plus (Qiagen), 0.25 µl of SUPERase-In RNase-Inhibitor (Invitrogen), and 0.1 µl of ERCC spike-Mix1 (Invitrogen) pre-diluted 1:500000 in RNAse-free water. For cell-population RNAseq, 50-100 cells per subpopulation per sample were sorted into the wells. Sorted cells were immediately frozen and stored at -80 °C. Single-cell libraries were prepared using Smart-seq2 protocol as previous described with minor modifications: Following cDNA amplification, ACTB expression was measured in each cDNA library by qPCR. All cDNA libraries were diluted aiming to an equivalent ct value for ACTB (average = 21.11, SD = 1.05) and were subsequently used as input for a tagmentation-based protocol (Nextera XT, Illumina) using one quarter of the recommended volumes, 10 min for tagmentation at 55°C20. The indexed libraries were quantified using Qubit dsDNA Hs Assay (Life Technologies) and fragment size of libraries was analysed using QIAxcel DNA high resolution Kit (Qiagen) and bioanalyser (Agilent). Libraries were normalized to 2 nM and pooled. Particularly, 218 of single-cell libraries were sequenced for HiSeq 2500 (Illumina).

value: 10 weeks old


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#9 , Mouse#8 , Left ear [L2002794_H1KO8L]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#9 , Mouse#8 , Left ear [L2002794_H1KO8L]


title: FT-99b_BR2

description: Library name: Tes387


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#7 , Mouse#7 , Left ear [L2002778_H1KO7L]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#7 , Mouse#7 , Left ear [L2002778_H1KO7L]


title: SAT30

description: Library name: SAT30


title: Uninfected-single cell#71 , Mouse#1_Right ear [3_H12]


title: Uninfected-single cell#70 , Mouse#5_Left ear [3_H11]


title: High-proliferating L. major infected,  wt compartment of BMC, cell-pool#1 , Mouse#2 , Right ear [L2002740_H1WT2R]

description:
SmartSeq2
High-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#1 , Mouse#2 , Right ear [L2002740_H1WT2R]

value: wt


title: FT-99b_BR1

description: Library name: Tes386

value: MDA-MB-231 cell culture


title: AGO-Control

description: Library name: Tes321

value: Breast cancer cells


title: SAT34

description: Library name: SAT34


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#6 , Mouse#6 , Right ear [L2002770_H1KO6R]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#6 , Mouse#6 , Right ear [L2002770_H1KO6R]


title: mack1_p77_m_3

description: Library name: p77_m3

value: muscle differentiation (serum reduction)


title: mack1_p77_s_3

description: Library name: p77_s3


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#4 , Mouse#5 , Right ear [L2002754_H1KO5R]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#4 , Mouse#5 , Right ear [L2002754_H1KO5R]


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#3 , Mouse#5 , Left ear [L2002815_H1KO5L]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#3 , Mouse#5 , Left ear [L2002815_H1KO5L]


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#8 , Mouse#7 , Right ear [L2002786_H1KO7R]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#8 , Mouse#7 , Right ear [L2002786_H1KO7R]


title: FT-Control

description: Library name: Tes320


title: SAT25

description: Library name: SAT25


title: Uninfected-single cell#60 , Mouse#1_Right ear [3_A1]


title: Uninfected-single cell#68 , Mouse#4_Right ear [3_E6]


title: mack1_p77_p_2

description: Library name: p77_p2

value: proliferation


title: mack1_p77_s_2

description: Library name: p77_s2


title: Uninfected-single cell#59 , Mouse#4_Right ear [2_G11]


title: Uninfected-single cell#58 , Mouse#3_Left ear [2_F9]


title: SAT28

description: Library name: SAT28


title: mack1_p77_f_3

description: Library name: p77_f3

value: lipid loading


title: SAT31

description: Library name: SAT31

value: subcutaneous adipose tissue


title: High-proliferating L. major infected,  IL7R-/- compartment of BMC, cell-pool#1 , Mouse#2 , Right ear [L2002739_H1KO2R]

description:
SmartSeq2
High-proliferating L. major infected, from IL7R-/- compartment of bone marrow chimeric, cell-pool#1 , Mouse#2 , Right ear [L2002739_H1KO2R]


title: mack1_p77_f_2

description: Library name: p77_f2


title: Uninfected-single cell#69 , Mouse#2_Right ear [3_G3]


title: SAT29

description: Library name: SAT29


title: SAT22

description: Library name: SAT22


title: Uninfected-single cell#67 , Mouse#4_Left ear [3_E5]


title: Uninfected-single cell#73 , Mouse#4_Left ear [3_H4]


title: Uninfected-single cell#65 , Mouse#4_Right ear [3_C6]


title: mack1_p77_p_3

description: Library name: p77_p3


title: mack1_p77_p_1

description: Library name: p77_p1


title: SAT26

description: Library name: SAT26


title: Uninfected-single cell#53 , Mouse#2_Left ear [2_D3]


title: SAT27

description: Library name: SAT27


title: Uninfected-single cell#64 , Mouse#1_Right ear [3_B7]


title: Uninfected-single cell#51 , Mouse#5_Left ear [2_C12]


title: mack1_p27_s_2

description: Library name: p27_s2


title: Uninfected-single cell#63 , Mouse#4_Left ear [3_B5]


title: Uninfected-single cell#66 , Mouse#4_Right ear [3_D6]


title: SAT19

description: Library name: SAT19


title: Uninfected-single cell#46 , Mouse#4_Left ear [1_E5]


title: mack1_p77_m_2

description: Library name: p77_m2


title: Uninfected-single cell#45 , Mouse#3_Left ear [1_E4]


title: Uninfected-single cell#62 , Mouse#2_Left ear [3_B3]


title: Uninfected-single cell#55 , Mouse#1_Left ear [2_D7]


title: mack1_p27_p_1

description: Library name: p27_p1


title: SAT16

description: Library name: SAT16


title: Uninfected-single cell#57 , Mouse#5_Left ear [2_E2]


title: Uninfected-single cell#54 , Mouse#4_Left ear [2_D5]


title: SAT15

description: Library name: SAT15


title: mack1_p27_m_3

description: Library name: p27_m3


title: SAT23

description: Library name: SAT23


title: Uninfected-single cell#50 , Mouse#1_Right ear [2_B7]


title: Uninfected-single cell#42 , Mouse#4_Right ear [1_C6]


title: mack1_p27_m_2

description: Library name: p27_m2


title: Uninfected-single cell#61 , Mouse#1_Right ear [3_B2]


title: SAT21

description: Library name: SAT21


title: mack1_p77_m_1

description: Library name: p77_m1


title: Uninfected-single cell#52 , Mouse#2_Right ear [2_C4]


title: mack1_p27_s_3

description: Library name: p27_s3


title: SAT24

description: Library name: SAT24


title: Uninfected-single cell#48 , Mouse#3_Left ear [1_G9]


title: SAT13

description: Library name: SAT13


title: SAT20

description: Library name: SAT20


title: mack1_p27_f_3

description: Library name: p27_f3


title: mack1_p77_f_1

description: Library name: p77_f1


title: SAT18

description: Library name: SAT18


title: SAT12

description: Library name: SAT12


title: Uninfected-single cell#47 , Mouse#3_Right ear [1_F10]


title: Uninfected-single cell#49 , Mouse#3_Left ear [1_H9]


title: mack1_p27_p_2

description: Library name: p27_p2


title: mack1_p27_s_1

description: Library name: p27_s1


title: Uninfected-single cell#56 , Mouse#2_Right ear [2_D9]


title: mack1_p27_p_3

description: Library name: p27_p3


title: Uninfected-single cell#43 , Mouse#2_Right ear [1_C9]


title: Uninfected-single cell#30 , Mouse#1_Left ear [3_E7]


title: Uninfected-single cell#29 , Mouse#1_Left ear [3_D7]


title: Uninfected-single cell#44 , Mouse#1_Right ear [1_E2]


title: SAT17

description: Library name: SAT17


title: Uninfected-single cell#39 , Mouse#1_Left ear [1_A3]


title: SAT14

description: Library name: SAT14


title: mack1_p27_f_2

description: Library name: p27_f2


title: Uninfected-single cell#37 , Mouse#3_Left ear [1_A10]


title: Uninfected-single cell#41 , Mouse#1_Right ear [1_C1]


title: Uninfected-single cell#33 , Mouse#5_Left ear [3_G11]


title: Uninfected-single cell#36 , Mouse#1_Left ear [1_A1]


title: Uninfected-single cell#38 , Mouse#4_Right ear [1_A12]


title: Uninfected-single cell#34 , Mouse#4_Left ear [3_G4]


title: mack1_p27_m_1

description: Library name: p27_m1


title: Uninfected-single cell#40 , Mouse#4_Right ear [1_B12]


title: Uninfected-single cell#32 , Mouse#5_Left ear [3_F6]


title: mack2_p2_1

description: Library name: P2_1


title: Uninfected-single cell#23 , Mouse#3_Right ear [2_F10]


title: SAT11

description: Library name: SAT11


title: Uninfected-single cell#35 , Mouse#2_Left ear [3_G8]


title: Uninfected-single cell#21 , Mouse#3_Left ear [2_E4]


title: SAT5

description: Library name: SAT5


title: Uninfected-single cell#19 , Mouse#2_Right ear [2_D4]


title: SAT9

description: Library name: SAT9


title: mack1_p27_f_1

description: Library name: p27_f1


title: SAT10

description: Library name: SAT10


title: Uninfected-single cell#28 , Mouse#2_Right ear [3_C9]


title: Uninfected-single cell#26 , Mouse#5_Left ear [2_H5]


title: SAT3

description: Library name: SAT3


title: Uninfected-single cell#27 , Mouse#4_Left ear [3_C1]


title: Uninfected-single cell#16 , Mouse#2_Right ear [2_B4]


title: mack2_p2_2

description: Library name: P2_2


title: mack2_p2_3

description: Library name: P2_3


title: SAT8

description: Library name: SAT8


title: Uninfected-single cell#25 , Mouse#4_Right ear [2_H11]


title: spRNA-Seq of tomato: seeding leaf-biorep2 LTSS

city: Urumqi

first: Ruiqiang

last: Xu

state: Xinjiang Uygur

address: No.311, Nongda East Road, Shaibak District, Urumqi, Xinjiang

institute: Xinjiang Academy of Agricultural Sciences

description:
Library name: LTSS-2-SP
BMK-S1000, Treatment replicate 2, seeding leaf under long term salt stress

data_processing:
snRNA-seq: Raw data processed with Cell Ranger v8.0 to generate feature-barcode matrices; filtered (genes in ≥5 cells, cells with ≥200 genes); Seurat object created. Spatial transcriptomics: Raw data processed with BSTMatrix v2.3j to obtain gene expression matrices and spot coordinates; tissue spots extracted with BSTViewer v3; bins merged (35-µm radius); Seurat object created.
Assembly: SL4.0
Supplementary files format and content: Seurat RDS files (.rds) containing count matrices, metadata, and dimensionality reductions.
Supplementary files format and content: Filtered feature-barcode matrices (.tar.gz) in 10x/CellRanger format (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) or BMS-S1000 (spatial RNA-seq).

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: Tomato seedlings (Solanum lycopersicum cv. M82) at four-leaf stage were grown under normal conditions. Control (CK) plants were irrigated with fresh water.

extract_protocol:
For snRNA-seq: Nuclei isolated from ~300 mg frozen leaf tissue using lysis buffer with NP-40 and RNase inhibitors, followed by filtration and quality control (RIN ≥ 7.0). For spatial transcriptomics: 10-µm cryosections from leaf basal region mounted on BMKMANU S1000 slides, fixed, and permeabilized.
snRNA-seq: Nuclei partitioned into GEMs using 10x Genomics Chromium Next GEM Single Cell 3′ kit; libraries prepared with standard protocol and sequenced PE150 on Illumina NovaSeq 6000. Spatial transcriptomics: Reverse transcription on BMKMANU S1000 bead-based slides; libraries constructed and sequenced PE150 on Illumina NovaSeq 6000 (≥50,000 reads/spot).

treatment_protocol: Long-term salt stress (LTSS): NaCl concentration gradually increased from 75 mmol/L to 250 mmol/L over 9 days, then maintained for 20 days. Upper young leaves were collected after treatment.

value: leaf

value: seeding leaf nuclei

value: WT

value: Long term salt stress


title: SAT7

description: Library name: SAT7

value: Mexican


title: mack2_p2_4

description: Library name: P2_4


title: Uninfected-single cell#31 , Mouse#5_Left ear [3_F11]

value: monocytes

value: ear tissue


title: mESC_Mettl3_cKO_rep2

city: Beijing

first: Li

last: Tang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

description:
Library name: mESC_Mettl3_cKO_rep2
mESC_D2_Mettl3_Virma_KO_raw_count.csv

data_processing:
Raw sequencing reads were quality assessed using FastQC (v.0.12.1) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), with sequencing adapters and low-quality bases trimmed using trim-galore. Trimmed reads were aligned to a mouse reference genome (mm39) using STAR (v.2.7.11b). Annotation files (vM29) were downloaded from the GENCODE database (https://www.gencodegenes.org/). Reads for each GENCODE annotated gene were annotated using Subread, and differentially expressed gene (DEG) analyses performed using the DESeq2 package in R.
Assembly: mm39
Supplementary files format and content: rawcount

source_name: mESC cultured in PrE-induce medium

extract_protocol:
TRIzol reagent (Invitrogen, 15596026) was added to cell samples to extract RNA. Briefly, 0.5 mL TRIzol reagent was added to wells in a 6-well plate and mixed thoroughly. Next, 0.2 mL chloroform was added (for phase separation), followed by centrifugation at 12,000 g at 4°C for 15 min. The upper aqueous phase was transferred to a new RNase-free tube and an equal volume of isopropanol added. After mixing, RNA was precipitated for 2 h at -20°C, and then centrifuged for 10 min at 12,000 g at 4°C. RNA pellets were washed twice in 75% ethanol and dissolved in RNase-free water. VE and EPI digested by 0.5% pronase E from 5-day embryoids.
The SMARTer Stranded Total RNA-Seq Kit v.2 (Takara, 634413) and the VAHTS Universal v.8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) were used to prepared total RNA-seq libraries, which were sequenced on an Illumina NovaSeq 6000 platform (Shanghai Jiema).

value: mESC cultured in PrE-induce medium


title: Resist51_BFRT_After

city: Ithaca

first: Philip

last: Ruppert

state: NY

address: 244 Garden Avenue

department: Division of Nutritional Sciences

institute: Cornell University

description:
Library name: S34
Resist51

data_processing:
Raw FASTQ were processed using nf-core/rnaseq v3.20.0 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects. The pipeline was executed with Nextflow v25.04.7 (Di Tommaso et al., 2017) with the following command: nextflow run nf-core/rnaseq -r 3.20.0 -profile mamba --max_cpus 32 --max_memory 180.GB --max_time 2400.h --input Samples.csv --outdir ./NF_core_results1 --fasta /Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz --gtf /Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz --gencode true --save_reference true This approach automates quality control, trimming, alignment (or pseudo‐alignment), quantification and reporting of RNA‐seq experiments. Read quality control (QC) was assessed using FastQC (version 0.12.1, ref), and adapter sequences were trimmed with Trim Galore! (version 0.6.10, ref), removing reads with Phred quality scores < 20. Quality summaries across samples were compiled using MultiQC (version 1.30, ref). Filtered reads were aligned to the Homo sapiens reference genome (GENCODE v44, GRCh38.primary_assembly) using the STAR aligner (version 2.7.11b, ref) and SALMON (version 1.10.3) (ref) with default parameters implemented in nf-core/rnaseq. Duplicate reads were marked, and gene-level counts were obtained using featureCounts (release 2.0.6, ref). Samples retained between approximately 41 and 62 million high-quality mapped reads (mapping quality > 0). All downstream statistical and differential expression analyses were performed in R (version 4.5.1) using the gene-level count matrix produced by the pipeline. All samples passed the sequencing QC. One subject was excluded from the BFRT group upon visual inspection of PCA and correlation matrices.
Count tables were reconstructed from quant.sf files per sequenced sample using tximport with the lengthScaledTPM option (version 1.36.1) (ref). Differential gene expression analysis was performed using DESeq2 (version 1.48.2) (ref) with shrinkage of fold-changes using apeglm (version 1.30.0) (ref). Genes with fewer than 10 total counts across all samples were excluded prior to normalization. The following interaction model was applied: ~ cohort + cohort:subject_within_cohort + cohort:timepoint, allowing detection of main before and after effects, and their statistical interaction. Specifically, the model tested: (i) the main effect of CREST (before vs. after), (ii) the main effect of BFRT (before vs. after), and (iii) their interaction (whether the effect of before and after differs between CREST and BFRT). Genes with an adjusted p-value < 0.05 and an absolute log2FC ≥ 0.585 were considered significantly differentially expressed. Gene set enrichment analysis (GSEA) was performed using the gseKEGG() function from the clusterProfiler package (version 4.16.0) (ref) with parameters: organism = "mmu", pvalueCutoff = 1, pAdjustMethod = "BH", minGSSize = 0, seed = TRUE, and eps = 0.
Assembly: GRCh38.p14
Supplementary files format and content: salmon.merged.gene_counts.tsv

source_name: Muscle

extract_protocol:
RNA_seq:Total ribonucleic acid (RNA) was extracted from tissues using the QIAzol Lysis Reagent (Qiagen, Hilden, Germany) followed by silica- membrane purification of total RNA (Qiagen, Hilden, Germany). The quality of RNA was validated by the Agilent RNA 6000 Nano-Kit in Agilent 2100 Bioanalyzer according to the manufacturer's protocol (Agilent Technologies, Waldbronn, Germany). mRNA sequencing was performed in-house.
RNA-seq: Input RNA was tested for quantity using the Qubit broad range RNA kit and for quality using Agilent Bioanalyzer 2100. Next, 1000 ng RNA was used for library prep using the Zephyr NGS workstation (Revvity), using the NEXTFLEX® Poly(A) Beads 2.0 and Rapid Directional RNA-Seq Kit 2.0.  The amplified libraries were tested for quality using Agilent Tapestation 2200 and quantity using the Qubit dsDNA high sensitivity kit. Finally, sequencing was performed on a S1 Flowcell using the NovaSeq 6000 S1 Reagent Kit v1.5 on an Illumina Novaseq 6000.

treatment_protocol: tbd

value: Muscle

value: BFRT

value: After


title: spRNA-Seq of tomato: seeding leaf-biorep2 CK

description:
Library name: CK-2-SP
BMK-S1000, Control replicate 2, seeding leaf under normal condition


title: Uninfected-single cell#9 , Mouse#1_Right ear [1_E6]

value: 10 weeks old


title: SAT6

description: Library name: SAT6

value: female


title: Uninfected-single cell#24 , Mouse#4_Left ear [2_H10]


title: Uninfected-single cell#20 , Mouse#3_Right ear [2_E10]


title: mack2_p180_1

description: Library name: P180_1

value: Muscle satellite cell


title: mack2_p180_4

description: Library name: P180_4

value: Muscle stem cell

value: proliferation


title: Uninfected-single cell#22 , Mouse#3_Left ear [2_E9]


title: snRNA-Seq of tomato: seeding leaf-biorep2 LTSS

description:
Library name: LTSS-2
10x Genomics, Treatment replicate 2, seeding leaf under long term salt stress


title: mack2_p180_2

description: Library name: P180_2


title: SAT4

description: Library name: SAT4

value: subcutaneous adipose tissue


title: Uninfected-single cell#18 , Mouse#1_Right ear [2_C8]


title: mack2_p180_3

description: Library name: P180_3


title: SAT1

description: Library name: SAT1


title: Uninfected-single cell#7 , Mouse#4_Left ear [1_D5]


title: Uninfected-single cell#6 , Mouse#3_Left ear [1_D4]


title: Uninfected-single cell#14 , Mouse#5_Left ear [1_G6]


title: spRNA-Seq of tomato: seeding leaf-biorep1 LTSS

description:
Library name: LTSS-1-SP
BMK-S1000, Treatment replicate 1, seeding leaf under long term salt stress

value: leaf


title: Uninfected-single cell#5 , Mouse#2_Left ear [1_D1]


title: snRNA-Seq of tomato: seeding leaf-biorep2 CK

description:
Library name: CK-2
10x Genomics, Control replicate 2, seeding leaf under normal condition

value: seeding leaf nuclei


title: Uninfected-single cell#12 , Mouse#1_Left ear [1_G2]


title: Uninfected-single cell#13 , Mouse#2_Left ear [1_G3]


title: Uninfected-single cell#17 , Mouse#4_Left ear [2_B5]


title: Uninfected-single cell#10 , Mouse#3_Left ear [1_E9]


title: SAT2

description: Library name: SAT2

value: male


title: Resist44_CREST_Before

description:
Library name: S27
Resist44

value: CREST

value: Before


title: Uninfected-single cell#15 , Mouse#4_Left ear [1_H10]

value: monocytes


title: snRNA-Seq of tomato: seeding leaf-biorep1 CK

description:
Library name: CK-1
10x Genomics, Control replicate 1, seeding leaf under normal condition

value: WT

value: Long term salt stress


title: snRNA-Seq of tomato: seeding leaf-biorep3 LTSS

description:
Library name: LTSS-3
10x Genomics, Treatment replicate 3, seeding leaf under long term salt stress


title: mESC_Virma_WT_rep1

description:
Library name: mESC_Virma_WT_rep1
mESC_D2_Mettl3_Virma_KO_raw_count.csv

value: mESC cultured in PrE-induce medium


title: Resist50_CREST_Before

description:
Library name: S31
Resist50

value: Muscle


title: Uninfected-single cell#3 , Mouse#4_Right ear [1_C2]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz

value: ear tissue


title: Uninfected-single cell#11 , Mouse#3_Left ear [1_F9]

value: 10 weeks old


title: mESC_Mettl3_cKO_rep1

description:
Library name: mESC_Mettl3_cKO_rep1
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: spRNA-Seq of tomato: seeding leaf-biorep1 CK

description:
Library name: CK-1-SP
BMK-S1000, Control replicate 1, seeding leaf under normal condition


title: Resist50_CREST_After

description:
Library name: S32
Resist50

value: After


title: TBLC2_rep2

description:
Library name: TBLC2_rep2
TBLC2_raw_count.csv

data_processing:
Raw sequencing reads were quality assessed using FastQC (v.0.12.1) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), with sequencing adapters and low-quality bases trimmed using trim-galore. Trimmed reads were aligned to a mouse reference genome (mm39) using STAR (v.2.7.11b). Annotation files (vM29) were downloaded from the GENCODE database (https://www.gencodegenes.org/). Reads for each GENCODE annotated gene were annotated using Subread, and differentially expressed gene (DEG) analyses performed using the DESeq2 package in R.
Assembly: mm39
Supplementary files format and content: rawcount
Supplementary files format and content: BED file for m6A peak

source_name: TBLC cultured in 2MYCP medium

extract_protocol:
TRIzol reagent (Invitrogen, 15596026) was added to cell samples to extract RNA. Briefly, 0.5 mL TRIzol reagent was added to wells in a 6-well plate and mixed thoroughly. Next, 0.2 mL chloroform was added (for phase separation), followed by centrifugation at 12,000 g at 4°C for 15 min. The upper aqueous phase was transferred to a new RNase-free tube and an equal volume of isopropanol added. After mixing, RNA was precipitated for 2 h at -20°C, and then centrifuged for 10 min at 12,000 g at 4°C. RNA pellets were washed twice in 75% ethanol and dissolved in RNase-free water.
The SMARTer Stranded Total RNA-Seq Kit v.2 (Takara, 634413) and the VAHTS Universal v.8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) were used to prepared total RNA-seq libraries, which were sequenced on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform.

value: TBLC cultured in 2MYCP medium


title: mESC_Mettl3_WT_rep2

description:
Library name: mESC_Mettl3_WT_rep2
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: TBLC_PlaB-_3h_rep2

description:
Library name: TBLC_PlaB-_3h_rep2
ActD_TBLC_PlaB-_raw_count.csv

source_name: TBLC cultured in SLM for 8 hours

value: TBLC cultured in SLM for 8 hours

value: Actinomycin D


title: Uninfected-single cell#2 , Mouse#4_Right ear [1_A6]


title: Resist51_BFRT_Before

description:
Library name: S33
Resist51

value: BFRT


title: mESC_Mettl3_WT_rep1

description:
Library name: mESC_Mettl3_WT_rep1
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: Resist48_BFRT_After

description:
Library name: S30
Resist48


title: TBLC_PlaB-_3h_rep1

description:
Library name: TBLC_PlaB-_3h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: Resist39_BFRT_Before

description:
Library name: S25
Resist39


title: Resist37_CREST_Before

description:
Library name: S23
Resist37


title: mESC_Virma_cKO_rep1

description:
Library name: mESC_Virma_cKO_rep1
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: Resist34_BFRT_After

description:
Library name: S22
Resist34


title: Uninfected-single cell#8 , Mouse#2_Right ear [1_D9]


title: EPSC_GLORI_sgCtrl_rep2

description:
Library name: EPSC_GLORI_sgCtrl_rep2
total_site_merged_sgGata6.txt

data_processing:
Analytical GLORI methods were performed using GLORI tools.
Assembly: mm39
Supplementary files format and content: m6A site information

source_name: EPSC

extract_protocol:
TRIzol reagent (Invitrogen, 15596026) was added to cell samples to extract RNA. Briefly, 0.5 mL TRIzol reagent was added to wells in a 6-well plate and mixed thoroughly. Next, 0.2 mL chloroform was added (for phase separation), followed by centrifugation at 12,000 g at 4°C for 15 min. The upper aqueous phase was transferred to a new RNase-free tube and an equal volume of isopropanol added. After mixing, RNA was precipitated for 2 h at -20°C, and then centrifuged for 10 min at 12,000 g at 4°C. RNA pellets were washed twice in 75% ethanol and dissolved in RNase-free water.
mRNA purification was performed as described; 50 ng mRNA was used as a starting material following a previous GLORI library protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform (JMDNA (Shanghai) Bio-Medical Technology Co., Ltd.).

value: EPSC


title: Low-proliferating Leishmania major infected-single cell#73 , Mouse#4_Left ear [3_G10]


title: Resist48_BFRT_Before

description:
Library name: S29
Resist48


title: EPSC_GLORI_sgGata6_rep2

description:
Library name: EPSC_GLORI_sgGata6_rep2
total_site_merged_sgGata6.txt


title: Resist44_CREST_After

description:
Library name: S28
Resist44


title: mESC_Virma_cKO_rep2

description:
Library name: mESC_Virma_cKO_rep2
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: snRNA-Seq of tomato: seeding leaf-biorep1 LTSS

description:
Library name: LTSS-1
10x Genomics, Treatment replicate 1, seeding leaf under long term salt stress

value: leaf

value: seeding leaf nuclei


title: TBLC_PlaB-_0h_rep2

description:
Library name: TBLC_PlaB-_0h_rep2
ActD_TBLC_PlaB-_raw_count.csv


title: TBLC_PlaB-_0h_rep1

description:
Library name: TBLC_PlaB-_0h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: TBLC_Ctrl_3h_rep2

description:
Library name: TBLC_Ctrl_3h_rep2
ActD_TBLC_PlaB-_raw_count.csv


title: mESC_Virma_WT_rep2

description:
Library name: mESC_Virma_WT_rep2
mESC_D2_Mettl3_Virma_KO_raw_count.csv


title: Uninfected-single cell#4 , Mouse#4_Left ear [1_C5]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: Resist39_BFRT_After

description:
Library name: S26
Resist39


title: Low-proliferating Leishmania major infected-single cell#74 , Mouse#4_Right ear [3_G5]


title: Resist37_CREST_After

description:
Library name: S24
Resist37

value: CREST


title: snRNA-Seq of tomato: seeding leaf-biorep3 CK

description:
Library name: CK-3
10x Genomics, Control replicate 3, seeding leaf under normal condition


title: TBLC2_rep1

description:
Library name: TBLC2_rep1
TBLC2_raw_count.csv


title: EPSC_GLORI_sgCtrl_rep1

description:
Library name: EPSC_GLORI_sgCtrl_rep1
total_site_merged_sgGata6.txt


title: Uninfected-single cell#1 , Mouse#3_Left ear [1_A2]


title: EPSC_GLORI_sgGata6_rep1

description:
Library name: EPSC_GLORI_sgGata6_rep1
total_site_merged_sgGata6.txt


title: Low-proliferating Leishmania major infected-single cell#75 , Mouse#5_Left ear [3_G6]


title: Low-proliferating Leishmania major infected-single cell#71 , Mouse#3_Left ear [3_F9]


title: Low-proliferating Leishmania major infected-single cell#72 , Mouse#4_Right ear [3_G1]


title: Kidney, old DQ

city: Greifswald

first: Yao

state: State

address: Felix-Hausdorff-Straße 3

institute: University Medicine Greifswald

description: Library name: Sample1

data_processing:
The FASTQ files were processed and aligned to GRCm39 mouse reference genome using MobiVision software (version 3.2 ) from 10x Genomics, with unique molecular identifier (UMI) counts summarized for each barcode.
Assembly: Mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Under sterile conditions, thefreshly collected kidneys  were washed twice with pre-cooled RPMI 1640 medium containing 0.04% BSA. The tissues were then mechanically dissociated into approximately 0.5 mm³ fragments using surgical scissors and transferred into freshly prepared enzymatic digestion solution. The digestion mixture contained RPMI 1640 (Conring, cat.no. 10-040-CVR), 0.04% BSA (MACS, cat.no. 1000076), and 0.2% collagenase II (Gibco, cat.no. 17101015). The samples were incubated at 37°C for 30-60 minutes with gentle inversion every 5-10 minutes.The digested cell suspension was filtered through a BD 40 μm cell strainer (Falcon, cat.no. 352340) 1-2 times. The filtrate was centrifuged at 300 × g for 5 minutes at 4°C. The cell pellet was resuspended in appropriate medium, mixed with an equal volume of red blood cell lysis buffer (Miltenyi, cat.no. 130-094-183), and incubated at 4°C for 10 minutes. After centrifugation at 300 × g for 5 minutes, the supernatant was discarded. The pellet was washed once with medium followed by another centrifugation at 300 × g for 5 minutes, and the final supernatant was removed.Finally，the cells were re-suspended with 1ml RPMI 1640 medium (Conring, cat.no.10-040-CVR) with 0.04% BSA added. Single-cell suspension concentration and cell viability were then evaluated by Luna-FL cell counter (Logos Biosystems，Korea) or Trypan Blue staining method.
The freshly prepared single-cell suspension was adjusted to a concentration of 700–1200 cells/μl. Library preparation and loading were performed following the manufacturer’s protocol for the MobiCube High-throughput Single Cell 3 ′ Transcriptome Set V2.1 (cat.no.PN-S050200301). The constructed libraries were sequenced on the Illumina Nova 6000 PE150  platform for high-throughput sequencing.

value: Kidney

value: old

value: DQ


title: TBLC_PlaB-_2h_rep1

description:
Library name: TBLC_PlaB-_2h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: Low-proliferating Leishmania major infected-single cell#66 , Mouse#1_Left ear [3_E2]

value: monocytes


title: Resist28_CREST_After

description:
Library name: S18
Resist28


title: Low-proliferating Leishmania major infected-single cell#70 , Mouse#4_Right ear [3_F5]


title: TBLC_Ctrl_1h_rep2

description:
Library name: TBLC_Ctrl_1h_rep2
ActD_TBLC_PlaB-_raw_count.csv


title: Resist34_BFRT_Before

description:
Library name: S21
Resist34

value: Before


title: Bnon_3

city: St. Louis

first: Brian

last: Laidlaw

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: Sample 9

data_processing:
Sequences reported as fastq files
Fastq files alligned to mm10 genome with STAR
Mappable reads counted with HTseq and imported into RStudio
DESeq2 used to analyze differential expression
Assembly: mm10
Supplementary files format and content: CSV sheet with normalized count for all samples

source_name: Lung

extract_protocol:
Cells were isolated by sorting using an Aria sorter and total RNA purified using the RNeasy Micro kit (Qiagen).
Barcoded sequencing libraries were generated using the SMARTer Ultra Low Input RNA Kit for Illumina Sequencing (takaraClontech). Paired-end sequencing was performed on an Illumina NovaSeq-6000.

value: Lung

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2- CXCR3-

value: Influenza PR8 day 30


title: Resist31_CREST_Before

description:
Library name: S19
Resist31

value: Muscle


title: Resist31_CREST_After

description:
Library name: S20
Resist31

value: After


title: TBLC_PlaB-_1h_rep2

description:
Library name: TBLC_PlaB-_1h_rep2
ActD_TBLC_PlaB-_raw_count.csv

value: TBLC cultured in SLM for 8 hours


title: Kidney, young

description: Library name: Sample3

value: young

value: control


title: EPSC_rep2

description:
Library name: EPSC_rep2
EPSC_raw_count.csv

value: EPSC


title: TBLC_PlaB-_2h_rep2

description:
Library name: TBLC_PlaB-_2h_rep2
ActD_TBLC_PlaB-_raw_count.csv

value: Actinomycin D


title: Bnon_2

description: Library name: Sample 8


title: TBLC_PlaB-_1h_rep1

description:
Library name: TBLC_PlaB-_1h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: Low-proliferating Leishmania major infected-single cell#69 , Mouse#1_Left ear [3_F2]

value: ear tissue

value: 10 weeks old


title: TBLC_Ctrl_3h_rep1

description:
Library name: TBLC_Ctrl_3h_rep1
ActD_TBLC_PlaB-_raw_count.csv

value: TBLC cultured in 2MYCP medium


title: Resist16_BFRT_After

description:
Library name: S12
Resist16

value: BFRT


title: Brm_2

description: Library name: Sample 5

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2- CXCR3+


title: EPSC_rep1

description:
Library name: EPSC_rep1
EPSC_raw_count.csv


title: Brm_3

description: Library name: Sample 6


title: TBLC_Ctrl_0h_rep1

description:
Library name: TBLC_Ctrl_0h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: Resist28_CREST_Before

description:
Library name: S17
Resist28

value: CREST


title: Low-proliferating Leishmania major infected-single cell#61 , Mouse#4_Left ear [3_C5]

value: monocytes


title: Brm_1

description: Library name: Sample 4

value: Lung


title: Resist14_CREST_Before

description:
Library name: S9
Resist14

value: Before


title: Resist14_CREST_After

description:
Library name: S10
Resist14


title: Low-proliferating Leishmania major infected-single cell#68 , Mouse#4_Left ear [3_F10]


title: Resist18_BFRT_After

description:
Library name: S14
Resist18


title: TBLC_Ctrl_2h_rep1

description:
Library name: TBLC_Ctrl_2h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: TBLC_Ctrl_2h_rep2

description:
Library name: TBLC_Ctrl_2h_rep2
ActD_TBLC_PlaB-_raw_count.csv


title: diffTBLC_m6A_IP_rep1

description:
Library name: diffTBLC_m6A_IP_rep1
diffTBLC_rep1_peaks.bed

source_name: TBLC cultured in SLM for 3 days

value: TBLC cultured in SLM for 3 days

value: anti-m6A (New England Biolabs, E1610S)


title: diffTBLC_input_rep2

description:
Library name: diffTBLC_input_rep2
diffTBLC_rep2_peaks.bed

value: Ctrl


title: Low-proliferating Leishmania major infected-single cell#60 , Mouse#3_Right ear [3_C4]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: Low-proliferating Leishmania major infected-single cell#65 , Mouse#1_Right ear [3_D8]


title: Resist12_BFRT_After

description:
Library name: S8
Resist12

value: Muscle

value: After


title: Resist26_BFRT_After

description:
Library name: S16
Resist26


title: Low-proliferating Leishmania major infected-single cell#58 , Mouse#1_Left ear [3_C2]


title: Resist18_BFRT_Before

description:
Library name: S13
Resist18


title: Resist11_CREST_After

description:
Library name: S6
Resist11


title: TBLC_Ctrl_1h_rep1

description:
Library name: TBLC_Ctrl_1h_rep1
ActD_TBLC_PlaB-_raw_count.csv


title: Bnon_1

description: Library name: Sample 7

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2- CXCR3-

value: Influenza PR8 day 30


title: Resist11_CREST_Before

description:
Library name: S5
Resist11


title: Kidney, old

description: Library name: Sample2

value: Kidney

value: old

value: control


title: Resist26_BFRT_Before

description:
Library name: S15
Resist26


title: diffTBLC_m6A_IP_rep2

description:
Library name: diffTBLC_m6A_IP_rep2
diffTBLC_rep2_peaks.bed


title: Left ventricular, MI+PBS

city: New York

first: Kaiyue

last: Zhang

address: 3960 Broadway

department: BME

institute: Columbia University

description: Library name: MI

data_processing:
Cell Ranger 7.0.1
Assembly: Mouse reference genome mm10
Supplementary files format and content: Count matrix from Cell Ranger

molecule: nuclear RNA

source_name: Heart

extract_protocol:
heart tissue was homogenized and lysed with Triton X‐100 in RNase‐free water for nucleus isolation. Isolated nuclei were purified, centrifuged, and resuspended in PBS with RNase inhibitor, then diluted to 700 nuclei/μL for standardized 10x Genomics capture
library preparation protocol with 10x Genomics Chromium Next GEM 3′ Single Cell Reagent kits version 3.1 (10x Genomics, Pleasanton, CA)

value: Heart

value: PBS


title: Resist06_BFRT_Before

description:
Library name: S3
Resist06

value: BFRT


title: Resist06_BFRT_After

description:
Library name: S4
Resist06


title: TBLC_PlaB-_input_rep1

description:
Library name: TBLC_PlaB-_input_rep1
TBLC_PlaB-_rep1_peaks.bed

value: TBLC cultured in SLM for 8 hours


title: Bcm_3

description: Library name: Sample 3

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2+


title: Low-proliferating Leishmania major infected-single cell#54 , Mouse#2_Right ear [3_A9]

value: monocytes

value: ear tissue

value: 10 weeks old


title: Low-proliferating Leishmania major infected-single cell#62 , Mouse#5_Left ear [3_D12]


title: TBLC_Ctrl_0h_rep2

description:
Library name: TBLC_Ctrl_0h_rep2
ActD_TBLC_PlaB-_raw_count.csv

value: TBLC cultured in 2MYCP medium

value: Actinomycin D


title: Cxcl12 WT, P5 wound, day 3 after wounding, rep 2

city: Cambridge

first: Hannah

middle: T

last: Tam

address: 7 Divinity Avenue

department: SCRB

institute: Harvard University

description:
Library name: E_47M_Cxcl12_fl
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were made using the cellranger pipeline (v7.1.0)
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format (H5)

source_name: Skin

extract_protocol:
To collect wound-responsive cells, we utilized a circular punch biopsy that was 1 mm larger than the wounds to collect cells immediately adjacent to the wound as well as those that had migrated into the wound bed. Single-cell suspensions were treated with ACK lysis buffer to remove red blood cells prior to FACS sorting. Live cells (DAPI-negative) were sorted out and used for library construction.
16.5K cells per sample were loaded into the 10X Genomics Chromium Next GEM Chip G. scRNAseq gene expression libraries were generated using the 10X Genomics Chromium Next GEM Single Cell Kit (v3.1) as per manufacturer’s protocol. Libraries were sequenced on a NovaSeq 6000 S4 lane.

value: Skin

value: WT

value: Wounded


title: Low-proliferating Leishmania major infected-single cell#53 , Mouse#1_Right ear [3_A8]

source_name: ear tissue


title: Low-proliferating Leishmania major infected-single cell#67 , Mouse#3_Left ear [3_E9]


title: diffTBLC_input_rep1

description:
Library name: diffTBLC_input_rep1
diffTBLC_rep1_peaks.bed

value: TBLC cultured in SLM for 3 days

value: Ctrl


title: Cxcl12 KO, P5 wound, day 3 after wounding, rep 2

description:
Library name: D_45M_PdgfraCre_Cxcl12_fl
10X Genomics

value: KO


title: TBLC_Ctrl_m6A_IP_rep1

description:
Library name: TBLC_Ctrl_m6A_IP_rep1
TBLC_Ctrl_rep1_peaks.bed

value: anti-m6A (New England Biolabs, E1610S)


title: Low-proliferating Leishmania major infected-single cell#64 , Mouse#4_Left ear [3_D5]


title: TBLC_Ctrl_m6A_IP_rep2

description:
Library name: TBLC_Ctrl_m6A_IP_rep2
TBLC_Ctrl_rep2_peaks.bed


title: Resist16_BFRT_Before

description:
Library name: S11
Resist16

value: Muscle

value: Before


title: 0618ADSC

first: Jingxiao

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

description:
Library name: 0618ADSC
column name in counts.txt: 0618ADSC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using STAR v2.7.10b and annotated using gencode v47 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: txt file with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted utilizing the TGuide S32 Blood/Cell/Tissue RNA kit in conjunction with the TGuide S32 nucleic acid extractor.
For the preparation of RNA-seq libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (provided by New England BioLabs, catalog number E7775) was used. The resultant libraries, comprising fragmented and randomly primed RNA molecules, were sequenced as paired-end reads of 2 x 150 base pairs

value: ADSC (Adipose-Derived Stem Cells)


title: Low-proliferating Leishmania major infected-single cell#63 , Mouse#1_Left ear [3_D2]

data_processing:
Raw fastq files were processed with Cutadapt (v3.7) to remove poly-A tails and adapter sequences introduced during library construction (SMART-seq: AAGCAGTGGTATCAACGCAGAGT & Nextera XT: CTGTCTCTTATACACATCT).
The first 15 bases of each read, bases with Qscore < 20 and reads left with less than 25 bases after trimming were also discarded.
Reads were mapped to a reference genome using STAR with default parameters.
The used reference genome has been built by combining the mouse (GRCm38) and Leishmania major (ASM272v2) genomes as well as spike-ins (ERCC92) and the Kikume Green-Red transcript sequences.
The raw count matrix was generated from the mapping results with featureCounts (Subread, v1.6.3)
Assembly: GRCm38,  ASM272v2, ERCC92
Supplementary files format and content: Tab-separated matrix files


title: Resist12_BFRT_Before

description:
Library name: S7
Resist12

value: BFRT


title: Low-proliferating Leishmania major infected-single cell#59 , Mouse#2_Right ear [3_C3]


title: Bcm_2

description: Library name: Sample 2

value: Lung

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2+

value: Influenza PR8 day 30


title: Low-proliferating Leishmania major infected-single cell#51 , Mouse#5_Left ear [3_A2]

value: monocytes

value: ear tissue

value: 10 weeks old


title: 1117HEF rep1

description:
Library name: 1117HEF rep1
column name in counts.txt: 1117HEF-1

value: HEF (Human Embryonic Fibroblasts)


title: TBLC_Ctrl_input_rep1

description:
Library name: TBLC_Ctrl_input_rep1
TBLC_Ctrl_rep1_peaks.bed

value: TBLC cultured in 2MYCP medium


title: Low-proliferating Leishmania major infected-single cell#50 , Mouse#5_Left ear [3_A12]


title: Low-proliferating Leishmania major infected-single cell#56 , Mouse#3_Right ear [3_B4]


title: S2-BTG2KO

description:
Library name: S2-BTG2KO
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: induced from hADSCs

extract_protocol:
Cells were harvested and resuspended at 1 x 106 cells per milliliter in PBS supplemented with 0.04% BSA.
Using Single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension containing 300-600 living cells per microliter was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol. On an S1000TM Touch Thermal Cycler (Bio Rad), captured cells were lysed, and the released RNA was barcoded through reverse transcription in individual GEM. These steps were carried out at 53 °C for 45 minutes, followed by 85 °C for 5 minutes, and held at 4 °C. Single-cell RNA sequencing libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics) and sequenced by IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150).

value: induced from hADSCs


title: Left ventricular, Sham

description: Library name: Control

value: Heart


title: TBLC_PlaB-_m6A_IP_rep1

description:
Library name: TBLC_PlaB-_m6A_IP_rep1
TBLC_PlaB-_rep1_peaks.bed

value: TBLC cultured in SLM for 8 hours


title: Left ventricular, MI+saNppa-LNP

description: Library name: LNP

value: saNppa-LNP


title: Ddx21_fl2

city: Chongqing

first: Yalan

last: Xiao

address: No. 1 Yixueyuan Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

description: Library name: Samples2

data_processing:
Illumina Casava1.7 software
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
About 5000 HSC (Lin-Sca-1+c-Kit+CD48-CD150+) were isolated by FACS and the mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols
The mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Hematopoietic stem cells (HSC)

value: WT


title: Low-proliferating Leishmania major infected-single cell#48 , Mouse#2_Right ear [2_H8]


title: TBLC_PlaB-_m6A_IP_rep2

description:
Library name: TBLC_PlaB-_m6A_IP_rep2
TBLC_PlaB-_rep2_peaks.bed

value: anti-m6A (New England Biolabs, E1610S)


title: diffTBLC_RIP_Ythdf2_input_rep2

description:
Library name: diffTBLC_RIP_Ythdf2_input_rep2
Ythdf2_RIP_raw_count.csv

value: TBLC cultured in SLM for 3 days

value: Ctrl


title: diffTBLC_RIP_Ythdf2_input_rep1

description:
Library name: diffTBLC_RIP_Ythdf2_input_rep1
Ythdf2_RIP_raw_count.csv


title: Bcm_1

description: Library name: Sample 1

value: Lung

value: B220+IgDloGL7-CD38+S1pr2-Zsgreen+ In vivo CD45.2+


title: Low-proliferating Leishmania major infected-single cell#57 , Mouse#5_Left ear [3_C12]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz

value: monocytes


title: Low-proliferating Leishmania major infected-single cell#55 , Mouse#4_Right ear [3_B11]

value: ear tissue


title: Ddx21_2

description: Library name: Samples2

library_source: genomic

data_processing:
Sequencing reads were processed through FASTQC (v0.11.5) for quality control and aligned to the mm10 genome using Bowtie2 (v2.2.9)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
The CUT&Tag assay was performed on fluorescence-activated cell-sorted HSCs (~10,000) from C57BL/6 mouse bone marrow using the NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein).
The library constructed using NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (Novoprotein) for sequencing, according to the manufacturer’s instruction

value: primary cell


title: Resist02_CREST_After

description:
Library name: S2
Resist02

value: Muscle

value: CREST

value: After


title: TBLC_PlaB-_input_rep2

description:
Library name: TBLC_PlaB-_input_rep2
TBLC_PlaB-_rep2_peaks.bed


title: Resist02_CREST_Before

description:
Library name: S1
Resist02

value: Before


title: D341 cells siCtrl_3 +RNase R

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: Library name: D341 cells siCtrl_3 +RNase R

data_processing:
RNASeq: Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
RNASeq: Reads were mapped using STAR_2.7.5a and count using featurecounts
circ-RNA: Back-spliced junctions (BSJs) were identified using CIRI-full algorithm, CIRIquant was used for quantification and differential analysis, with RNAse-treated and -untreated samples. Annotations of circRNAs was done using GRCh38 genome and GENCODE v32 annotations.
circ-RNA: circRNAs were detected in RNAse-treated samples, but quantification was done on untreated samples to evaluate and take into account the efficiency of RNAse treatment (CIRIquant option).
Assembly: hg38
Supplementary files format and content: RNASeq: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2022_1 were also provide.
Supplementary files format and content: circ-RNA: Tab-delimited text file includes edgeR normalized expression values for each detected circRNA and for each sample.

growth_protocol: D341 cells were cultured in Minimal Essential Medium (MEM, Gibco) supplemented with sodium pyruvate 1mM (Gibco), MEM Non-Essential Amino Acids Solution 1X (Gibco), 20% fetal bovine serum (FBS, Gibco), 100U/ml penicillin and 10μg/ml streptomycin (Euroclone).

extract_protocol:
Total RNA was extracted using miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Universal Plus™ Total RNA-Seq with NuQuant® following manufacturer’s instructions.

treatment_protocol: D341 cells were transfected with 50nM of specific siRNAs using Lipofectamine RNAiMax Transfection Reagent (Cat. No. 13778150, Invitrogen) according to manufacturer’s instructions.

value: human medulloblastoma cell line

value: D341 cells silenced with 50 nM siCtrl for 72h, plus RNAse R, replicate 3


title: 1117HEF rep2

description:
Library name: 1117HEF rep2
column name in counts.txt: 1117HEF-2

value: HEF (Human Embryonic Fibroblasts)


title: Ddx21_fl1

description: Library name: Samples1

value: Bone marrow

value: Hematopoietic stem cells (HSC)


title: diffTBLC_RIP_Igf2bp3_input_rep2

description:
Library name: diffTBLC_RIP_Igf2bp3_input_rep2
Igf2bp3_RIP_raw_count.csv


title: Pooled SHARE-seq libraries, batch 1 containing sub-libraries 1.1, 1.2, 2.1, 2.2, 3.1, 3.2, 4.1, 4.2

first: Bruno

last: Gegenhuber

state: Massachusetts

address: 220 Longwood Ave

department: Neuroscience

institute: Harvard Medical School

description: Library name: Pooled_ATAC_RNA_libraries_batch_1

library_source: other

data_processing:
SHARE-seq data were processed using the SHARE-seq-alignmentV2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2), generating gene x nucleus matrices for the snRNA assay and fragment files for the snATAC assay.
snRNA gene x nucleus matrices were loaded into Seurat (v5.3.0), and nuclei with fewer than 600 gene counts were removed. Scrublet was used to predict and remove doublets, and post-doublet removal, nuclei were further filtered on the basis of gene counts, retaining nuclei that have between 750 and 80,000 gene counts.
snATAC fragment files were loaded into Signac (v1.14.0), and initial 5000 bp x cell genome bin matrices were constructed using the GenomeBinMatrix function. Chromatin assay objects were then created using the CreateChromatinAssay function, and these objects were subsequently filtered to keep cell barcodes present in the snRNA assay. Peaks were called on the dataset using MACS2 (CallPeaks).
Assembly: mm10
Supplementary files format and content: V1_SHAREseq_seurat_obj.rds: a Seurat object containing gene expression, peak accessibility, chromVAR scores, and all relevant metadata (time point, rearing condition, replicate) for the final processed dataset (70,907 cells).

molecule: other

extract_protocol: SHARE-seq was performed on V1 tissue harvested from P7, P14, P21, P28, and P35 C57BL/6 mice raised in DR or NR conditions (n = 4 mice per condition and time point). Mice were deeply anesthetized with isoflurane, and V1 was dissected. The tissue was dounce homogenized in 1.5 mL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH pH 7.8, 1X EDTA-free protease inhibitor cocktail (PIC) tablet (Sigma Aldrich 11873580001), 1 mM dithiothreitol (DTT), 0.15 mM spermine, 0.5 mM spermidine, 0.1 U/μL Enzymatics RNase inhibitor (Y9240L), 0.05 U/μL SUPERase inhibitor (AM2696)) with a tight pestle for 20 strokes. The sample was then supplemented with 0.3% IGEPAL CA-630 and further dounced 5 strokes with a tight pestle. Homogenate was filtered through a 40-μm strainer into a 15 mL conical tube, and 3.5 mL of homogenization buffer and 5 mL of 50% OptiPrep solution (50% OptiPrep (Sigma D1556), 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1X PIC, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 0.1 U/μL Enzymatics RNase inhibitor, 0.05 U/μL SUPERase inhibitor) were added. Tissue lysate was underlaid with 1 mL of 30% OptiPrep solution and 1 mL of 40% OptiPrep solutions. Samples were then centrifuged at 10,000g for 18 min at 4°C in an ultracentrifuge. Following centrifugation, approximately 250 μL of nuclei were collected at the 30/40% OptiPrep interface and diluted in NIB-RI buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1 U/μL Enzymatics RNase inhibitor, 0.05 U/μL SUPERase inhibitor). The nuclei were then centrifuged at 500g for 10 min at 4°C in a swinging-bucket centrifuge and subsequently resuspended in NIB-RI buffer containing 0.2% formaldehyde. Samples were incubated at room temperature for 5 min and then quenched on ice for 5 min with the addition of 125 mM glycine, 40 mM Tris pH 8, and 0.08% BSA. Nuclei were then washed two times in NIB-RI buffer by centrifuging at 500g for 10 min at 4°C and replacing the supernatant without disturbing the pellet. After the second wash, the supernatant was removed. Nuclei were flash-frozen in liquid nitrogen and then stored at -80°C until all samples were collected.

treatment_protocol: DR or NR

value: WT

value: DR or NR


title: Cxcl12 WT, P5 wound, day 3 after wounding, rep 1

description:
Library name: A_40F_Cxcl12_fl
10X Genomics

value: Skin

value: Wounded


title: D341 cells siCtrl_2 +RNase R

description: Library name: D341 cells siCtrl_2 +RNase R

value: D341 cells silenced with 50 nM siCtrl for 72h, plus RNAse R, replicate 2


title: diffTBLC_RIP_Ythdf2_IP_rep2

description:
Library name: diffTBLC_RIP_Ythdf2_IP_rep2
Ythdf2_RIP_raw_count.csv

value: TBLC cultured in SLM for 3 days

value: anti-YTHDF2 (Abcam, ab246514)


title: Low-proliferating Leishmania major infected-single cell#42 , Mouse#1_Right ear [2_G6]

first: Yan

address: Haus 26, Institut für Molekulare und Klinische Immunologie, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44

institute: Otto-von-Guericke-Universität Magdeburg

value: monocytes

value: ear tissue

value: 10 weeks old


title: D341 cells sihnRNPC_3 +RNase R

description: Library name: D341 cells sihnRNPC_3 +RNase R

value: D341 cells silenced with 50 nM sihnRNPC for 72h, plus RNAse R, replicate 3


title: D341 cells sihnRNPC_3 -RNase R

description: Library name: D341 cells sihnRNPC_3 -RNase R

value: D341 cells silenced with 50 nM sihnRNPC for 72h, minus RNAse R, replicate 3


title: Low-proliferating Leishmania major infected-single cell#52 , Mouse#3_Right ear [3_A4]


title: Low-proliferating Leishmania major infected-single cell#47 , Mouse#1_Right ear [2_H7]


title: Ddx21_CKO1

description: Library name: Samples3

value: KO


title: t_3h_FPL, rep 4

first: Tim

last: Halim

address: Robinson Way

department: CRUK CI

country: United Kingdom

institute: University of Cambridge

description: Library name: t_3h_FPL4

data_processing:
Quantification of gene expression was performed using Salmon (v 1.9.0) in mapping-based mode versus the Ensembl release 108 transcriptome
Assembly: GRCm39
Supplementary files format and content: Tar file containing full salmon output

source_name: murine naive CD8+ isolated from spleen

growth_protocol: naive murine CD8+ T cells isolated with Naive CD8a+ T Cell Isolation Kit, mouse (Miltenyi, Cat no. 130-096-543). Isolated murine CD8+ T cells were resuspended in RPMI media (Gibco, Cat no. 21875- 034) supplemented with 10% HI-FCS, 10mM HEPES (Sigma, Cat no. H0887), 1mM Sodium Pyruvate (Gibco, Cat no. 11360-039), 50μM β-Mercaptoethanol (Gibco, Cat no. 31350-010), 100U/mL Penicillin/Streptomycin (Gibco, Cat no. 15140-122) and 10ng/mL recombinant murine IL-2 (Peprotech, Cat no. 212-121).

extract_protocol:
RNA was extracted using the PurelinkTM RNA Mini Kit (Thermo, Cat no. 12183025) according to the manufacturer’s instructions.
Library preparation was conducted according to the Illumina Stranded mRNA Prep reference guide (Illumina, Cat no. 1000000124518 v02). PCR cycles were adjusted based on RNA input (12 and 11 cycles for 3h and 24h samples, respectively). A pool of 24 libraries with paired-end and 50 bp-long reads was sequenced on the NovaSeq system (Illumina). The average number of reads per sample was approximately 25 million. There are 6 replicates for each sample group.

treatment_protocol: Cells were counted, washed and resuspended at 1million/ml in complete T cell media in the presence of 10μM FPL 64176 (made up in 100% ethanol, Tocris, Cat no. 1403) or carrier control (100% ethanol) and incubated in a humidified incubator for 50 mins. Following pre-incubation, 500μl cells in carrier- or FPL 64176- containing media were plated on the stimulation plates. Cells were stimulated with plate-bound anti-CD3 (1ug/mL, eBioscience, Cat no. 16-0033) and anti-CD28 (2ug/mL, eBioscience, Cat no. 16-0281) antibodies for 3h and 24h

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+FPL64176

tag: time


title: diffTBLC_RIP_Ythdf2_IP_rep1

description:
Library name: diffTBLC_RIP_Ythdf2_IP_rep1
Ythdf2_RIP_raw_count.csv


title: Cxcl12 KO, P5 wound, day 3 after wounding, rep 1

description:
Library name: B_42F_PdgfraCre_Cxcl12_fl
10X Genomics


title: Low-proliferating Leishmania major infected-single cell#40 , Mouse#3_Left ear [2_G4]

last: Fu

extract_protocol:
Ears of mice were separated in two sheets (ventral and dorsal) using forceps and enzymatically digested in RPMI 1640 medium containing 1 mg/ml collagenase and 50 ng/ml DNase for 60 min at 600 rpm and 37°C and passed through a 70 μm cell strainer. Cells were centrifuged at 4°C with 300 g for 10 min. Mouse CD45 MicroBeads (Miltenyi Biotec) were used to isolate leukocytes prior to cell surface staining according to manufacturer’s instructions. Afterwards, cells were washed with PBS and FACS buffer before surface staining of cells was done by using surface marker specific antibodies (APC-CD11c and APC-cy7-Ly6c). Samples were blocked with Fc-block using anti-CD16/32 antibody (1:25 in FACS buffer) for 15 min on ice before the antibody staining. Antibodies were applied with a final concentration of 1:200. mKikume G&R Leishmania major infections were analyzed with a FACS ARIA III flow cytometer/sorter. Specifically, mKikumeGreen refers to high-proliferating L. major infected monocytes, while mKikumeRed refers to low-proliferating L. major infected monocytes.
Single cells were sorted into different wells from a 96-well plate (Costar) filled with 4.65 µl of Buffer RLT Plus (Qiagen), 0.25 µl of SUPERase-In RNase-Inhibitor (Invitrogen), and 0.1 µl of ERCC spike-Mix1 (Invitrogen) pre-diluted 1:500000 in RNAse-free water. For cell-population RNAseq, 50-100 cells per subpopulation per sample were sorted into the wells. Sorted cells were immediately frozen and stored at -80 °C. Single-cell libraries were prepared using Smart-seq2 protocol as previous described with minor modifications: Following cDNA amplification, ACTB expression was measured in each cDNA library by qPCR. All cDNA libraries were diluted aiming to an equivalent ct value for ACTB (average = 21.11, SD = 1.05) and were subsequently used as input for a tagmentation-based protocol (Nextera XT, Illumina) using one quarter of the recommended volumes, 10 min for tagmentation at 55°C20. The indexed libraries were quantified using Qubit dsDNA Hs Assay (Life Technologies) and fragment size of libraries was analysed using QIAxcel DNA high resolution Kit (Qiagen) and bioanalyser (Agilent). Libraries were normalized to 2 nM and pooled. Particularly, 218 of single-cell libraries were sequenced for HiSeq 2500 (Illumina).


title: Low-proliferating Leishmania major infected-single cell#45 , Mouse#1_Left ear [2_H2]


title: D341 cells sihnRNPC_1 +RNase R

description: Library name: D341 cells sihnRNPC_1 +RNase R

value: human medulloblastoma cell line

value: D341 cells silenced with 50 nM sihnRNPC for 72h, plus RNAse R, replicate 1


title: Ddx21_CKO2

description: Library name: Samples4

value: Bone marrow

value: Hematopoietic stem cells (HSC)


title: Low-proliferating Leishmania major infected-single cell#46 , Mouse#2_Left ear [2_H3]


title: t_3h_FPL, rep 3

description: Library name: t_3h_FPL3


title: diffTBLC_RIP_Igf2bp3_IP_rep2

description:
Library name: diffTBLC_RIP_Igf2bp3_IP_rep2
Igf2bp3_RIP_raw_count.csv

value: anti-IGF2BP3 (CST, 25864)


title: Low-proliferating Leishmania major infected-single cell#44 , Mouse#2_Right ear [2_G8]


title: Low-proliferating Leishmania major infected-single cell#49 , Mouse#3_Left ear [2_H9]


title: TBLC_Ctrl_input_rep2

description:
Library name: TBLC_Ctrl_input_rep2
TBLC_Ctrl_rep2_peaks.bed

value: TBLC cultured in 2MYCP medium

value: Ctrl


title: PrEdiff_2h_rep1

description:
Library name: Sample41
ActD_EPSC_PrEdiff_raw_count.csv

source_name: EPSC cultured in PrE-induce medium

value: EPSC cultured in PrE-induce medium

value: Actinomycin D


title: diffTBLC_RIP_Igf2bp3_IP_rep1

description:
Library name: diffTBLC_RIP_Igf2bp3_IP_rep1
Igf2bp3_RIP_raw_count.csv

value: TBLC cultured in SLM for 3 days


title: t_3h_FPL, rep 1

description: Library name: t_3h_FPL1


title: Low-proliferating Leishmania major infected-single cell#37 , Mouse#2_Left ear [2_F3]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz

value: monocytes

value: ear tissue

value: 10 weeks old


title: D341 cells sihnRNPC_2 +RNase R

description: Library name: D341 cells sihnRNPC_2 +RNase R

value: D341 cells silenced with 50 nM sihnRNPC for 72h ,plus RNAse R, replicate 2


title: D341 cells siCtrl_1 -RNase R

description: Library name: D341 cells siCtrl_1 -RNase R

value: D341 cells silenced with 50 nM siCtrl for 72h, minus RNAse R, replicate 1


title: Ddx21_1

description: Library name: Samples1

value: primary cell


title: diffTBLC_RIP_Igf2bp3_input_rep1

description:
Library name: diffTBLC_RIP_Igf2bp3_input_rep1
Igf2bp3_RIP_raw_count.csv


title: U-2 OS clone C32 ChIP, input, replicate 2

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Library name: CTCF ChIP input, R2

data_processing:
Reads trimmed with Cutadapt (version 2.6) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Reads aligned with Bowtie2 (version 2.4.5) with the following options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Bowtie2 .sam output converted to .bam with samtools (version 1.15.1)
.bam files sorted and indexed with samtools (version 1.15.1)
duplicates removed with samtools (version 1.15.1)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.4) with the following options: --binSize 20 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads --ignoreDuplicates
MACS2 (version 2.2.7.1) peak calling using input samples as control and the following options: macs2 callpeak -B -f BAMPE -g hs
Peak coordinates merged and/or intersected with bedtools (version 2.27.1) or bedops (version 2.4.39)
Assembly: hg38
Supplementary files format and content: *.bw files: coverage files generated with deepTools

source_name: U-2 OS

growth_protocol: U-2 OS cells were cultured at 37 °C with 5% CO2 in low-glucose Dulbecco's Modified Eagle Medium (DMEM; Thermo Fisher #10567022) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. During the incubation, the lysates were repeatedly pipetted up and down every 5 minutes. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 11 cycles of 30" on and 30" off). Sonicated lysates were cleared by centrifugation and 500 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein G Dynabeads (Fisher 1009D) for 2 hours at 4°C and immunoprecipitated overnight with 1.25 μg of normal rabbit IgGs or anti-CTCF antibodies. 10% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 36 μl of water, 25 ul of which were used used for library prep.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (using half of the recommended volumes); adaptors diluted 1:10; 9 PCR cycles; 20 ng starting material for inputs; 25 ul for CTCF ChIP samples.

treatment_protocol: Cells were cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final).

value: U-2 OS

value: Osteosarcoma

tag: antibody

value: Endogenous knock-in FLAG-Halo-CTCF (ATCC CRL-3625)

value: 1% formaldehyde crosslinking for 6 minutes


title: Low-proliferating Leishmania major infected-single cell#34 , Mouse#2_Left ear [2_D8]

city: Magdeburg


title: t_3h_FPL, rep 5

description: Library name: t_3h_FPL5

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+FPL64176


title: Pooled SHARE-seq libraries, batch 2 containing sub-libraries 3.3, 3.4, 4.3, 4.4

description: Library name: Pooled_ATAC_RNA_libraries_batch_2

value: WT

value: DR or NR


title: t_3h_FPL, rep 6

description: Library name: t_3h_FPL6