title: PrEdiff_3h_rep2

description:
Library name: Sample44
ActD_EPSC_PrEdiff_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

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: EPSC cultured in PrE-induce medium

value: Actinomycin D


title: Low-proliferating Leishmania major infected-single cell#43 , Mouse#1_Right ear [2_G7]

status: Public on Mar 20 2026

type: SRA

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
Raw_count_matrix_scRNAseq_20230314.gz

library_source: transcriptomic single cell

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. 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).

tag: cell type

value: monocytes

tag: tissue

value: ear tissue

tag: strain

tag: age

value: 10 weeks old


title: PrEdiff_3h_rep1

city: Beijing

first: Li

last: Tang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

description:
Library name: Sample43
ActD_EPSC_PrEdiff_raw_count.csv

library_source: transcriptomic

source_name: EPSC cultured in PrE-induce medium

tag: treatment

tag: time


title: EPS_3h_rep2

description:
Library name: Sample36
ActD_EPSC_PrEdiff_raw_count.csv

source_name: EPSC

value: EPSC


title: D341 cells siCtrl_1 +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_1 +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.

organism: Homo sapiens

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.

tag: cell line

value: human medulloblastoma cell line

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


title: D341 cells sihnRNPC_1 -RNase R

description: Library name: D341 cells sihnRNPC_1 -RNase R

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


title: Low-proliferating Leishmania major infected-single cell#41 , Mouse#4_Right ear [2_G5]

department: Institut für Molekulare und Klinische Immunologie


title: t_3h_Carrier, rep 3

city: Cambridge

first: Tim

last: Halim

address: Robinson Way

department: CRUK CI

country: United Kingdom

institute: University of Cambridge

description: Library name: t_3h_Carrier3

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+carrier


title: D341 cells siCtrl_3 -RNase R

description: Library name: D341 cells siCtrl_3 -RNase R

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


title: EPS_3h_rep1

description:
Library name: Sample35
ActD_EPSC_PrEdiff_raw_count.csv


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, minus RNAse R, replicate 2


title: PrEdiff_1h_rep1

description:
Library name: Sample39
ActD_EPSC_PrEdiff_raw_count.csv


title: t_3h_Carrier, rep 1

description: Library name: t_3h_Carrier1


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, minus RNAse R, replicate 2


title: t_3h_Carrier, rep 5

description: Library name: t_3h_Carrier5


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

city: Berkeley

first: Robert

last: Tjian

state: CA

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

department: MCB

country: USA

institute: UC Berkeley

description: Library name: CTCF ChIP pulldown, R2

library_source: genomic

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

molecule: genomic DNA

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

tag: genotype

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#39 , Mouse#2_Left ear [2_G3]

value: monocytes


title: PrEdiff_2h_rep2

description:
Library name: Sample42
ActD_EPSC_PrEdiff_raw_count.csv

value: EPSC cultured in PrE-induce medium

value: Actinomycin D


title: Low-proliferating Leishmania major infected-single cell#35 , Mouse#2_Left ear [2_E3]

value: ear tissue

value: 10 weeks old


title: t_3h_FPL, rep 2

description: Library name: t_3h_FPL2

value: plate-bound CD3/CD28+FPL64176


title: t_3h_Carrier, rep 6

description: Library name: t_3h_Carrier6


title: Low-proliferating Leishmania major infected-single cell#30 , Mouse#3_Right ear [2_D10]


title: PBMC, Covid Vaccine, Responder 6

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
Library name: XV321
10X Genomics

data_processing:
Raw base call (BCL) files were demultiplexed using cellranger mkfastq (10x Genomics, v4.0.0). Alignment to the GRCh38 human reference genome, barcode processing, and UMI counting were performed using the cellranger count pipeline (v4.0.0). The resulting filtered gene-barcode matrices were used for downstream analysis. Processed data were converted to .h5ad format for deposition. (Reference: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human GRCh38
Supplementary files format and content: H5AD matrix file

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coat preparations by density gradient centrifugation using Ficoll-Hypaque (GE Healthcare). Cells were washed with DPBS and cryopreserved in 90% fetal bovine serum (FBS) and 10% dimethyl sulfoxide (DMSO) in liquid nitrogen. Prior to library preparation, PBMCs were thawed, washed, and resuspended in DPBS with 0.04% bovine serum albumin (BSA). Cell viability and concentration were assessed using trypan blue and Countess II FL (Thermo Fisher). Approximately 10,000 viable cells per sample were loaded onto a 10x Genomics Chromium Single Cell 3’ Chip (v3.1 chemistry) for gel bead-in-emulsion (GEM) generation and cDNA synthesis. cDNA was amplified by PCR (11 cycles), and sequencing libraries were prepared following the manufacturer's protocol.
Single-cell RNA-seq libraries were prepared according to the manufacturer's protocol (10x Genomics, Chromium Single Cell 3’ v3.1). Briefly, approximately 10,000 viable PBMCs per sample were resuspended in the master mix and loaded into a Chromium Single Cell Chip alongside partitioning oil and gel beads to generate gel bead-in-emulsion (GEMs). Polyadenylated RNA from each cell was reverse-transcribed into barcoded cDNA within individual GEMs. Each cDNA molecule incorporated an Illumina R1 primer sequence, a 10x barcode, and a unique molecular identifier (UMI). After reverse transcription, emulsions were broken and the cDNA was purified with Silane DynaBeads. cDNA was then amplified by PCR (11 cycles), and sequencing libraries were prepared using SPRIselect reagent for size selection. During library construction, Illumina R2 primer sequence, P5 and P7 adapters, and a sample index were added to enable paired-end sequencing.

value: Peripheral blood

value: PBMC

tag: donor id

tag: vaccine status

value: Two vaccine doses

tag: vaccine

value: BNT162b2 COVID-19 mRNA

tag: Sex

value: Male

tag: responder status

value: Responder

tag: batch


title: t_3h_Carrier, rep 4

description: Library name: t_3h_Carrier4

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+carrier


title: Low-proliferating Leishmania major infected-single cell#38 , Mouse#1_Left ear [2_G2]


title: PrEdiff_0h_rep1

description:
Library name: Sample37
ActD_EPSC_PrEdiff_raw_count.csv


title: PrEdiff_0h_rep2

description:
Library name: Sample38
ActD_EPSC_PrEdiff_raw_count.csv


title: t_24h_FPL, rep 3

description: Library name: t_24h_FPL3


title: U-2 OS clone C32 CTCF ChIP, replicate 1

description: Library name: CTCF ChIP pulldown, R1

value: U-2 OS

value: Osteosarcoma

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


title: PBMC, Covid Vaccine, Non-responder 4

description:
Library name: XV269
10X Genomics

value: Female

value: Non-responder


title: Low-proliferating Leishmania major infected-single cell#33 , Mouse#1_Right ear [2_D6]

value: monocytes

value: ear tissue


title: Low-proliferating Leishmania major infected-single cell#27 , Mouse#4_Left ear [2_C5]

value: 10 weeks old


title: PrEdiff_1h_rep2

description:
Library name: Sample40
ActD_EPSC_PrEdiff_raw_count.csv

value: EPSC cultured in PrE-induce medium

value: Actinomycin D


title: Low-proliferating Leishmania major infected-single cell#26 , Mouse#1_Right ear [2_B6]


title: PBMC, Covid Vaccine, Non-responder 3

description:
Library name: XV257
10X Genomics

value: Peripheral blood

value: PBMC

value: Two vaccine doses


title: Low-proliferating Leishmania major infected-single cell#31 , Mouse#5_Left ear [2_D12]


title: diffTBLC_siIgf2bp3_3h_rep2

description:
Library name: Sample60
diffTBLC_siIgf2bp3-2-3

source_name: TBLC cultured in SLM for 3 days

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 SLM for 3 days

value: Actinomycin D & siIgf2bp3


title: Low-proliferating Leishmania major infected-single cell#25 , Mouse#1_Left ear [2_B3]


title: Low-proliferating Leishmania major infected-single cell#36 , Mouse#2_Left ear [2_E8]


title: t_24h_FPL, rep 6

description: Library name: t_24h_FPL6

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+FPL64176


title: U-2 OS clone C32 ChIP, input, replicate 1

description: Library name: CTCF ChIP input, R1

value: U-2 OS

value: Osteosarcoma

value: 1% formaldehyde crosslinking for 6 minutes


title: EPS_2h_rep2

description:
Library name: Sample34
ActD_EPSC_PrEdiff_raw_count.csv

value: EPSC


title: PBMC, Covid Vaccine, Non-responder 6

description:
Library name: XV324
10X Genomics

value: BNT162b2 COVID-19 mRNA

value: Female

value: Non-responder


title: PBMC, Covid Vaccine, Responder 3

description:
Library name: XV256
10X Genomics

value: Male

value: Responder


title: PBMC, Covid Vaccine, Responder 4

description:
Library name: XV301
10X Genomics

value: Peripheral blood


title: t_24h_FPL, rep 5

description: Library name: t_24h_FPL5


title: PBMC, Covid Vaccine, Responder 5

description:
Library name: XV313
10X Genomics

value: PBMC


title: Low-proliferating Leishmania major infected-single cell#28 , Mouse#1_Right ear [2_C6]

value: monocytes

value: ear tissue

value: 10 weeks old


title: EPS_1h_rep2

description:
Library name: Sample32
ActD_EPSC_PrEdiff_raw_count.csv

value: Actinomycin D


title: t_3h_Carrier, rep 2

description: Library name: t_3h_Carrier2

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+carrier


title: PBMC, Covid Vaccine, Non-responder 5

description:
Library name: XV309
10X Genomics

value: Two vaccine doses


title: Low-proliferating Leishmania major infected-single cell#29 , Mouse#1_Left ear [2_C7]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: t_24h_Carrier, rep 4

description: Library name: t_24h_Carrier4


title: EPS_0h_rep1

description:
Library name: Sample29
ActD_EPSC_PrEdiff_raw_count.csv


title: PBMC, Covid Vaccine, Responder 2

description:
Library name: XV232
10X Genomics


title: Low-proliferating Leishmania major infected-single cell#22 , Mouse#1_Left ear [2_A3]


title: Low-proliferating Leishmania major infected-single cell#32 , Mouse#4_Right ear [2_D2]


title: t_24h_FPL, rep 4

description: Library name: t_24h_FPL4

value: plate-bound CD3/CD28+FPL64176


title: EPS_2h_rep1

description:
Library name: Sample33
ActD_EPSC_PrEdiff_raw_count.csv

value: EPSC


title: t_24h_Carrier, rep 3

description: Library name: t_24h_Carrier3


title: diffTBLC_siIgf2bp3_3h_rep1

description:
Library name: Sample59
diffTBLC_siIgf2bp3-1-3

value: TBLC cultured in SLM for 3 days

value: Actinomycin D & siIgf2bp3


title: EPS_0h_rep2

description:
Library name: Sample30
ActD_EPSC_PrEdiff_raw_count.csv


title: t_24h_Carrier, rep 6

description: Library name: t_24h_Carrier6


title: diffTBLC_siIgf2bp3_2h_rep2

description:
Library name: Sample58
diffTBLC_siIgf2bp3-2-2


title: t_24h_Carrier, rep 5

description: Library name: t_24h_Carrier5


title: diffTBLC_siIgf2bp3_2h_rep1

description:
Library name: Sample57
diffTBLC_siIgf2bp3-1-2


title: t_24h_Carrier, rep 1

description: Library name: t_24h_Carrier1


title: t_24h_FPL, rep 2

description: Library name: t_24h_FPL2


title: 0618_OCT4_positive

first: Jingxiao

last: Cao

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

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

description: Library name: 0618_OCT4_positive

data_processing:
Data processing was conducted using the RNAi Gene Enrichment Ranking (RIGER) algorithm (Luo B et al. Highly parallel identification of essential genes in cancer cells. Proc. Natl. Acad. Sci. USA, 105, 20380–20385)
Supplementary files format and content: xlsx files containg the enrichment score (ES), normalized enrichment score (NES), p value, and average fold change (avgFC) for each gene.
Library strategy: CRISPR Screen

source_name: induced from hADSC

extract_protocol:
OCT4 positive or negative cells were sorted by FACS, and genome DNAs were isolated with TIANamp FFPE DNA kit (DP331-02)
A two-step PCR method was used to build the library. The first step is to obtain the target fragment through PCR. After amplification, each reaction section is merged and enriched, and purified using magnetic beads; The second step of PCR is to amplify the purified PCR product 15ul with a primer (index). After the two-step PCR is completed, magnetic beads are used for recycling to obtain a single target band. After purification, the library was subjected to agarose electrophoresis to confirm the bands (fragment size of about 280bp), quantified using Qubit, and diluted to 3ng/ul. The library was then placed on the machine according to the QC standard of the library.

value: induced from hADSC

value: OCT4-positive cells after chemical reprogramiming


title: EPS_1h_rep1

description:
Library name: Sample31
ActD_EPSC_PrEdiff_raw_count.csv


title: diffTBLC_siIgf2bp3_1h_rep1

description:
Library name: Sample55
diffTBLC_siIgf2bp3-1-1


title: t_24h_FPL, rep 1

description: Library name: t_24h_FPL1


title: 0618_OCT4_negative

description: Library name: 0681_OCT4_negative

value: OCT4-negative cells after chemical reprogramiming


title: Low-proliferating Leishmania major infected-single cell#18 , Mouse#1_Left ear [1_H2]


title: diffTBLC_siNC2_3h_rep2

description:
Library name: Sample52
diffTBLC_siNC2-2-3

value: Actinomycin D & siNC2


title: diffTBLC_siIgf2bp3_1h_rep2

description:
Library name: Sample56
diffTBLC_siIgf2bp3-2-1


title: Low-proliferating Leishmania major infected-single cell#20 , Mouse#4_Left ear [2_A11]


title: PBMC, Covid Vaccine, Responder 1

description:
Library name: XV127
10X Genomics

value: Peripheral blood

value: PBMC

value: BNT162b2 COVID-19 mRNA

value: Male

value: Responder


title: Low-proliferating Leishmania major infected-single cell#23 , Mouse#3_Right ear [2_A5]

value: monocytes

value: ear tissue

value: 10 weeks old


title: PBMC, Covid Vaccine, Non-responder 1

description:
Library name: XV177
10X Genomics

value: Two vaccine doses

value: Female

value: Non-responder


title: Low-proliferating Leishmania major infected-single cell#21 , Mouse#2_Right ear [2_A2]


title: S3D12

description:
Library name: S3D12
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

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).


title: Low-proliferating Leishmania major infected-single cell#19 , Mouse#3_Left ear [2_A10]


title: S_KO_rep2

city: Wuhan

first: Yihao

last: Zhou

state: Hubei

address: Luojiashan Road

department: College of Life Sciences

institute: Wuhan university

description: Library name: Sample_6

data_processing:
RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
bcl2fastq2 Conversion Software v2.19 for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to(ensembl_106_mus_musculus_grcm39_primary) whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: ensembl_106_mus_musculus_grcm39_primary
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 1°C).

extract_protocol:
RNA was harvested using Trizol reagent. 0.2 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were fasted for 16 hours  with free access to water supplemented with or without serine

value: liver

value: GapAlb KO

value: Fasting 16h+5%serine in drinking water


title: S_KO_rep1

description: Library name: Sample_5


title: S2D8

description:
Library name: S2D8
10x Genomics

value: induced from hADSC


title: Low-proliferating Leishmania major infected-single cell#17 , Mouse#2_Left ear [1_F8]


title: diffTBLC_siIgf2bp3_0h_rep1

description:
Library name: Sample53
diffTBLC_siIgf2bp3-1-0

value: TBLC cultured in SLM for 3 days

value: Actinomycin D & siIgf2bp3


title: t_24h_Carrier, rep 2

description: Library name: t_24h_Carrier2

value: murine naive CD8+ isolated from spleen

value: murine naive CD8+

value: plate-bound CD3/CD28+carrier


title: Low-proliferating Leishmania major infected-single cell#15 , Mouse#2_Left ear [1_E8]


title: CT_WT_rep2

description: Library name: Sample_2

value: Gapfl

value: Fasting 16h+drinking water


title: diffTBLC_siIgf2bp3_0h_rep2

description:
Library name: Sample54
diffTBLC_siIgf2bp3-2-0


title: CT_KO_rep1

description: Library name: Sample_3


title: diffTBLC_siNC2_2h_rep1

description:
Library name: Sample49
diffTBLC_siNC2-1-2

value: Actinomycin D & siNC2


title: Low-proliferating Leishmania major infected-single cell#24 , Mouse#5_Left ear [2_B12]

value: monocytes

value: ear tissue


title: S3D4

description:
Library name: S3D4
10x Genomics


title: Low-proliferating Leishmania major infected-single cell#16 , Mouse#2_Left ear [1_F1]

value: 10 weeks old


title: PBMC, Covid Vaccine, Non-responder 2

description:
Library name: XV229
10X Genomics

value: Peripheral blood

value: PBMC

value: Two vaccine doses

value: BNT162b2 COVID-19 mRNA

value: Male


title: diffTBLC_siNC2_2h_rep2

description:
Library name: Sample50
diffTBLC_siNC2-2-2


title: diffTBLC_siNC2_1h_rep1

description:
Library name: Sample47
diffTBLC_siNC2-1-1


title: S2D4

description:
Library name: S2D4
10x Genomics

value: induced from hADSC


title: Low-proliferating Leishmania major infected-single cell#12 , Mouse#1_Right ear [1_D3]


title: diffTBLC_siNC2_1h_rep2

description:
Library name: Sample48
diffTBLC_siNC2-2-1

value: TBLC cultured in SLM for 3 days


title: Low-proliferating Leishmania major infected-single cell#13 , Mouse#1_Right ear [1_D6]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: diffTBLC_siNC2_3h_rep1

description:
Library name: Sample51
diffTBLC_siNC2-1-3


title: CT_KO_rep2

description: Library name: Sample_4

value: liver

value: GapAlb KO


title: CT_WT_rep1

description: Library name: Sample_1


title: S1D2

description:
Library name: S1D2
10x Genomics


title: diffTBLC_siVirma_rep1

description:
Library name: Sample11
siNC_siMettl3_siVirma_raw_count.csv

value: siVirma


title: S1D12

description:
Library name: S1D12
10x Genomics


title: Low-proliferating Leishmania major infected-single cell#11 , Mouse#3_Right ear [1_D10]


title: S1D4

description:
Library name: S1D4
10x Genomics


title: diffTBLC_siMettl3_rep2

description:
Library name: Sample10
siNC_siMettl3_siVirma_raw_count.csv


title: Low-proliferating Leishmania major infected-single cell#14 , Mouse#3_Right ear [1_E10]


title: ENDO_sample136

city: Berne

first: Lea

last: Duempelmann

address: Murtenstrasse 35

department: DBMR

country: Switzerland

institute: University of Berne

data_processing:
The workflow was embedded in the workflow management engine Snakemake (Köster and Rahmann, 2012) for automation and to ensure reproducibility. The software MultiQC (Ewels et al., 2016) was used for the quality control of the raw reads. Gene indexing, cell debarcoding, deduplication, read mapping, and estimation of transcript-level expression by pseudo-alignment were performed with the Salmon software package AlevinQC (Srivastava et al., 2019). The Seurat (Satija et al., 2015) and scater (McCarthy et al., 2017) packages were used to perform quality control and visualization of the data on the sample-, cell- and gene-level. Included are the detection and removal of outlier cells based on transcript and gene metrics, detection of possible doublet cells, and batch effects. Samples not fulfilling the following quality criteria were excluded: median cell-wise mitochondrial expression < 30%, median number of genes per cell > 1000, and median number of unique transcripts per cell > 1000. Dimension reduction was done by selecting the 3000 highly variable genes that account for the most variation in a cell population.
Assembly: hg38 / GRCh38
Supplementary files format and content: Seurat object of the endometrial single-cell atlas encompassing all samples

source_name: endometrial biopsy

extract_protocol:
An endometrial biopsy was obtained from each study participant using Pipelle-de-Cornier (Laboratoire CCD, 1103000) just before their laparoscopy. After removal from the uterus, endometrial biopsies were immediately processed into single-cell suspensions and cryopreserved. Briefly, each endometrial biopsy was washed twice in PBS, cut into small pieces with a scalpel and digested in 5 ml of IMDM (Gibco, 31980022) supplemented with 1 mg ml-1 Collagenase type I-A (Sigma-Aldrich, C2674) and 1 mg ml-1 Collagenase type II (Worthington, LS004174) at 37°C for 30-60 minutes. During digestion, the tissue containing tube was inverted several times every 10 minutes until tissue pieces appeared visually dissociated. Enzymatic dissociation was terminated by addition of 5 ml 4°C PBS. Cells were mechanically dissociated in a gentleMACS™ C Tube (Miltenyi Biotec, 130-093-237) using the gentleMACS™ Dissociator (Miltenyi Biotec, 130-093-235), with the Program mLung 02.01. The resulting cell suspension was filtered through a 100µm and 40µm strainer (Corning, 352340 and 352360) and rinsed with an additional 30 ml 4°C PBS. To remove red blood cells, cell suspension was pelleted by centrifugation (300g, 10 min), suspended in 6 ml of 1x red cell lysis buffer (Invitrogen, 00-4300-54) and incubated for 5 min at room temperature. The lysis was stopped by the addition of 35 ml 4°C PBS and endometrial cells were filtered using a 20µm strainer (pluriSelect, 43-50020-01). Following centrifugation (300g, 10 min), the cells were cryopreserved in 90% FCS (Sigma-Aldrich, F7524), 10% DMSO  (Sigma-Aldrich, D8418), frozen in a Bicell freezing vessel (Nihon Freezer, 1-6263-01) at -80°C and subsequently stored long term in liquid nitrogen.
Selected endometrial single-cell aliquots for 10x capture were thawed in a 37°C water bath and suspended in 37°C IMDM supplemented with 10% FCS. After centrifugation (300g, 5 min), cell suspension was washed with 4°C PBS + 0.2% BSA (Sigma, A4503). After centrifugation (300g, 5 min), the cell pellet was carefully resuspended in 4°C PBS + 0.2% BSA) to a concentration of  ~1*10^6 cells ml-1 and  strained using a 35µm nylon mesh (Corning, 352235) or a 40µm Flowmi cell strainer (Sigma-Aldrich, BAH136800040) to ensure the absence of cell aggregates. Cell concentration and viability (propidium iodide-negative population) was measured after 5 min incubation of cell aliquot in 2 µg ml-1 propidium iodide (Sigma, 81845) using the portable flow cytometer Moxi Flow (ORFLO Technologies, cassette Typ MF-M, MXC021). Only samples with a post-thawing viability of >70% were included for single-cell capture.  Single-cell capture and cDNA library generation were performed with the 10x Genomics Chromium Single Cell Gene Expression workflow (Chromium NextGEM Single Cell 5' Library and Gel Bead Kit v1.1, Chromium Controller). 25000 viable cells per sample were captured in a single reaction. cDNA libraries were balanced by shallow iSeq and sequenced with a NovaSeq 6000 System (Illumina, S4, 2 x 100 cycles).

value: endometrial biopsy

tag: endometriosis status

value: Endometriosis

tag: endometriosis grade

value: severe-ENDO

value: female


title: diffTBLC_siNC2_0h_rep2

description:
Library name: Sample46
diffTBLC_siNC2-2-0

tag: cell type

value: Actinomycin D & siNC2


title: diffTBLC_siVirma_3h_rep2

description:
Library name: Sample44
diffTBLC_siVirma-2-3

value: Actinomycin D & siVirma


title: diffTBLC_siVirma_rep2

description:
Library name: Sample12
siNC_siMettl3_siVirma_raw_count.csv


title: ENDO_sample135

tag: tissue


title: diffTBLC_siMettl3_rep1

description:
Library name: Sample9
siNC_siMettl3_siVirma_raw_count.csv


title: Low-proliferating Leishmania major infected-single cell#10 , Mouse#2_Left ear [1_C8]

value: monocytes

value: ear tissue

tag: strain

value: 10 weeks old


title: Low-proliferating Leishmania major infected-single cell#9 , Mouse#1_Left ear [1_C7]

tag: age


title: diffTBLC_siNC2_0h_rep1

description:
Library name: Sample45
diffTBLC_siNC2-1-0

tag: treatment


title: ENDO_sample134

value: mild-ENDO


title: diffTBLC_siVirma_3h_rep1

description:
Library name: Sample43
diffTBLC_siVirma-1-3

tag: time


title: diffTBLC_siNC_rep2

description:
Library name: Sample8
siNC_siMettl3_siVirma_raw_count.csv

value: siNC


title: diffTBLC_siVirma_2h_rep1

description:
Library name: Sample41
diffTBLC_siVirma-1-2


title: ENDO_sample132


title: Low-proliferating Leishmania major infected-single cell#8 , Mouse#5_Left ear [1_C12]


title: Low-proliferating Leishmania major infected-single cell#7 , Mouse#3_Right ear [1_C10]


title: CTL_sample133

value: No Endometriosis

value: non-ENDO


title: Low-proliferating Leishmania major infected-single cell#6 , Mouse#3_Right ear [1_B5]


title: diffTBLC_siVirma_2h_rep2

description:
Library name: Sample42
diffTBLC_siVirma-2-2

value: TBLC cultured in SLM for 3 days


title: TBLC_rep2

description:
Library name: Sample6
TBLC_PrE-T_EPI_T_raw_count.csv

source_name: TBLC cultured in 2MYCP medium

value: TBLC cultured in 2MYCP medium


title: TBLC_rep1

description:
Library name: Sample5
TBLC_PrE-T_EPI_T_raw_count.csv


title: ENDO_sample130


title: Low-proliferating Leishmania major infected-single cell#5 , Mouse#1_Left ear [1_B3]


title: diffTBLC_siVirma_1h_rep1

description:
Library name: Sample39
diffTBLC_siVirma-1-1


title: PrE-T_rep2

description:
Library name: Sample4
TBLC_PrE-T_EPI_T_raw_count.csv

value: CD140+ cells


title: diffTBLC_siVirma_1h_rep2

description:
Library name: Sample40
diffTBLC_siVirma-2-1


title: Low-proliferating Leishmania major infected-single cell#4 , Mouse#4_Left ear [1_B2]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: diffTBLC_siNC_rep1

description:
Library name: Sample7
siNC_siMettl3_siVirma_raw_count.csv


title: PrE-T_rep1

description:
Library name: Sample3
TBLC_PrE-T_EPI_T_raw_count.csv


title: ENDO_sample128


title: diffTBLC_siNC1_3h_rep2

description:
Library name: Sample36
diffTBLC_siNC1-2-3

value: Actinomycin D & siNC


title: diffTBLC_siVirma_0h_rep1

description:
Library name: Sample37
diffTBLC_siVirma-1-0


title: EPI-T_rep1

description:
Library name: Sample1
TBLC_PrE-T_EPI_T_raw_count.csv

value: CD140- cells


title: Low-proliferating Leishmania major infected-single cell#2 , Mouse#5_Left ear [1_A7]


title: CTL_sample131

value: endometrial biopsy


title: diffTBLC_siVirma_0h_rep2

description:
Library name: Sample38
diffTBLC_siVirma-2-0


title: EPI-T_rep2

description:
Library name: Sample2
TBLC_PrE-T_EPI_T_raw_count.csv


title: High-proliferating Leishmania major infected-single cell#70 , Mouse#1_Right ear [3_H6]


title: ENDO_sample125

value: Endometriosis

value: severe-ENDO


title: diffTBLC_siNC1_3h_rep1

description:
Library name: Sample35
diffTBLC_siNC1-1-3


title: embryoid_EPI_rep5

description:
Library name: Sample27
VE_EPI_raw_count.csv

source_name: Embryoid producted by EPSC and GBL-1

value: Embryoid producted by EPSC and GBL-1


title: Low-proliferating Leishmania major infected-single cell#1 , Mouse#3_Right ear [1_A5]


title: embryoid_EPI_rep6

description:
Library name: Sample28
VE_EPI_raw_count.csv


title: ENDO_sample126

value: female


title: CTL_sample124


title: diffTBLC_siNC1_2h_rep1

description:
Library name: Sample33
diffTBLC_siNC1-1-2


title: ENDO_sample129


title: CTL_sample123


title: Low-proliferating Leishmania major infected-single cell#3 , Mouse#4_Left ear [1_B11]

value: monocytes


title: diffTBLC_siNC1_2h_rep2

description:
Library name: Sample34
diffTBLC_siNC1-2-2


title: ENDO_sample127


title: ENDO_sample122


title: High-proliferating Leishmania major infected-single cell#69 , Mouse#4_Left ear [3_H10]

value: ear tissue


title: embryoid_EPI_rep4

description:
Library name: Sample26
VE_EPI_raw_count.csv


title: High-proliferating Leishmania major infected-single cell#65 , Mouse#1_Right ear [3_G12]

value: 10 weeks old


title: diffTBLC_siNC1_0h_rep2

description:
Library name: Sample30
diffTBLC_siNC1-2-0


title: diffTBLC_siNC1_1h_rep2

description:
Library name: Sample32
diffTBLC_siNC1-2-1


title: High-proliferating Leishmania major infected-single cell#68 , Mouse#3_Right ear [3_G9]


title: High-proliferating Leishmania major infected-single cell#67 , Mouse#1_Left ear [3_G7]


title: diffTBLC_siNC1_0h_rep1

description:
Library name: Sample29
diffTBLC_siNC1-1-0


title: embryoid_VE_rep5

description:
Library name: Sample21
VE_EPI_raw_count.csv


title: embryoid_EPI_rep3

description:
Library name: Sample25
VE_EPI_raw_count.csv


title: diffTBLC_siNC1_1h_rep1

description:
Library name: Sample31
diffTBLC_siNC1-1-1


title: High-proliferating Leishmania major infected-single cell#66 , Mouse#1_Left ear [3_G2]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: embryoid_EPI_rep2

description:
Library name: Sample24
VE_EPI_raw_count.csv


title: ENDO_sample121

value: mild-ENDO


title: diffTBLC_3h_rep1

description:
Library name: Sample27
diffTBLC_h3-1

value: Actinomycin D


title: ENDO_sample120


title: High-proliferating Leishmania major infected-single cell#62 , Mouse#2_Right ear [3_F3]


title: embryoid_VE_rep4

description:
Library name: Sample20
VE_EPI_raw_count.csv


title: embryoid_EPI_rep1

description:
Library name: Sample23
VE_EPI_raw_count.csv


title: embryoid_VE_rep6

description:
Library name: Sample22
VE_EPI_raw_count.csv


title: ENDO_sample119


title: diffTBLC_2h_rep2

description:
Library name: Sample26
diffTBLC_h2-2


title: CTL_sample117

value: No Endometriosis


title: diffTBLC_3h_rep2

description:
Library name: Sample28
diffTBLC_h3-2


title: High-proliferating Leishmania major infected-single cell#63 , Mouse#1_Left ear [3_F7]


title: High-proliferating Leishmania major infected-single cell#61 , Mouse#2_Right ear [3_E3]


title: diffTBLC_2h_rep1

description:
Library name: Sample25
diffTBLC_h2-1


title: CTL_sample116

value: non-ENDO


title: embryoid_VE_rep3

description:
Library name: Sample19
VE_EPI_raw_count.csv


title: embryoid_VE_rep2

description:
Library name: Sample18
VE_EPI_raw_count.csv


title: High-proliferating Leishmania major infected-single cell#60 , Mouse#5_Left ear [3_E12]


title: High-proliferating Leishmania major infected-single cell#64 , Mouse#1_Right ear [3_F8]


title: High-proliferating Leishmania major infected-single cell#58 , Mouse#4_Left ear [3_E1]


title: CTL_sample113


title: diffTBLC_1h_rep1

description:
Library name: Sample23
diffTBLC_h1-1

value: TBLC cultured in SLM for 3 days


title: PrE-E_rep2

description:
Library name: Sample14
PrE-E_EPI-E_raw_count.csv

value: EPSC cultured in PrE-induce medium


title: CTL_sample114


title: CTL_sample112


title: EPI-E_rep2

description:
Library name: Sample16
PrE-E_EPI-E_raw_count.csv


title: EPI-E_rep1

description:
Library name: Sample15
PrE-E_EPI-E_raw_count.csv


title: High-proliferating Leishmania major infected-single cell#56 , Mouse#4_Right ear [3_D11]


title: High-proliferating Leishmania major infected-single cell#55 , Mouse#3_Right ear [3_D10]


title: embryoid_VE_rep1

description:
Library name: Sample17
VE_EPI_raw_count.csv


title: TBLC_3h_rep2

description:
Library name: Sample20
TBLC_h3-2

value: TBLC cultured in 2MYCP medium


title: High-proliferating Leishmania major infected-single cell#59 , Mouse#3_Right ear [3_E10]


title: ENDO_sample111


title: diffTBLC_0h_rep2

description:
Library name: Sample22
diffTBLC_h0-2


title: CTL_sample118


title: CTL_sample115


title: PrE-E_rep1

description:
Library name: Sample13
PrE-E_EPI-E_raw_count.csv


title: diffTBLC_0h_rep1

description:
Library name: Sample21
diffTBLC_h0-1


title: PrEdiff_siIgf2bp3_rep1

description:
Library name: Sample11
siIgf2bp3_raw_count.csv

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 platform (Shanghai Jiema).


title: CTL_sample110


title: PrEdiff_siIgf2bp3_rep2

description:
Library name: Sample12
siIgf2bp3_raw_count.csv


title: ENDO_sample108


title: TBLC_3h_rep1

description:
Library name: Sample19
TBLC_h3-1


title: High-proliferating Leishmania major infected-single cell#54 , Mouse#1_Right ear [3_C8]


title: ENDO_sample109


title: PrEdiff_siNC_rep2

description:
Library name: Sample10
siIgf2bp3_raw_count.csv

value: siNC


title: High-proliferating Leishmania major infected-single cell#52 , Mouse#1_Right ear [3_B8]


title: diffTBLC_1h_rep2

description:
Library name: Sample24
diffTBLC_h1-2


title: TBLC_1h_rep2

description:
Library name: Sample16
TBLC_h1-2


title: ENDO_sample107


title: High-proliferating Leishmania major infected-single cell#53 , Mouse#3_Right ear [3_C10]


title: High-proliferating Leishmania major infected-single cell#51 , Mouse#4_Right ear [3_B6]


title: High-proliferating Leishmania major infected-single cell#50 , Mouse#2_Right ear [3_B1]


title: PrEdiff_Mettl3_cKO_rep1

description:
Library name: Sample7
Mettl3_cKO_raw_count.csv


title: PrEdiff_Mettl3_cKO_rep2

description:
Library name: Sample8
Mettl3_cKO_raw_count.csv


title: TBLC_2h_rep2

description:
Library name: Sample18
TBLC_h2-2


title: TBLC_0h_rep2

description:
Library name: Sample14
TBLC_h0-2


title: ENDO_sample105


title: PrEdiff_siNC_rep1

description:
Library name: Sample9
siIgf2bp3_raw_count.csv


title: TBLC_1h_rep1

description:
Library name: Sample15
TBLC_h1-1


title: High-proliferating Leishmania major infected-single cell#57 , Mouse#2_Right ear [3_D3]

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz


title: TBLC_2h_rep1

description:
Library name: Sample17
TBLC_h2-1


title: PrEdiff_Mettl3_WT_rep2

description:
Library name: Sample6
Mettl3_cKO_raw_count.csv

value: WT


title: snRNA-seq on P21 V1 from DR astrocyte GR-Con animal, replicate 1

city: Boston

first: Bruno

last: Gegenhuber

state: Massachusetts

address: 220 Longwood Ave

department: Neuroscience

institute: Harvard Medical School

description: Library name: P21_DR_GRCon_R1

data_processing:
Reads were demultiplexed and aligned to the reference genome using cellranger (v8.0.1) count.
Gene expression matrices were constructed using cellranger (v8.0.1) software.
Predicted doublets and low-quality nuclei were removed using Seurat (v5.3.0).
Assembly: mm10
Supplementary files format and content: Matrix.mtx.gz file contains the gene x cell matrix for all samples. Barcodes.tsv.gz file contains the cell barcodes. Features.tsv.gz file contains the gene names. metadata.tsv.gz file contains the corresponding metadata for each cell.

molecule: nuclear RNA

growth_protocol: P21 GRfl/fl animals injected at birth with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-CAAX-4x6T-WPRE (GR-Con) or AAV2/5-GfaABC1D-Cre-T2A-EGFP-CAAX-4x6T-WPRE (GR-KO).

extract_protocol:
Sections of 1 mm spanning V1 were collected in an adult mouse brain matrix (Alto) on ice, and V1 was microdissected. Tissue samples were immediately flash-frozen in a dry ice ethanol bath and stored at -80°C prior to nuclei extraction. V1 tissue was transferred to a 1.5 mL tube containing 350 μL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH pH 7.8 supplemented with 1X PIC, 1 mM DTT, 0.15 mM spermine and 0.5 mM spermidine). 1 U/μL (snRNA-seq) of Protector RNase inhibitor (Sigma) was added. The tissue was dounced in a 2 mL glass homogenizer (Sigma D8938) with a loose pestle for 20 strokes. Samples were supplemented with 0.3% IGEPAL CA-630 and further dounced for an additional 10 strokes with a tight pestle. Homogenate was filtered through a small 40-μm strainer (pluriSelect 43-10040-50) into a 1.5 mL tube before diluting 1:1 with homogenization buffer and adding DRAQ5 (Abcam ab108410) at a 1:500 dilution. Nuclei were then sorted by DRAQ5 signal using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip into a 1.5 mL tube (precoated with 30% BSA) containing 300 μL of cold ATAC-RSB supplemented with 1 mM DTT, 1 U/μL Protector RNase inhibitor, and 1% BSA (Sigma A8577-10mL). After collection, nuclei were centrifuged two times at 200g for 2 min in a swinging-bucket centrifuge at 4°C. The supernatant was then carefully aspirated from the surface of the liquid until approximately 40 μL remained.
snRNA-seq libraries were prepared with the 10X Genomics Single Cell 3’ Gene Expression Kit v4 (PN-1000686), following the manufacturer’s instructions.

treatment_protocol: DR or NR

value: GR-Con

value: DR


title: High-proliferating Leishmania major infected-single cell#48 , Mouse#4_Left ear [3_A11]


title: CTL_sample104

value: endometrial biopsy


title: High-proliferating Leishmania major infected-single cell#46 , Mouse#1_Right ear [2_H6]


title: snRNA-seq on P21 V1 from DR astrocyte GR-KO animal, replicate 2

description: Library name: P21_DR_GRKO_R2

value: GR-KO


title: High-proliferating Leishmania major infected-single cell#49 , Mouse#1_Right ear [3_A7]


title: High-proliferating Leishmania major infected-single cell#44 , Mouse#1_Right ear [2_H12]


title: ENDO_sample99

value: Endometriosis

value: severe-ENDO

value: female


title: ENDO_sample100


title: ENDO_sample106


title: snRNA-seq on P21 V1 from NR astrocyte GR-Con animal, replicate 2

description: Library name: P21_NR_GRCon_R2

value: NR


title: TBLC_0h_rep1

description:
Library name: Sample13
TBLC_h0-1


title: TBLC_GLORI_siVirma_rep2

description: Library name: Sample4

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

source_name: TBLC cultured in MYCP 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.
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: TBLC cultured in MYCP medium

value: siVirma


title: High-proliferating Leishmania major infected-single cell#45 , Mouse#3_Right ear [2_H4]

value: monocytes

value: ear tissue

value: 10 weeks old


title: High-proliferating Leishmania major infected-single cell#42 , Mouse#5_Left ear [2_F2]


title: PrEdiff_Mettl3_WT_rep1

description:
Library name: Sample5
Mettl3_cKO_raw_count.csv

value: EPSC cultured in PrE-induce medium


title: CTL_sample95

value: No Endometriosis

value: non-ENDO


title: snRNA-seq on P21 V1 from NR astrocyte GR-KO animal, replicate 1

description: Library name: P21_NR_GRKO_R1


title: High-proliferating Leishmania major infected-single cell#41 , Mouse#2_Left ear [2_F1]


title: ENDO_sample103

value: mild-ENDO


title: snRNA-seq on P21 V1 from DR astrocyte GR-Con animal, replicate 2

description: Library name: P21_DR_GRCon_R2

value: GR-Con


title: ENDO_sample101


title: TBLC_GLORI_siNC_rep2

description: Library name: Sample2

value: siNC


title: CTL_sample96

value: endometrial biopsy


title: PrEdiff_Virma_cKO_rep2

description:
Library name: Sample4
Virma_cKO_raw_count.csv


title: High-proliferating Leishmania major infected-single cell#39 , Mouse#1_Right ear [2_E6]


title: High-proliferating Leishmania major infected-single cell#43 , Mouse#1_Right ear [2_G12]


title: PrEdiff_Virma_WT_rep1

description:
Library name: Sample1
Virma_cKO_raw_count.csv

value: WT


title: High-proliferating Leishmania major infected-single cell#47 , Mouse#3_Right ear [3_A10]


title: CTL_sample88


title: miR_Cer_4, miR146a KO pancreas, Cerulein, replicate 4

city: Adelaide

first: Kristen

last: Feher

address: North Terrace

country: Australia

institute: SAiGENCI

description: Library name: 24-05836

data_processing:
RNA-seq libraries were sequenced on the DNBSEQ G400 FCL platform to produce 100bp long paired end reads.
Reads are trimmed using "fastp --detect_adapter_for_pe -- cut_tail --correction -- overrepresentation analysis --dedup"
Trimmed reads are aligned to genome using STAR aligner and read counts are extracted
Assembly: GRCm39
Supplementary files format and content: Tab delimited text files with CPM values of filtered genes for each sample

source_name: Pancreas

growth_protocol: Age-matched (6-8 weeks old) littermates of wild-type (WT) and miR146a knockout (KO) mice were used for experimentation. Mice were housed under specific pathogen-free conditions. Experiments were approved by the Adelaide University Animal Ethics Committee.

extract_protocol:
Total RNA was isolated from snap-frozen mouse pancreatic tissues using TRIzol (Sigma).
Libraries were generated using stranded polyA libraries prepared using Nugen Universal Plus mRNA-seq (Part No. 0508), protocol M01442 v2 at South Australian Genomics Centre (SAGC), Adelaide, Australia. PE100 sequencing (R1 – 98; R2 – 98; Barcode – 16; Dual Barcode – 8) was done using MGI DNBSEQ G400 FCL PE100 chemistry..

treatment_protocol: The cerulein-induced mouse model of AP was established via intraperitoneal (IP) injections (1 injection per hour for 7 hours) of cerulein (50 μg/kg; Sigma, USA) or phosphate-buffered saline (PBS; 50 μl, as a control). Mice were humanely culled one hour after the last injection.

value: Pancreas

value: miR146a KO

value: Cerulein


title: snRNA-seq on P21 V1 from DR astrocyte GR-KO animal, replicate 1

description: Library name: P21_DR_GRKO_R1

value: GR-KO

value: DR


title: High-proliferating Leishmania major infected-single cell#38 , Mouse#4_Left ear [2_E5]


title: PrEdiff_Virma_WT_rep2

description:
Library name: Sample2
Virma_cKO_raw_count.csv


title: CTL_sample87

value: female


title: High-proliferating Leishmania major infected-single cell#37 , Mouse#4_Right ear [2_E11]

value: monocytes


title: TBLC_GLORI_siVirma_rep1

description: Library name: Sample3

value: TBLC cultured in MYCP medium

value: siVirma


title: PrEdiff_Virma_cKO_rep1

description:
Library name: Sample3
Virma_cKO_raw_count.csv

value: EPSC cultured in PrE-induce medium


title: E16.5 wound, day 3 after wounding, injected with AAV-tdTomato, AAV-negative cells, rep 2

first: Hannah

middle: T

last: Tam

state: MA

address: 7 Divinity Avenue

department: SCRB

institute: Harvard University

description: 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: Wounded, injected with AAV


title: snRNA-seq on P21 V1 from NR astrocyte GR-KO animal, replicate 2

description: Library name: P21_NR_GRKO_R2

value: NR


title: snRNA-seq on P21 V1 from NR astrocyte GR-Con animal, replicate 1

description: Library name: P21_NR_GRCon_R1

value: GR-Con


title: ENDO_sample94

value: Endometriosis

value: severe-ENDO


title: TBLC_GLORI_siNC_rep1

description: Library name: Sample1

value: siNC


title: E16.5 wound, day 3 after wounding, injected with AAV-tdTomato, AAV-positive cells, rep 2

description: 10X Genomics

value: WT


title: High-proliferating Leishmania major infected-single cell#40 , Mouse#1_Left ear [2_E7]

value: ear tissue

value: 10 weeks old


title: miR_Cer_3, miR146a KO pancreas, Cerulein, replicate 3

description: Library name: 24-05835

value: Pancreas

value: miR146a KO

value: Cerulein


title: miR_Cer_2, miR146a KO pancreas, Cerulein, replicate 2

description: Library name: 24-05834


title: E16.5 wound, day 3 after wounding, injected with AAV-tdTomato, AAV-negative cells, rep 1

description: 10X Genomics


title: ENDO_sample102

value: endometrial biopsy

value: mild-ENDO

value: female


title: ENDO_sample91


title: ENDO_sample86


title: E16.5 wound, day 3 after wounding, injected with AAV-tdTomato, AAV-positive cells, rep 1

description: 10X Genomics


title: High-proliferating Leishmania major infected-single cell#36 , Mouse#4_Right ear [2_D11]

value: monocytes


title: miR_PBS_5, miR146a KO pancreas, PBS, replicate 5

description: Library name: 24-05832

value: PBS


title: High-proliferating Leishmania major infected-single cell#35 , Mouse#4_Right ear [2_C2]


title: ENDO_sample84


title: P0 unwounded, rep 2

description: 10X Genomics

value: Skin

value: Unwounded


title: ENDO_sample83


title: P0 unwounded, rep 1

description: 10X Genomics


title: miR_PBS_3, miR146a KO pancreas, PBS, replicate 3

description: Library name: 24-05830


title: High-proliferating Leishmania major infected-single cell#34 , Mouse#1_Left ear [2_C1]


title: miR_Cer_1, miR146a KO pancreas, Cerulein, replicate 1

description: Library name: 24-05833


title: miR_Cer_5, miR146a KO pancreas, Cerulein, replicate 5

description: Library name: 24-05837


title: CTL_sample82

value: No Endometriosis

value: non-ENDO


title: ENDO_sample85

value: Endometriosis


title: High-proliferating Leishmania major infected-single cell#33 , Mouse#2_Right ear [2_B9]


title: High-proliferating Leishmania major infected-single cell#32 , Mouse#4_Left ear [2_B2]


title: E16.5 wound, day 3 after wounding, rep 1

description: 10X Genomics

value: Wounded


title: High-proliferating Leishmania major infected-single cell#30 , Mouse#2_Right ear [2_A9]


title: E16.5 wound, day 3 after wounding, rep 2

description: 10X Genomics

value: WT


title: WT_Cer_5, WT pancreas, Cerulein, replicate 5

description: Library name: 24-05827


title: WT_Cer_4, WT pancreas, Cerulein, replicate 4

description: Library name: 24-05826


title: WT_Cer_3, WT pancreas, Cerulein, replicate 3

description: Library name: 24-05825


title: miR_PBS_2, miR146a KO pancreas, PBS, replicate 2

description: Library name: 24-05829


title: ENDO_sample76

value: severe-ENDO


title: P8 unwounded, rep 2

description: 10X Genomics


title: CTL_sample77


title: ENDO_sample74


title: High-proliferating Leishmania major infected-single cell#31 , Mouse#3_Left ear [2_B10]

value: ear tissue

value: 10 weeks old


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

description: 10X Genomics


title: ENDO_sample72


title: High-proliferating Leishmania major infected-single cell#29 , Mouse#1_Right ear [2_A8]


title: High-proliferating Leishmania major infected-single cell#26 , Mouse#2_Left ear [2_A4]


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

description: 10X Genomics


title: CTL_sample81


title: High-proliferating Leishmania major infected-single cell#25 , Mouse#1_Right ear [1_H7]


title: WT_PBS_5, WT pancreas, PBS, replicate 5

description: Library name: 24-05822

value: Pancreas


title: CTL_sample73


title: High-proliferating Leishmania major infected-single cell#27 , Mouse#5_Left ear [2_A6]


title: HpNSCs, 10-6 M Dex and 20ng/mL BMP4, rep1

city: Xi 'an

first: Yuan

middle: Jia

last: Lan

state: Shaanxi Province

address: Yanta West Road

institute: The First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
CUT&Tag reads were removed adapter and low-quality reads by trim_galore(v0.6.7).
Clean reads were aligned to the mouse mm10 genome using Hisat2 (v2.1.0) with default parameters.
Gene expression levels were quantified as Fragments Per Kilobase Million (FPKM) using Stringtie (v1.3.6).
Differentially expressed genes (DEGs) were determinedusing the DESeq2 software package (R version: 3.6.1) with a threshold of adjusted p value < 0.05 and an absolute log2 (Fold Change, FC) ≥0.584.
Gene Ontology enrichment analyses of the DEGs were conducted separately using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (v2021) (https://david.ncifcrf.gov), with statistical significance set at P-value < 0.05.
The visualization of results included the generation of volcano plots by the R-ggplot2 package (v3.3.6) and heatmaps using pheatmap (v1.0.12) in R (v3.6.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes FPKM values for each sample

source_name: HpNSC

growth_protocol: HpNSCs were cultured in the proliferation condition containing 1% B27 supplement, 20 ng/ml EGF, 20 ng/ml FGF2 and 1x Penicillin-Streptomycin in DMEM/F12 medium with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using Trizol (TAKARA), 2ug of total RNA was used for the construction of sequencing libraries.
The RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: To assess the roles of Dex and BMP4, 10-6 M Dex or/and 20 ng/mL BMP4 was added to DMEM/F12 medium containing 1% N2 supplement, 20 ng/mL FGF2 and 1x penicillin-streptomycin for 3 days.

tag: cell line

value: HpNSC

value: Neural stem cell

value: 10-6 M Dex and 20ng/mL BMP4, 3 days


title: miR_PBS_4, miR146a KO pancreas, PBS, replicate 4

description: Library name: 24-05831

value: miR146a KO


title: miR_PBS_1, miR146a KO pancreas, PBS, replicate 1

description: Library name: 24-05828


title: CTL_sample71

value: endometrial biopsy

value: female


title: P8 unwounded, rep 1

description: 10X Genomics

value: Skin


title: HpNSCs, 20ng/mL BMP4, rep3

value: 20ng/mL BMP4, 3 days


title: WT_Cer_2, WT pancreas, Cerulein, replicate 2

description: Library name: 24-05824

value: Cerulein


title: High-proliferating Leishmania major infected-single cell#28 , Mouse#1_Right ear [2_A7]

value: monocytes


title: HpNSCs, 10-6 M Dex and 20ng/mL BMP4, rep2


title: High-proliferating Leishmania major infected-single cell#24 , Mouse#2_Left ear [1_H3]


title: ENDO_sample75

value: Endometriosis


title: WT_PBS_3, WT pancreas, PBS, replicate 3

description: Library name: 24-05820

value: PBS


title: CTL_sample65

value: No Endometriosis

value: non-ENDO


title: WT_PBS_2, WT pancreas, PBS, replicate 2

description: Library name: 24-05819

value: WT


title: WT_Cer_1, WT pancreas, Cerulein, replicate 1

description: Library name: 24-05823


title: CTL_sample64


title: High-proliferating Leishmania major infected-single cell#23 , Mouse#1_Right ear [1_H12]

value: ear tissue

value: 10 weeks old


title: HpNSCs, 20ng/mL BMP4, rep1

value: HpNSC


title: HpNSCs, 10-6 M Dex and 20ng/mL BMP4, rep3

value: Neural stem cell


title: CTL_sample70


title: WT_PBS_4, WT pancreas, PBS, replicate 4

description: Library name: 24-05821

value: Pancreas


title: HepAD38 (Tet-), ZNF638

first: Sifan

last: Meng

address: Beijing

institute: Capital Medical University

data_processing:
Sequence were multiplexed and sequenced with 2× 50-bp pair-end reads on Illumina Novaseq platform
Assembly: hg38 with HBV genome
Supplementary files format and content: bed

growth_protocol: DMEM，10%FBS，1%P/S，cells were cultured at 37 with 5% CO2

extract_protocol:
cells were fixed with 1% formaldehyde at 37 °C for 20min.After cell lysis and separation, use ultrasound to break chromatin.
ChIP-seq was subjected to library preparation (VAHTS Universal Pro DNA Library Prep Kit for Illumina.

value: HBV integrated cell line

tag: chip antibody


title: High-proliferating Leishmania major infected-single cell#19 , Mouse#3_Right ear [1_G4]

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: WT_PBS_1, WT pancreas, PBS, replicate 1

description: Library name: 24-05818

tag: genotype


title: High-proliferating Leishmania major infected-single cell#18 , Mouse#1_Right ear [1_G12]


title: High-proliferating Leishmania major infected-single cell#21 , Mouse#2_Left ear [1_G8]


title: HpNSCs, 20ng/mL BMP4, rep2


title: HepAD38 (Tet+), MPP8


title: High-proliferating Leishmania major infected-single cell#17 , Mouse#4_Right ear [1_G11]


title: HepAD38 (Tet+), ZNF638


title: High-proliferating Leishmania major infected-single cell#22 , Mouse#4_Right ear [1_H11]


title: HpNSCs, no treatment, rep2

value: No treatment, 3 days


title: HpNSCs, 10-6 M Dex, rep2

value: 10-6 M Dex, 3 days


title: High-proliferating Leishmania major infected-single cell#20 , Mouse#1_Right ear [1_G7]


title: HepAD38 (Tet-), Input


title: HepAD38 (Tet-), MPP8


title: HpNSCs, 10-6 M Dex, rep3


title: High-proliferating Leishmania major infected-single cell#16 , Mouse#1_Left ear [1_F7]


title: HpNSCs, 10-6 M Dex, rep1


title: HpNSCs, no treatment, rep1


title: High-proliferating Leishmania major infected-single cell#14 , Mouse#3_Right ear [1_F4]


title: 3T3-L1 cells, 6 day-2

city: Shanghai

first: Xuyun

last: Zhao

state: Shanghai

address: South Chongqing Road

department: Medical school

institute: Shanghai Jiaotong University

description: 3T3L1 day 0 and day6.xlsx

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: embryo

growth_protocol: Cells were maintained in DMEM growth medium supplemented with 10% fetal bovine serum (FBS) and antibiotics(Penicillin Streptomycin) in humified amosphere with 8% CO2 at 37℃

extract_protocol:
RNA were extracted from cells using  Trizol method.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Two days after the cells confluenced (disignated day 0), adipogenic differentiation was induced by adding an induction medium (DMEM containing 10% FBS, 0.5 mM IBMX, 125 mM indomethacin, 1 mM dexamethasone, 20 nM insulin and 1 nM T3) until day2. Then Cells were switched to differentiation medium (DMEM, 10% FBS, 20 nM insulin and 1 nM T3), and changed fresh differentiation medium every two days.

value: embryo

value: fibroblast

value: adipogenic differentiation


title: HpNSCs, no treatment, rep3


title: High-proliferating Leishmania major infected-single cell#15 , Mouse#4_Left ear [1_F5]

source_name: ear tissue

value: monocytes


title: 3T3-L1 cells, 0 day-3

description: 3T3L1 day 0 and day6.xlsx


title: HepAD38 (Tet+), Input


title: TRA2B siRNA#1

type: RNA

city: Tokushima

first: Yuki

last: Kuwano

country: Japan

institute: Tokushima University

description: miRNA expression in TRA2B siRNA-transfected cells

hyb_protocol: For hybridization, the samples were resuspended in 17 microliters of DEPC-treated water. To each sample, 1 microliter of diluted Hybridization Spike Control, 4.5 mkl of 10X GE Blocking Agent (Agilent Technologies) and 22.5 microliters of 2X HiRPM Hybridization Buffer (Agilent Technologies) were added. The samples were heated to 100oC for 5 minutes and transferred immediately to an ice water bath for 5 minutes. The samples were then loaded onto Human miRNA Microarray (V3, 8x15K array). Hybridization was performed at 55oC for 20 hours.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX11 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: RNA was labeled with Cyanine 3-Cytidine biphosphate (pCp) using the Agilent’s miRNA Complete Labeling and Hybridization Kit (Agilent Technologies).Briefly, 100 ng of total RNA was combined with diluted Labeling Spike In controls. The samples were dephosphorylated using Calf Intestinal Phosphatase at 37oC for 30 minutes, followed by denaturation with 10% DMSO at 100oC for 10 minutes and incubation in an ice water bath. The Cyanine 3-pCp was then ligated onto the miRNA molecule using T4 RNA Ligase at 16oC for 2 hr.

extract_protocol: The total RNA was extracted using RNAiso Plus reagent (Thermo Fisher Scientific) and pulified by miRNeasy Kit (Qiagen).

treatment_protocol: HCT116 cells were transfected with control or TRA2B siRNA (Qiagen) using Lipofectamine RNAiMax (Thermo Fisher Scientific) for 48 hours according to the manufacturer’s protocol.

value: HCT116  cells


title: High-proliferating Leishmania major infected-single cell#13 , Mouse#1_Right ear [1_F12]

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: 3T3-L1 cells, 0 day-2

description: 3T3L1 day 0 and day6.xlsx


title: HpNSCs, GR, CUT&Tag

data_processing:
CUT&Tag reads were removed adapter and low-quality reads by trim_galore(v0.6.7).
The clean reads were mapped onto the reference mouse genome mm10 Peak-calling was performed using MACS2 (v2.1.4) with the following parameters: macs2 callpeak -t aligned.sorted.bam --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B --SPMR.
BigWig files were generated using the bamCoverage command in deeptools
Assembly: mm10
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed using the NovoNGS CUT&Tag 3.0 High-Sensitivity kit (N259-YH01, Novoprotein) according to the manufacturer's instructions. Briefly, 1x105 HpNSCs were harvested, immobilized and permeabilized with NovoNGS ConA Beads. Cells were incubated with GR antibody (Santa Cruz, sc-1004) or IgG control antibody (Millipore, 12-370) overnight at 4 °C, followed by incubation with an unlabeled secondary antibody (Millipore, AP132) for 1 h at room temperature. Subsequently, pAG-Tn5 was added to the samples for 1 h. The cells were then incubated in Tagmentation Buffer at 37 °C for 1 h. DNA fragments were purified with the Tagment DNA Extract Beads.
Libraries were amplified by PCR following the provided cycling conditions by the NovoNGS CUT&Tag 3.0 High-Sensitivity kit. Library quality was assessed using an Agilent Bioanalyzer, and sequencing was performed on an Illumina Novaseq 6000 platform.

treatment_protocol: 10-6 M Dex was added to DMEM/F12 medium containing 1% N2 supplement, 20 ng/mL FGF2 and 1x penicillin-streptomycin for 3 days.

tag: cut&tag antibody

value: Santa Cruz, sc-1004


title: PAR-CLIP_MOV10 - rep2

city: Guangzhou

first: Jinshuai

last: Sun

address: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Illumia bcl2fastq2.17 software was used for basecalling and adapters, reads length shorter than 15 nucleotides and reads with low complexity (< 30%) were removed by FASTP.
Only the Reverse reads were used in the data analysis and uploaded. Bowtie was applied to map sequencing reads against GRCh38 genome with up to two mismatches allowed.
Distribution of aligned reads was calculated according to NCBI with featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph files were generated using using the utility bamCoverage from the bioinformatics suite deeptools v3.5.1.

source_name: HeLa

growth_protocol: HeLa cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, SH30022.01) supplemented with 10% fetal bovine serum (FBS, Natocor, SFBE) and 1× nonessential amino acids.

extract_protocol:
For PAR-CLIP samples, RNA was subsequently purified with acidic phenol:chloroform and ethanol precipitation.
PAR-CLIP DNA library was constructed by a SMART-Seq® Stranded Kit according to the manufacturer’s instructions.
For PAR-CLIP experiment, the final purified library was evaluated using the Agilent 2100 TapeStation and diluted for cluster generation and high-throughput sequencing (2 × 150 bp) on NovaSeq 6000 (Illumina).

treatment_protocol: For PAR-CLIP experiment, eight 10 cm-plates of HeLa cells or HeLa cells stably expressing Flag-tagged RBP candidates were treated with 0.2 mM 4sU for 16 h, followed by washing with prechilled PBS for three times, then irradiated with 365 nm UV light at 0.4 J/cm2. Afterwards, the mitochondria were purified as mentioned above. Then the mitochondrial pellets were lysed, and homogenized by a syringe with narrow needle (29 G), centrifuged at 13,000 g for 15 min at 4 °C. The supernatant was digested with nuclease and then immunoprecipitated using MOV10 antibodies (Proteintech) or FLAG antibody-conjugated magnetic beads (Sigma) for 2 h at 4 °C. After that, beads were collected, washed, and digested with nuclease again, followed by washing with high-salt washing buffer. Then the beads were resuspended and treated with calf intestinal alkaline phosphatase. The resultant protein-RNA complexes were then divided into two portions: one was labelled with biotin according to the instructions of the Chemiluminescent Nucleic Acid Detection Module Kit (Thermo Fisher Scientific) and the other was used for PAR-CLIP sequencing.

value: HeLa

value: Derived from cervical cancer cells

value: Uterus; Cervix

value: mitochondria purified from HeLa cells with 4sU labelling

tag: target

value: pull down mitochondrial RNA


title: PAR-CLIP_MOV10 - rep1


title: control siRNA#1

description: miRNA expression in control siRNA-transfected cells


title: CE1

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimed from 3' and 5' until the final base had  a score >30, using Trimmomatic V0.33, discarding reads left with <20bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using HISAT2 version 2.2.1. Only uniquely mapping reads with at most two mismatches were retained.
To create Cut & Tag coverage plots, the locations of the mapped Cut & Tag-Seq reads were extended to 150bp to represent sequenced fragments, renormalized(to reads per million, rpm) and reformatted in the bed file format.
Peaks were called using MACS2 v2.2.7 with the significance fut-off q-value<=.0.01
bed files were generated using the MACS2
Assembly: mm10
Supplementary files format and content: bed
Library strategy: Cut & Tag

source_name: brown adipose tissue

extract_protocol:
BAC were differentiated and harvested, counted and centrifuged at 600xg for 5 min. 5x104 cells were used for one sample.
experiment was conducted using Commercial Cut & Tag Assay kit (Vazyme, TD903)
Cut&Tag libraries were prepared using CAM from Cut & Tag assay kit (Vazyme, TD903) complemented with  DNA Barcodes  from TruePrep Index Kit (Vazyme, TD-202)

value: BAC-Cre

value: mouse preadipocyte

value: brown adipose tissue

tag: antibody


title: PAR-CLIP_GTPBP6 - rep1


title: CE2


title: 3T3-L1 cells, 6 day-1

description: 3T3L1 day 0 and day6.xlsx

value: WT


title: mitoRICK - EUPD.rep2

data_processing:
Illumia bcl2fastq2.17 software was used for basecalling
Data were aligned to the GRCh38 human genome assembly using hisat2 (v2.1.012) with '--rna-strandness RF'.
Distribution of aligned reads was calculated according to NCBI with featureCounts.
Genome_build: GRCh38 and ERCC
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt file was generated using Samtools and featureCounts script.

extract_protocol:
For mitoRICK samples samples, cells were lysed by 1 ml TRI Reagent, followed by adding 200 μl chloroform with robust vortex for 15 s. The mixture was centrifuged at 12,000 g at 4ºC for 15 min, than the RNA was precipitated with isopropanol at -20ºC for 30 min or overnight. And to facilitate precipitation, glycogen (Roche) was added if necessary.
For mitoRICK RNA and total RNA, EpiTM mini longRNA-seq kit was used for library preparation. In brief, 10 μl IP RNA and 50 ng input RNA were used for library construction, total RNAs were digested by DNase I to remove residual DNAs, and RNAs were fragmented. Then the first cDNA was synthesized based on SMART (Switching Mechanism At the 5' end of RNA Transcript technology).
For mitoRICK and OG2 mESCs experiments, followed by two-round of PCR amplifications and purification, the resultant cDNA library was evaluated using Bioptic Qsep100 Analyzer, and diluted to 500 pM for cluster generation and high-throughput sequencing (2 ×150 bp) on NovaSeq 6000 (Illumina).

treatment_protocol: For the mitoRICK experiment, 120 mg mitochondrial pellet with or without 0.3 mM EU labelling was weighed Every 100 mg of mitochondrial pellet was resuspended with 1 ml lysis buffer [20 mM Tris-HCl pH 7.5, 500 mM LiCl, and 0.5% lithium-dodecylsulfate (LiDS) supplemented with 1× EDTA-free protease inhibitor cocktail (Roche), 200 U ml-1 RNase inhibitor (Thermo Scientific) and 400 U ml-1 DNase I], and placed on ice for 10 min with occasional upside-down mixing. Lysate was homogenized by passing through a syringe with a narrow needle (29G) for 5 times, centrifuged at 12,000 g at 4ºC for 10 min, and then the supernatant was transferred to a new tube. Diluted the supernatant by adding with ten volumes of the prechilled 50 mM Tris-HCl (pH 7.5), and concentrated the mixture using a 15-ml ultrafiltration tube (molecular weight cutoff: 10 KDa) to a final volume of ≤ 1 mL, then repeated dilution and concentration steps. The final concentrate was used for click reaction as previously described. Briefly, click reaction buffer (containing 100 μM Biotin-PEG3-Azide, 0.5 M CuSO4, 2 mM THPTA, 1 mM aminoguanidine, and 5 mM sodium ascorbate stock) was added to the final concentrate and mixed well, the mixture was placed at room temperature with continuously gentle rotation for 2 h. Then the click reaction was quenched by adding with EDTA at a final concentration of 5 mM at room temperature for 5 min. RNA and protein complexes were precipitated with prechilled methanol at -20ºC for 30 min, and then were washed with methanol twice. Resuspended the pellet with suspending buffer [0.5% sodium dodecyl sulfate (SDS), 1 mM EDTA, 1% Brij-97, 150 mM NaCl, 50 mM triethanolamine supplemented with 200 U ml-1 RNase inhibitor], pipetted up and down to completely dissolve the pellet. Centrifuged the mixture at 4,000 g at 4ºC for 10 min. Subsequently, transferred the supernatant to a new tube and took 1% of the supernatant as input for quality control for Western blot or RNA detection. Next the RNA and protein complexes were incubated with streptavidin agarose beads (Thermo) at 4ºC overnight. Then the RNA-bound agarose beads were collected and washed twice with buffer I (2% SDS in PBS), buffer II (8 M urea and 0.25 M NH4HCO3 in water), buffer III (2.5 M NaCl in PBS) and 50 mM Tris-HCl (pH 7.5) in sequential order for 10 min respectively. The resultant proteins or RNA eluted from the beads were prepared for further RNA extraction.

value: mitochondria purified from HeLa cells with EU labelling


title: BAC cells, 4 day-2

description:
Day4-2
BAC day0 and day 4.xlsx

value: BAC

value: preadipocyte


title: VE2

value: BAC-V


title: control siRNA#2


title: High-proliferating Leishmania major infected-single cell#10 , Mouse#1_Left ear [1_D7]

first: Yan

last: Fu

value: ear tissue

value: 10 weeks old


title: TRA2B siRNA#2

value: HCT116  cells


title: mitoRICK - EUPD.rep1


title: HpNSCs, IgG, CUT&Tag

value: HpNSC

value: Neural stem cell

value: Millipore, 12-370


title: PAR-CLIP_GTPBP6 - rep2

value: HeLa

value: Derived from cervical cancer cells

value: Uterus; Cervix


title: BAC cells, 4 day-1

description:
Day4-1
BAC day0 and day 4.xlsx

value: adipogenic differentiation


title: BAC cells, 0 day-2

description:
Day0-2
BAC day0 and day 4.xlsx


title: High-proliferating Leishmania major infected-single cell#12 , Mouse#1_Left ear [1_E7]

value: monocytes


title: VE1

value: mouse preadipocyte

value: brown adipose tissue


title: High-proliferating Leishmania major infected-single cell#9 , Mouse#2_Right ear [1_C4]


title: BAC cells, 0 day-1

description:
Day0-1
BAC day0 and day 4.xlsx

value: WT


title: mitoRICK - EUinput.rep2

value: mitochondria purified from HeLa cells with EU labelling

value: total mitochondrial RNA


title: CH2

value: BAC-Cre


title: High-proliferating Leishmania major infected-single cell#11 , Mouse#4_Left ear [1_E11]

value: ear tissue


title: CH1


title: High-proliferating Leishmania major infected-single cell#8 , Mouse#4_Left ear [1_C11]

value: 10 weeks old


title: mitoRICK - CtrlPD.rep2

value: mitochondria purified from HeLa cells without EU labelling

value: pull down mitochondrial RNA


title: mitoRICK - EUinput.rep1


title: CarS2-AKO, S29BAT-6

description:
CKO3
raw_counts.text

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

extract_protocol:
RNA were extracted from brown adipose tissue using  Trizol method.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: cold tolerance experiment


title: High-proliferating Leishmania major infected-single cell#7 , Mouse#2_Right ear [1_B9]


title: VH1

value: BAC-V


title: mitoRICK - CtrlPD.rep1

value: HeLa


title: WTa_like

first: Lei

last: Gao

address: East Building of Resources, No. 5 Yiheyuan Road, Haidian District, Beijing

description: Library name: T2

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor contamination, low-quality bases, and reads with excessive ambiguous nucleotides, yielding high-quality clean reads. Clean reads were aligned to the Arabidopsis thaliana reference genome using a standard short-read alignment workflow. Based on the alignment results, single-nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels) were identified and annotated using established variant-calling pipelines.Read filtering and quality control. Raw sequencing reads contained adaptor contamination and low-quality bases and were therefore subjected to stringent quality filtering prior to downstream analyses. Read pairs containing adaptor sequences were removed. For each single-end read within a pair, if the proportion of ambiguous nucleotides (N) exceeded 10% of the read length, the entire read pair was discarded. Similarly, read pairs were removed when more than 50% of bases in either read had a quality score ≤ 5. The remaining high-quality reads were retained as clean reads and used for all subsequent analyses.
Assembly: Arabidopsis thaliana Col-0 genome at Tair 10(https://www.arabidopsis.org/) and Sequnceing genome of WT sample
Supplementary files format and content: Delta_All.index.xls

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Genomic DNA was extracted from Arabidopsis thaliana leaves using a standard CTAB protocol with minor modifications. Briefly, frozen leaf tissue (~50–100 mg) was ground in liquid nitrogen and incubated in CTAB extraction buffer (2% CTAB, 100 mM Tris-HCl pH 8.0, 20 mM EDTA, 1.4 M NaCl, 1% PVP-40, and 0.2% β-mercaptoethanol) at 65 °C for 30 min. After chloroform:isoamyl alcohol extraction and isopropanol precipitation, DNA was washed with 70% ethanol, air-dried, dissolved in TE, and treated with RNase A
High-quality genomic DNA was sheared to an average fragment size of ~350 bp using a Covaris ultrasonicator. Sequencing libraries were constructed with the TruSeq DNA Library Preparation Kit following the manufacturer’s instructions and using all recommended reagents and consumables. Briefly, fragmented DNA underwent end repair, A-tailing, and adaptor ligation, followed by bead-based purification. Libraries were enriched by limited-cycle PCR amplification, purified, and assessed for size distribution and concentration prior to sequencing.

value: leaf