title: MV411_KO-539_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 12

value: 21 days of treatment


title: MCF-7 Vehicle 1

status: Public on Nov 30 2025

type: SRA

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

library_source: transcriptomic

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc
The resultant quality controlled fastq files were aligned to the Ensembl annoted Human genome (GRCh38.83) using STAR
Gene expression was quantified using FeatureCounts
Assembly: GRCh38.83
Supplementary files format and content: Tab delimited text file contain gene expression in counts

molecule: total RNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: Cells were maintained at 37C and 5% CO2. MCF-7 were maintained in phenol-red free RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate, and  10% charcoal “depleted” FBS. MDA-MB-231 cells were maintained in in RPMI-1640 medium supplemented with 100 µg/mL penicillin, 100 µg/mL streptomycin, 1 mM sodium pyruvate and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with oncolumn DNase treatment
Illumina

treatment_protocol: MCF-7 cells were either treated with vehicle (DMSO) or estradiol (10nM), alone or in combination with the STM2457 (10µM) METTL3 inhibitor.  MDA-MB-231 cells were treated with either vehicle (DMSO) or STM2457 (10µM). Cells were treated twice over 6 days (day 0 and day 3) and RNA harvested on day 6. The effect on global gene expression and alternative splicing was determined by RNA sequencing.

tag: tissue

value: Cell line

tag: cell line

tag: cell type

value: Breast cancer (ER positive)

tag: treatment

value: Vehicle (DMSO)


title: Duodenum, HFD, KO4

city: Beijing

first: Xiaowei

last: Xing

state: Beijing

address: No.1 Xian Nong Tan St. Xi Cheng District

department: Institute of Materia Medica

country: China

institute: Peking Union Medical College

description: Library name: SAMPLE 13

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Paired-end clean reads were aligned to the reference mouse Ensemble genome GRCm38 using Hisat2 v2.0.5 and counted by featureCounts v1.5.0-p3.
Differential expressed genes were analyzed using the DESeq2 R package (1.20.0). After Benjamini and Hochberg’s approach for controlling the false discovery rate, genes with an adjusted P-value < 0.05 were assigned as differentially expressed.
Assembly: mm10
Supplementary files format and content: Microsoft excel file includes gene counts normalized by DESeq2 for each sample

organism: Mus musculus

source_name: duodenal epithelium

extract_protocol:
Frozen tissues were homogenized and total RNA was extracted by TRIzol method, the integrity was assessed by Bioanalyzer 2100 system.
mRNA was purified using poly-T oligo-attached magnetic beads. NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) was used for library preparation following manufacturer's recommendations.

treatment_protocol: Ephb4 fl/fl and Ephb4-IKO mice were fed with HFD for 19 weeks. Mice were sacrificed and duodenal epithelium were collected, snap frozen in liquid nitrogen and transferred to -80 degree refrigerator.

value: duodenal epithelium

tag: genotype

value: KO

value: fed with HFD for 19 weeks


title: SD.AG43

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

country: USA

institute: University of California Los Angeles

description: Library name: Sample37

data_processing:
Demultiplexed sequence data were imported into QIIME2, and quality filtering was performed using DADA2 to ensure sequence quality. A total of ? reads were obtained from pre-gestational and gestational adult samples, and ? reads from postnatal samples, with an average of ? reads per sample. A feature table and representative sequence table containing amplicon sequence variants (ASVs) were generated, and ASVs with low counts were removed. A rooted phylogenetic tree was constructed to infer evolutionary relationships. Outputs from QIIME2, along with metadata, were imported into R (version 4.2.1).
Assembly: mm10
Supplementary files format and content: Rds file contains abundance counts of amplicon sequence variants (ASVs) across different samples,taxonomic classification table  and sample data
Library strategy: 16S rDNA-seq

molecule: nuclear RNA

source_name: feces

growth_protocol: C57/BL6 strain mice were purchased from Jackson Lab, Bar Harbor, ME. Mice were maintained in 12:12-h light-dark cycles and care/treatment provided according to UCLA Animal Research Committee’s approved protocol

extract_protocol:
Feces were collected from non-pregnant, age-matched females and GD19 pregnant mothers, each housed individually in separate cages. Additionally, feces were collected separately from male and female PN21 pups just before weaning.
DNA was extracted using bead beating and the Qiagen PowerSoil kit. Libraries were prepared following methods adapted from Caporaso et al. The V4 region of the 16S rRNA gene was amplified with barcoded universal primers. PCR products were purified, pooled in equimolar concentrations, and sequenced on the Illumina MiSeq platform with a 2X250 bp reagent kit for paired-end sequencing.

treatment_protocol: study was conducted with a 4-week pre-conceptional exposure to air pollutants, followed by continued exposure during gestation (GD0 to GD18), based on previous research. Mice were exposed every third day, with two exposures per period under light restraint: a) the Air Pollutant (AP) group was administered 20 μl of SRM1649b (300 μg/mouse) suspension, divided and instilled intra-nasally into each nare; b) the Control (CON) group was administered 20 μl of sterile saline, similarly instilled. Vaginal delivery was allowed for the pregnant dams, who then cared for their litters.

value: feces

tag: group

tag: gender

value: Female


title: SD.AG3

description: Library name: Sample33


title: MV411_KO-539_WT_A_G_Editor_Day_21_Rep2

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 11

library_source: genomic

data_processing:
Data processing was performed with the genomic perturbation platform (GPP) at the Broad institute.
An internal software tool, PoolQ, deconvolutes and quantitates perturbation barcodes from multiplexed sequencing data.
Count matrix files were log normalized to standardize read counts.
The log normalized read counts for each condition after 21 days of drug treatment were compared to the log normalized read counts for each condition at the start of the screen (Day 0).
Assembly: GRCh38/hg38
Supplementary files format and content: CRISPR Base editor screen details and results in Excel .xlsx format
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 1% L-glutamine at 37 °C with 5% CO2.

extract_protocol:
Genomic DNA was extracted from 5 million cells per condition with the Machery Nagel NucleoSpin Blood Kit
Library construction performed utilizing genomic perturbation platform at Broad Institute: Sangree, A.K., et al. Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2. Nat Commun 13, 1318 (2022).
Briefly, PCR amplification of unique barcodes was performed and sequencing (Hiseq 2500) performed to assess and quantify the abundance of each barcode.

treatment_protocol: Cells were treated with DMSO control or 13.8 nM DS-1594, 17.3 nM JNJ-6617, 23.4 nM KO-539, 51.6 nM SNDX-5613, 25.2 nM DSP-5336 for 21 days.

value: Overexpression of A>G base editor:ABE8e (V106W), SpG-SpyoCas9 (D10A), pRDA_867, addgene plasmid #231109

tag: timepoint


title: Duodenum, HFD, KO3

description: Library name: SAMPLE 12


title: SD.AG38

description: Library name: Sample31


title: MV411_KO-539_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 10


title: NEP-2 RNA-seq

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq data were trimmed and aligned to human genome (GRCH38/hg38), then HISAT2.2.4 was used to mapping the reads with default parameters.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of false discovery rate (FDR) < 0.05 and log2 fold change > 1.
Assembly: GRCH38/hg38

molecule: polyA RNA

source_name: neuroepithelial progenitors cells

growth_protocol: The hESC (Line H9, passages 39–55, Shanghai Chuan Qiu Biotechnology Co.,Ltd.) were cultured on a feeder layer of mouse embryonic fibroblast (MEFs). The MEFs were treated with mitomycin C (10 μg/mL) for 3 h. The hESC medium consisted of Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12), 0.1 mM β–mercaptoethanol, 1 % GlutaMaxTM, Knockout serum replacement (KSR), 10 ng/mL basic fibroblast growth factor 2 and 1 % Nonessential amino acid solution (NEAA).

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries was prepared using the NEBNext Ultra RNA Library Prep kit (NEB#7530, New England Biolabs, Ipswich, MA, USA), following the manufacturer's protocol

treatment_protocol: For differentiation of hESCs into NEP cells, hESCs were dissociated with dispase and seeded on the mitomycin C treated mouse embryonic fibroblast cells. On the following day (D1), the hESC medium was replaced with NEP medium, including DMEM/F12 and neurobasal medium (1:1) with 0.1 mM ascorbic acid, 1 X N2 supplement, 1 X B27 supplement, 3 μM CHIR99021, 1 % GlutaMaxTM, 2 μM DMH1 and 2 μM SB431542 for 6 days. For differentiation of ME cells, the hESC medium was changed to advanced RPMI1640, supplemented with 1x penicillin/streptomycin, CHIR99021 (5 μM) and 1 % GlutaMaxTM for 36 h.

value: neuroepithelial progenitors cells

tag: developmental stage

value: differentiation for 6 days


title: ME-2 RNA-seq

source_name: mesendoderm cells

value: mesendoderm cells

value: differentiation for 36 h


title: SD.AG37

description: Library name: Sample30

value: Male


title: ME-1 RNA-seq


title: NEP-1 RNA-seq


title: SD.AG36

description: Library name: Sample29


title: Duodenum, HFD, KO1

description: Library name: SAMPLE 10


title: Duodenum, HFD, F10

description: Library name: SAMPLE 9

value: fl/fl


title: MV411_JNJ-6617_WT_A_G_Editor_Day_21_Rep2

description: Library name: Sample 8


title: Duodenum, HFD, KO2

description: Library name: SAMPLE 11


title: SD.AG35

description: Library name: Sample28


title: MV411_JNJ-6617_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 7


title: MV411_DS-1594_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 6


title: SD.AG40

description: Library name: Sample34


title: MCF-7 Vehicle 2


title: Duodenum, HFD, F9

description: Library name: SAMPLE 8


title: hESC-1 RNA-seq

value: human embryonic stem cells


title: Duodenum, HFD, F7

description: Library name: SAMPLE 7


title: SD.AG34

description: Library name: Sample27


title: NEP-2.IP

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: hg19

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® ac4C-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4 °C for 4 h. The RNA/antibody complexes were then digested with Proteinase K and the eluted RNA was purified by phenol:chloroform extraction.
RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

tag: antibody

value: anti-ac4C (ab252215, Abcam)


title: Duodenum, HFD, F6

description: Library name: SAMPLE 6


title: SD.AG33

description: Library name: Sample26


title: MV411_DS-1594_WT_A_G_Editor_Day_21_Rep2

description: Library name: Sample 5

value: 21 days of treatment


title: MV411_JNJ-6617_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 9


title: MV411_DS-1594_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 4


title: SD.AG32

description: Library name: Sample25


title: SD.AG39

description: Library name: Sample32


title: Duodenum, HFD, F5

description: Library name: SAMPLE 5


title: SD.AG31

description: Library name: Sample24


title: NEP-1.IP


title: MV411_DMSO_WT_A_G_Editor_Day_21_Rep3

description: Library name: Sample 3

value: DMSO


title: MV411_DMSO_WT_A_G_Editor_Day_21_Rep2

description: Library name: Sample 2


title: Duodenum, HFD, F4

description: Library name: SAMPLE 4


title: hESC-2 RNA-seq


title: Duodenum, HFD, F3

description: Library name: SAMPLE 3


title: ME-2.IP


title: MV411_DMSO_WT_A_G_Editor_Day_21_Rep1

description: Library name: Sample 1


title: ME-2.Input


title: Duodenum, HFD, F2

description: Library name: SAMPLE 2


title: SD.AG29

description: Library name: Sample21


title: SD.AG30

description: Library name: Sample23


title: Duodenum, HFD, F1

description: Library name: SAMPLE 1


title: NEP-1.Input


title: SD.AG28

description: Library name: Sample20


title: ME-1.IP


title: SD.AG27

description: Library name: Sample19


title: HL-60，shRNA_control-1

city: Guangzhou

first: XiaPing

last: Miao

state: GuangDong

address: 10 Luoxuan 3rd Road, Guangzhou International Biotech Island, Guangdong, China

institute: Guangzhou KingMed Center for Clinical Laboratory

data_processing:
Reads were aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”
The reads mapped the genome were calculated using feature Counts (v1.6.3).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: leukemia

growth_protocol: HL-60 cells were maintained in DEME supplemented with 20% fetal bovine serum and antibiotics in humidiffied atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted by the QIAsymphony RNA Kit (QIAGEN, China) according to the manufacturer’s instructions
The RNA-seq libraries were prepared with VAHTS Stranded mRNA-seq Library Prep Kit for Illumina V2 (Vazyme Biotech, China) and sequenced with Illumina HiSeq 2500 with 150 bp paired-end reads.

value: leukemia

value: suspension

value: WT


title: HL-60，shRNA_control-2


title: NEP-2.Input


title: ME-1.Input


title: Mettl14_cko_a

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

data_processing:
Basecalls performed using CASAVA
clean reads were aligned to the mouse reference genome (mm10) using Hisat2
featureCounts was used to count the reads numbers mapped to each genes
Assembly: mm10
Supplementary files format and content: read counts for each genes were given in the processed data files

source_name: retina

extract_protocol:
RNAs were extracted using TRIzol reagent
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol

value: retina


title: HL-60，shRNA_OSGEP-3

value: OSGEP konckdown


title: Ctrl_c.


title: SD.AG26

description: Library name: Sample18

value: feces

value: Female


title: SD.AG2

description: Library name: Sample22


title: SD.AG25

description: Library name: Sample17


title: Ctrl_a.


title: ESC-1.IP

tag: strain

value: hESCs


title: HL-60，shRNA_OSGEP-2


title: HL-60，shRNA_control-3


title: ESC-2.Input


title: Mesenchymal stem cells,expressing GFP, control_3

first: Xu

last: Yongyue

address: Tsinghua University

institute: Tsinghua University

data_processing:
HISAT2
DESeq2
Assembly: Mus_musculus.GRCm38.97.chr
Supplementary files format and content: csv. FPKM value of genes for all samples.

source_name: fat

growth_protocol: MSCs were cultured in DMEM/F-12 medium with 10% FBS.

extract_protocol:
Trizol (Vazyme, R401-01) was used for RNA extraction. Illumina RNA-seq and subsequent analysis were performed by ANNOROAD Corporation (Beijing, China).
Libraries were constructed following  protocol for Illumina PE library

treatment_protocol: MSCs were transduction with lentivirus expressing mutated dephosphorylated GYS1(GYSmut group). While MSCs of the contron group expressed GFP. MSCs were cultured in 100-mm dishes (5×106 cells per dish) in DMEM/F-12 medium. Trizol (Vazyme, R401-01) was used for RNA extraction. Illumina RNA-seq and subsequent analysis were performed by ANNOROAD Corporation (Beijing, China).

value: fat

value: Mesenchymal stem cells

value: GFP


title: 26193-P,19.5 months,rep8

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!(v0.6.10) using the default parameters
Sequence reads were aligned to mouse genome (mm10) using Salmon (v1.10.1 )
Read count extraction using Salmon (Version 1.10.1)
Read count were normalized using the DESeq2 in R (Version 1.40.2)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including the normalized counts for each sample in a matrix table

source_name: kidney

extract_protocol:
miRNeasy Mini Kit (Qiagen,  74104)
TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: Deoxycorticosterone acetate (DOCA) treatment: 18 month-old mice (n=8) were given two sequential subcutaneous DOCA pellet implants (50mg/pellet, 21-day release, Innnovative Research of America, Sarasota, FL) 3 weeks apart for a total of 6 weeks of sustained DOCA release. Animals were provided ad libitum access to saline water for the duration of the experiment. After 6 weeks, kidneys were extracted, and podocytes isolated by MACS using anti-Nephrin antibodies.

value: kidney

value: podocyte

value: wildtype

value: untreated


title: SD.AG24

description: Library name: Sample16


title: SD.AG23

description: Library name: Sample15


title: HL-60，shRNA_OSGEP-1


title: Mettl14_cko_b


title: ESC-1.Input

value: human embryonic stem cells


title: Mesenchymal stem cells,expressing GFP, control_1


title: ESC-2.IP

value: anti-ac4C (ab252215, Abcam)


title: 26191-P,19.5 months,rep6


title: SD.AG21

description: Library name: Sample13


title: SD.AG20

description: Library name: Sample12


title: Mesenchymal stem cells,expressing GYSmut, GYSmut_3

value: GYSmut


title: Ctrl_b.


title: Mesenchymal stem cells,expressing GYSmut, GYSmut_2


title: 26190-P,19.5 months,rep5


title: SD.AG1

description: Library name: Sample11


title: Mesenchymal stem cells,expressing GYSmut, GYSmut_1


title: 26189-P,19.5 months,rep4


title: SD.AG19

description: Library name: Sample10


title: Mesenchymal stem cells,expressing GFP, control_2


title: 26187-P,19.5 months,rep3


title: 26192-P,19.5 months,rep7


title: SD.AG22

description: Library name: Sample14


title: hippocampal CA1 region, enriched condition, right hemisphere, biological replication 3

city: Kanazawa

first: Azusa

last: Kubota

state: Ishikawa

address: 13-1 Takara-machi

department: Graduate School of Advanced Preventive Medical Sciences

country: Japan

institute: Kanazawa University

data_processing:
Quality control and trimming were done by fastp (version 0.23.4)
Transcript quantification was done by salmon (version 1.10.3)
Read count data conversion was done by tximport (version 1.34.0)
Assembly: mRatBN7.2 cDNA assembly (Ensembl release 113)
Supplementary files format and content: Excel file contains: 1. Raw gene count matrix, 2. Scaled TPM count matrix.

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Total RNA was extracted from rat CA1 region tissues using the RNeasy® Mini Kit (Qiagen, Germany), according to the manufacturer’s protocol.
The cDNA libraries for RNA-seq were prepared from 500 ng of extracted RNA using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina, USA), according to the manufacturer’s instructions.

value: hippocampus

value: long-evans

tag: Sex

value: male

tag: time

value: four weeks after weaning

value: enrichment


title: SD.AG18

description: Library name: Sample9

value: feces

value: Female


title: hippocampal CA1 region, enriched condition, left hemisphere, biological replication 3


title: hippocampal CA1 region, enriched condition, right hemisphere, biological replication 2


title: SD.AG16

description: Library name: Sample7


title: 26102-P,19.5 months with DOCA,rep7

value: DOCA


title: 26186-P,19.5 months,rep2


title: 26185-P,19.5 months,rep1


title: SD.AG17

description: Library name: Sample8


title: 26099-P,19.5 months with DOCA,rep6


title: SD.AG14

description: Library name: Sample5


title: hippocampal CA1 region, enriched condition, left hemisphere, biological replication 1


title: SD.AG15

description: Library name: Sample6


title: 26098-P,19.5 months with DOCA,rep5


title: 26096-P,19.5 months with DOCA,rep4


title: hippocampal CA1 region, isolated condition, right hemisphere, biological replication 3

value: isolation


title: SD.AG12

description: Library name: Sample3


title: hippocampal CA1 region, enriched condition, right hemisphere, biological replication 1


title: 26013-P,19.5 months with DOCA,rep3


title: SD.AG11

description: Library name: Sample2


title: SD.AG10

description: Library name: Sample1


title: hippocampal CA1 region, isolated condition, right hemisphere, biological replication 2


title: hippocampal CA1 region, isolated condition, left hemisphere, biological replication 3


title: 26012-P,19.5 months with DOCA,rep2


title: hippocampal CA1 region, enriched condition, left hemisphere, biological replication 2


title: 26010-P,19.5 months with DOCA,rep1


title: hippocampal CA1 region, isolated condition, left hemisphere, biological replication 2


title: C2_LPS_rep2

first: Bowen

last: Xie

address: Chengfu Road, Haidian District

data_processing:
For RNA-seq: Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4. For ATAC-seq: Sequencing was performed using Hiseq-PE150 (Illumina) made by Novogene. Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters ‘-q 10-length 30-stringency 5′. Paired-end reads were mapped to the mm10 reference genome using Bowtie2 with-x2000. Reads that aligned to the mitochondrial genome were filtered and PCR duplicates were removed with picard MarkDuplicates. To identify peaks, the bam files containing unique, non-chrM reads were used to call peaks with MACS2 using parameters “–nomodel–keep-dup all -q 0.01–shift −100–extsize 200–call-summits -g mm.” For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATAC-seq reads were counted by featureCounts. Differentially expressed peaks were identified by at least 2-fold change and FDR adjusted p value of 0.01.
The clean reads were aligned to Mus musculus genome (mm10) by bowtie2 with default parameter, and uniquely mapping reads were summarized by featureCounts (from Subread package)
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by DESeq2 with a cut-off threshold of 1.5-fold change and FDR adjusted p-value 0.05.
Assembly: mm10
Supplementary files format and content: txt file for storing FPKM values for RNA-seq data, and a bw file for ATAC-seq data.

source_name: Bone marrow

growth_protocol: For in vitro samle:cDC1 and cDC2 cells were treated with PBS or LPS (100 ng/ml) for 12 hours, total RNA from the indicated cell types were extracted and collected for bulk RNA-seq. For in vivo sample: GFP- and GFP+ cDCs, GFP- and GFP+ non-cDC APCs (nAPCs) from E.G7-GFP tumors or draining lymph nodes in C57BL/6J mice were isolated using flow cytometry followed by RNA extraction and sequencing.

extract_protocol:
For RNA-seq: Total RNA was extracted from sorted cells using TRIzol (Invitrogen, cat#15596018) according to the manufacturer’s protocol. For ATAC-seq: For ATAC-seq analysis, 5×104 splenic cDC1s and cDC2s were resuspended in 35 μl of lysis buffer (10 mM Tris-Hcl PH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and incubated on ice for 10 minutes with vortex 3 times. After adding 10 μl of TTBL and 5 μl of TTE Mix, the mixture was shaken at 37°C for 30 minutes for DNA fragmentation.
RNA-seq library was constructed for deep sequencing by BGI Genomics (in vivo) or Novogene (in vitro).  For ATAC-seq: Fragmented DNA was purified by 1.8-fold of AMPure beads, barcoded with dual indexes and amplified by PCR. Size selection and purification of DNA were performed using 0.4-fold and 1.6-fold of AMPure beads, respectively. The size distribution and molarity of library DNA were determined by Agilent 2100 bioanalyzer and Qubit.

value: Bone marrow

value: LPS


title: NIL-Gn1-R5-2

city: Nagoya

first: Hiroyuki

last: Tsuji

address: Furocho

department: Bioscience and Biotechnology Center

institute: Nagoya University

data_processing:
Read alignment software Bowtie2
Feature count Subread 2.1
Genome_build: Oryza sativa MSU7
Supplementary_files_format_and_content: UMIcounts

organism: Oryza sativa

growth_protocol: Plants were grown in climate chambers at 70% humidity under short day conditions with daily cycles of 10 h of light at 27 °C and 14 h of dark at 25 °C. Light was provided by fluorescent white light tubes (400–700 nm, 100 μmol m-2·s-1).

extract_protocol:
Total RNA was extracted from the tissue using Plant Total RNA Mini Kit (Favogen)
Library construction was conducted according to the CEL-Seq2 method (10) with modifications. Briefly, 100 pg of RNA were used for amplification by in vitro transcription. Libraries were amplified by 11 -15 cycles of PCR, which was empirically determined.

tag: cultivar


title: hippocampal CA1 region, isolated condition, right hemisphere, biological replication 1


title: NIL-Gn1-R5-1


title: C2_PBS_rep2

value: PBS


title: NIL-Gn1-R4-1


title: NIL-Gn1-R2-9


title: C2_PBS_rep1


title: SD.AG13

description: Library name: Sample4


title: NIL-Gn1-R2-8


title: C1_LPS_rep1


title: C1_PBS_rep2


title: HUC12504

city: Notre Dame

first: Alyssa

last: La Bella

state: IN

address: 278 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

description: Library name: Sample 27

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Candida_albicans_30-877911309 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer- defined groups of samples was performed. The Wald test was used to generate p- values and log2 fold changes. Genes with an absolute log2 fold change > 2 were identified as differentially expressed genes for each comparison.
For urinary catheter RNA, the total of the gene hit counts for each sample was summed. For each gene in every sample, counts per million (CPM) were calculated using the following formula: (Gene Hit Count/Total Gene Hit Counts of Sample) *10 6 . The counts per million of each gene were then normalized to the counts per million value of the housekeeping gene ARP3 for each sample. Expression values are graphed as CPM normalized to ARP3.
Assembly: The trimmed reads were mapped to the Candida_albicans_30-877911309 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Candida albicans

source_name: Candida albicans

extract_protocol:
Total RNA was extracted from biofilms with the Zymogen RNA extraction kit (Zymo Research catalog no. R2071), and subsequently DNase I–treated (Thermofisher scientific catalog no. 89836).
Extracted RNA was sent to Azenta Life Science for RNA sequencing and bioinformatics analysis. Whole transcriptome sequencing was done following rRNA depletion via PolyA selection.

value: Candida albicans

value: WT


title: HUC12304

description: Library name: Sample 25


title: NIL-Gn1-R2-5


title: HUC13506

description: Library name: Sample 28


title: HUC12303

description: Library name: Sample 24


title: NIL-Gn1-R2-6


title: NIL-Gn1-R2-7


title: C1_PBS_rep1


title: HUC12302

description: Library name: Sample 23


title: KO_C2_LPS_rep2


title: NIL-Gn1-R2-4


title: HUC11906

description: Library name: Sample 22


title: NIL-Gn1-R2-2


title: C1_LPS_rep2


title: hippocampal CA1 region, isolated condition, left hemisphere, biological replication 1


title: HUC11701

description: Library name: Sample 21


title: KO_C2_LPS_rep1


title: C2_LPS_rep1


title: NIL-Gn1-R2-1


title: KO_C2_PBS_rep2


title: U87-MG-RFP CHI3L1 KO2 (5B5) biol rep 3

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

description: CHI3L1 knock-out

data_processing:
Reads trimming by Trimmomatic
Alignment bu STAR to hg38
Mark optical duplicates by Picard MarkDuplicates
Counts fragments to genes by featurecounts
Data normalization and statistical analysis by DESeq2
Assembly: hg38
Supplementary files format and content: text format containing sequencing fragments counts assigned to ensembl gene ids

source_name: Brain

growth_protocol: Standard, subpassage every 2-3 days or when confluency above 80%; DMEM 1 g Glc with 10% fetal bovine serum and penicillin/streptamycin supplementation, standard incubation 5% CO2, 37C, humidity 95%

extract_protocol:
According to manufacturer's protocol: Qiagen RNeasy Micro Kit (50), cat. no. 74004, ddH2O elution
KAPA Stranded mRNA-Seq Kit (Roche)

value: Brain

value: Astrocytoma

value: CHI3L1 knock-out


title: HUC12306

description: Library name: Sample 26


title: U87-MG-RFP CHI3L1 KO2 (5B5) biol rep 2

description: CHI3L1 knock-out


title: KO_C2_PBS_rep1


title: HUC103

description: Library name: Sample 19


title: NIL-Gn1-R1-8


title: EFG1CompYPD3

description: Library name: Sample 18

value: SN250 EFG1 Complement


title: U87-MG-RFP CHI3L1 KO2 (5B5) biol rep 1

description: CHI3L1 knock-out


title: KO_C1_LPS_rep2


title: NIL-Gn1-R1-6


title: NIL-Gn1-R1-7


title: EFG1CompYPD2

description: Library name: Sample 17


title: U87-MG-RFP CHI3L1 KO1 (2G2) biol rep 1

description: CHI3L1 knock-out


title: NIL-Gn1-R1-4


title: U87-MG-RFP CHI3L1 KO1 (2G2) biol rep 2

description: CHI3L1 knock-out


title: KO_C1_PBS_rep2


title: KO_C1_LPS_rep1


title: NIL-Gn1-R1-5


title: EFG1CompYPD1

description: Library name: Sample 16


title: NIL-Gn1-R1-3


title: U87-MG-RFP wild-type (WT) biol rep 3

description: wild-type

value: wild-type


title: KO_C1_PBS_rep1


title: EFG1CompUrine3

description: Library name: Sample 15


title: WT_C2_LPS_rep2


title: HUC110

description: Library name: Sample 20


title: U87-MG-RFP wild-type (WT) biol rep 2

description: wild-type


title: WT_C2_LPS_rep1


title: U87-MG-RFP wild-type (WT) biol rep 1

description: wild-type


title: EFG1CompUrine1

description: Library name: Sample 13


title: NIL-Gn1-R1-1


title: WT_C2_PBS_rep2


title: EFG1CompUrine2

description: Library name: Sample 14


title: efg1YPD3

description: Library name: Sample 12

value: SN250 efg1


title: U87-MG-RFP CHI3L1 KO1 (2G2) biol rep 3

description: CHI3L1 knock-out


title: NIL-Gn1-R1-2


title: Botrytis_TasA_2

city: Malaga

first: Alicia

last: Pérez Lorente

address: Av Louis Pasteur 49. IHSM

country: Spain

institute: University of Malaga

description:
Library name: Botrytis_TasA_2
COND_TasA_vs_COND_control_all.xlsx

data_processing:
The raw reads were pre-processed with SeqTrimNext using the specific NGS technology configuration parameters (Falgueras et al., 2010). This pre-processing removes low quality, ambiguous and low complexity stretches, linkers, adapters, vector fragments, and contaminated sequences while keeping the longest informative parts of the reads. SeqTrimNext also discarded sequences below 25 bp. Subsequently, clean reads were aligned and annotated using the Cucumis melo genome as the reference with Bowtie2 (Langmead and Salzberg, 2012) in BAM files, which were then sorted and indexed using SAMtools v1.484110 (Li et al., 2009).
Uniquely localized reads were used to calculate the read number value for each gene via Sam2counts (https://github.com/vsbuffalo/sam2counts). Differentially expressed genes (DEGs) between treatments were analyzed via DEgenes Hunter, which provides a combined p value calculated (based on Fisher’s method) using the nominal p values provided by from edgeR113 (Robinson et al., 2010) and DEseq2114 (Anders and Huber, 2010).
Assembly: ASM34474v1 (B. subtilis) and ASM14353v4 (Botrytis cinerea)
Supplementary files format and content: tab-delimited Excel files include Log2FC of the comparison between treated and non-treated Botrytis with purified compounds or with Bacillus (or Bacillus in coculture with Botrytis), with p-value, gene names and descriptions

organism: Botrytis cinerea

source_name: Fungi

growth_protocol: Liquid culture of PDB

extract_protocol:
Liquid growth cultures of B. subtilis and B. cinerea were grown 6h inPDB medium at 28°C. Overnight cultures were diluted and, after 3-4 hours (exponential phase), B. subtilis cells were treated with Tse1 or with control buffer. Cultures were grown for 3 h.  Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with Nucleo-Spin RNA Plant (Macherey–Nagel) kit. The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fungi


title: efg1YPD2

description: Library name: Sample 11


title: Botrytis_TasA_1

description:
Library name: Botrytis_TasA_1
COND_TasA_vs_COND_control_all.xlsx


title: Koshihikari-R5-5

value: Koshihikari


title: WT_C1_LPS_rep2


title: Koshihikari-R5-2


title: efg1YPD1

description: Library name: Sample 10


title: WT_C2_PBS_rep1


title: Botrytis_Bacillus_Bo_1

description:
Library name: Botrytis_Bacillus_Bo_1
COND_coculture_vs_COND_control_all_Bo.xlsx


title: WT_C1_LPS_rep1


title: Botrytis_Fengycin_2

description:
Library name: Botrytis_Fengycin_2
COND_Fengycin_vs_COND_control_all.xlsx


title: Koshihikari-R4-4


title: efg1Urine3

description: Library name: Sample 9


title: WT_C1_PBS_rep2


title: efg1Urine2

description: Library name: Sample 8


title: Koshihikari-R4-3


title: WT_C1_PBS_rep1


title: efg1Urine1

description: Library name: Sample 7


title: Botrytis_Fengycin_1

description:
Library name: Botrytis_Fengycin_1
COND_Fengycin_vs_COND_control_all.xlsx


title: TME GFP+cDCs_rep2

source_name: Tumor

value: Tumor

value: GFP+ cDCs


title: Koshihikari-R4-2


title: WTYPD3

description: Library name: Sample 6

value: SC5314 WT


title: Botrytis_control_2

description:
Library name: Botrytis_control_2
COND_coculture_vs_COND_control_all_Bo.xlsx


title: Koshihikari-R2-5


title: WTYPD2

description: Library name: Sample 5


title: TME GFP+cDCs_rep1


title: Botrytis_control_1

description:
Library name: Botrytis_control_1
COND_coculture_vs_COND_control_all_Bo.xlsx


title: Koshihikari-R2-4


title: WTYPD1

description: Library name: Sample 4


title: CT27 TSC derived Trophoblast cells, Control 3

city: Manchester

first: Peter

last: Ruane

state: England

address: 5th Floor Research, St Mary's Hospital, Oxford Road

institute: University of Manchester

description: Library name: TC3

data_processing:
Salmon quantification of RNA seq reads
Normalisation and differential expression using EdgeR
Assembly: hg38
Supplementary files format and content: EdgeR processed log2 CPM
Supplementary files format and content: Raw count quantification

source_name: CT27 TSC

growth_protocol: STB was differentiated from TSC line CT27 over 8 days according to protocol set out by Okae et al 2018 Cell Stem Cell. 22(1):50-63.e6

extract_protocol:
RNA was extracted from adherent STB using MicroPlus RNeasy kit (Qiagen), according to manufacturer’s instructions.
DNBseq platform was used to sequence BV01 cDNA libraries constructed from STB RNA at a read depth of 100bp paired end reads (BGI Group, Hong Kong)

treatment_protocol: STB was treated with endometrial organoid secretions for 24h (basal culture media conditioned with secretions by centrifugation of isolated organoids so that they burst and release secretions). Control STB were treated with unconditioned basal culture media.

value: CT27 TSC

value: Trophoblast stem cells


title: WTUrine3

description: Library name: Sample 3


title: TME GFP+nAPCs_rep2

value: GFP+ nAPCs


title: Koshihikari-R2-3


title: Koshihikari-R5-3


title: Koshihikari-R2-2


title: CT27 TSC derived Trophoblast cells, Control 2

description: Library name: TC2


title: CT27 TSC derived Trophoblast cells, Control 1

description: Library name: TC1


title: TME GFP-cDCs_rep2

value: GFP- cDCs


title: TME GFP+nAPCs_rep1


title: CT27 TSC derived Syncytiotrophoblast cells, Receptive 3

description: Library name: SR3

source_name: CT27 TSC derived STB

value: CT27 TSC derived STB

value: Syncytiotrophoblast stem cells


title: WTUrine1

description: Library name: Sample 1

value: Candida albicans


title: Botrytis_Bacillus_Bo_2

description:
Library name: Botrytis_Bacillus_Bo_2
COND_coculture_vs_COND_control_all_Bo.xlsx


title: Koshihikari-R1-5


title: TME GFP-cDCs_rep1


title: TME GFP-nAPCs_rep2

value: GFP- nAPCs


title: pig PBMC CF 2

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

country: Germany

institute: Klinikum rechts der Isar – Technical University Munich

description: 10X Genomics

data_processing:
Cell Ranger workflow using the DropletUtils was used to generate FASTQ files
Assembly: hg19, Sscorfa11.1
Supplementary files format and content: barcodes.tsv.gz features.tsv.gz matrix.mtx.gz

organism: Sus scrofa

source_name: Bone Marrow

extract_protocol:
MNC were isolated from pig lung and bone-marrow as well as human or pig blood and stored in liquid nitrogen. For each genotype and species constellation, cryopreserved samples were thawn and equal numbers of cells from n=4 donors were pooled. Bone marrow specimens were FACS-sorted for live CD45-positive cells after thawing.
10 000 cells for each sample (targeted cell recovery) were processed using Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 (1000128, 10x Genomics) and the Chromium Chip B Single Cell Kit (10x Genomics; PN- 1000073) to generate Gel Bead-In-EMulsions (GEMs) and single cell sequencing libraries. Libraries were sequenced using The NextSeq2000 (Ilumina, San Diego USA, P2 flowcell with a depth of  > 16 000 pair reads per cell.

value: Bone Marrow

value: CD45-positive BM cells

value: CF

value: neonatal piglets


title: Koshihikari-R1-4


title: CT27 TSC derived Syncytiotrophoblast cells, Receptive 2

description: Library name: SR2


title: CT27 TSC derived Syncytiotrophoblast cells, Receptive 1

description: Library name: SR1


title: TME GFP-nAPCs_rep1


title: Koshihikari-R1-3


title: dLN GFP+cDCs_rep2

source_name: lymph node

value: lymph node


title: pig PBMC WT 2

description: 10X Genomics

value: WT


title: pig lung-derived CF

description: 10X Genomics

source_name: Lung-derived (small airway tissue)

value: Lung-derived (small airway tissue)

value: Density gradient enriched mononuclear cells


title: CT27 TSC derived Syncytiotrophoblast cells, Decidual 3

description: Library name: SD3


title: WTUrine2

description: Library name: Sample 2

value: SC5314 WT


title: dLN GFP+cDCs_rep1

value: GFP+ cDCs


title: Koshihikari-R1-2

value: Koshihikari


title: CT27 TSC derived Syncytiotrophoblast cells, Decidual 2

description: Library name: SD2

value: Syncytiotrophoblast organoid stem cells


title: Koshihikari-R2-1


title: pig lung-derived MNC WT

description: 10X Genomics


title: CT27 TSC derived Syncytiotrophoblast cells, Decidual 1

description: Library name: SD1


title: dLN GFP+nAPCs_rep2

value: GFP+ nAPCs


title: CT27 TSC derived Syncytiotrophoblast cells, Control 3

description: Library name: SC3

value: CT27 TSC derived STB


title: pig PBMC CF 1

description: 10X Genomics

source_name: Peripheral Blood

value: Peripheral Blood

value: PBMC


title: pig PBMC WT 1

description: 10X Genomics


title: BJ-5ta control, rep4

city: Zürich

first: Shana

middle: J

last: Strula

address: Schmelzbergstrasse 9

country: Switzerland

institute: ETH Zürich

description: Library name: BJ-5ta_control_rep4

data_processing:
RNA sequencing analysis was performed using the SUSHI framework (Hatakeyama et al., 2016), which encompassed the following steps: Read quality was inspected using FastQC, and sequencing adaptors removed using fastp; Alignment of the RNA-Seq reads using the STAR aligner (Dobin et al., 2013) and with the GENCODE human genome build GRCh38.p13 (Release 32) as the reference (Frankish et al., 2021); the counting of gene-level expression values using the ‘featureCounts’ function of the R package Rsubread (Liao et al., 2013); All R functions were executed on R version 4.0
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited .txt file containing gene-level counts generated by featureCounts

growth_protocol: BJ-5ta human foreskin fibroblasts (ATCC, CRL-4001™) were maintained in a 4:1 mixture of Dulbecco's Modified Eagle Medium DMEM high glucose (DMEM; ThermoFischer Scientific) and Medium 199 (ThermoFischer Scientific), which was supplemented with 10 % fetal bovine serum (FBS; ThermoFisher Scientific) and 0.01 % mg/ml Hygromycin B from Streptomyces hygroscopicus (Sigma-Aldrich).

extract_protocol:
Qiagen RNeasy + DNase
Illumina Trueseq mRNA

treatment_protocol: Cells were grown to 70-80% confluency in 15 cm Petri dishes for UV exposure. Prior to irradiation, the culturing medium was changed to serum-free DMEM (ThermoFischer Scientific) without antibiotics. Cells were irradiated in a UV irradiation chamber (BS-02 Opsytec Dr. Grödel) according to the schemes shown in the corresponding figures. For UVA, dishes were covered with a soda-lime glass (150 x 25 mm, Faust Laborbedarf) to filter the low UVB emitted by the irradiation system. A dosimeter was used to monitor the UVA level.

value: hTERT-immortalized fibroblast cell

value: wild type

value: control


title: CT27 TSC derived Syncytiotrophoblast cells, Control 2

description: Library name: SC2

value: Syncytiotrophoblast stem cells


title: dLN GFP-cDCs_rep2

value: GFP- cDCs


title: dLN GFP+nAPCs_rep1

value: lymph node


title: Mouse, ATAC, 6-OHDA+NDST3

city: Seoul

first: Yujung

last: Chang

address: 98 Hannamdaero, Yongsan-gu

country: South Korea

institute: Stand Up Therapeutics Inc.

description: Library name: Mouse_ATAC_6N_R1

library_source: other

data_processing:
RNA-seq : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN reads are trimmed using TrimGalore and CUT&RUN data are aligned using Bowtie. ATAC-seq : Raw sequencing reads were preprocessed using Trim Galore to remove adapter sequences and trim low-quality bases from both ends. The low-quality bases were filtered using a sliding window trimming approach. scRNA-seq : Raw BCL files generated by the Illumina HiSeq X Ten were demultiplexed into FASTAQ files using ‘cellranger mkfastq’ pipeline.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts and reads in peak for each sample

molecule: other

extract_protocol:
RNA-seq:Total RNA was isolated using an RNA extraction kit (Qiagen).A total of 1 µg of high-quality total RNA from each sample was utilized for library preparation following the manufacturer's protocol. CUT&RUN : The released DNA fragment were extracted using CUT&RUN Kit following manufacture's protocol. ATAC-seq : 50,000 nuclei were used transposition reaction using the Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) following manufacture's protocol. scRNA-seq : Tissue samples were enzymatically dissociated into single cell suspension using Multi Tissue Dissociation kit 1 (Miltenyi Biotec) in combination with the gentleMACS Dissociator, following the manufacturer's protocol. Post dissociation, myelin debris was removed via Percoll density gradient centrifugation, and red blood cells were eliminated using Red Blood Cell Lysis Solution (Miltenyi Biotec). Cell viability and concentration were assessed using the LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems).
RNA-seq :TruSeq Stranded mRNA Library Prep Kit following manufacture's protocol. CUT&RUN : TruSeq DNA Sample prep Kit following manufacture's protocol. ATAC-seq : Manual ATAC-Seq library preparation involves separate cell lysis, Tn5 transposase tagmentation, DNA purification, and PCR amplification steps performed individually. scRNA-seq : Single-cell libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 protocol (10x Genomics).

value: Brain

value: CNS

value: ICR

value: WT

value: 6-OHDA with NDST3 treatment


title: BJ-5ta control, rep3

description: Library name: BJ-5ta_control_rep3


title: dLN GFP-cDCs_rep1


title: CT27 TSC derived Syncytiotrophoblast cells, Control 1

description: Library name: SC1


title: BJ-5ta control, rep2

description: Library name: BJ-5ta_control_rep2


title: dLN GFP-nAPCs_rep2

value: GFP- nAPCs


title: Mouse, ATAC, sham

description: Library name: Mouse_ATAC_CTRL_R1

value: Sham-control


title: Mouse, ATAC, 6-OHDA

description: Library name: Mouse_ATAC_6_R1


title: BJ-5ta control, rep1

description: Library name: BJ-5ta_control_rep1


title: Mouse, H3K27ac,6-OHDA+NDST3, rep2

description: Library name: Mouse_CR_6N_R2

data_processing:
RNA-seq : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN : The base calls binary is converted into FASTQ utilizing illumina package bcl2fastq. CUT&RUN reads are trimmed using TrimGalore and CUT&RUN data are aligned using Bowtie. ATAC-seq : Raw sequencing reads were preprocessed using Trim Galore to remove adapter sequences and trim low-quality bases from both ends. The low-quality bases were filtered using a sliding window trimming approach. scRNA-seq : Raw BCL files generated by the Illumina HiSeq X Ten were demultiplexed into FASTAQ files using ‘cellranger mkfastq’ pipeline.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts and reads in peak for each sample
Library strategy: CUT&Run


title: BJ-5ta control, rep5

description: Library name: BJ-5ta_control_rep5


title: BJ-5ta exposed to an accumulated dose off 100 J/cm2, rep5

description: Library name: BJ-5ta_UVA_rep5

value: UVA 100 J/cm2


title: MprA_pBAD_MprA_R1

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

description:
Library name: MprA_pBAD_MprA_R1
The mprA-deleted E.coli strain carrying the pBAD-MprA plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 1.0. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 1 of the control group.

data_processing:
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor，or with unknown bases more than 5%  ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome with Bowtie2： v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated  (http://deweylab.biostat.wisc.edu/RSEM）
Assembly: Salmonella Typhimurium LT2 Genome  (NC_003197) Chromosome (https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_003277.2) , E.coli K-12 MG1655 genome (NC_000913.3) chromosome, (https://www.ncbi.nlm.nih.gov/nuccore/556503834)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: Escherichia coli str. K-12 substr. MG1655

growth_protocol: M9CA broth plus 0.1% glucose-6-phosphate (G6P) to OD~0.4

extract_protocol:
Bacterial total RNA was isolated using the hot phenol method. Briefly, Cells were resuspended in lysozyme, 10% SDS and 3M sodium acetate (pH5.2). The cleared lysate was mixed with saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. After mixing with chloroform and centrifugation in a Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech), the aqueous phase was collected and mixed the with 30:1 ethanol: sodium acetate (pH 6.5) and precipitated at -80°C overnight. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and the RNA concentration was determined using NanoDrop 2000.
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine. Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform

treatment_protocol: 0.2& L-Arabinose induction or not


title: dLN GFP-nAPCs_rep1


title: MprA_pBAD_Ctr_R2

description:
Library name: MprA_pBAD_Ctr_R2
The mprA-deleted E.coli strain carrying the empty pBAD plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 1.0. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 2 of the control group.

value: Escherichia coli str. K-12 substr. MG1655


title: mSG, whole epithelium (Epcam+), irradiated [scRNAseq], HTO

city: Nutley

first: Piero

last: Dalerba

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation (CDI)

institute: Hackensack Meridian Health

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read 1 file contains cell barcode and UMI; read 2 file contains Hashtag Antibody Derived Tag reads
PS056_barcodes.tsv.gz
PS056_features.tsv.gz
PS056_matrix.mtx.gz
PS056_HTO

data_processing:
*library strategy: CITE-seq
Sequencing data were processed using the CellRanger software (version 6.1.2) provided by 10X Genomics
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files for both gene-expression (GEX) and hashtag-oligo (HTO) libraries libraries include the following categories: "features.tsv.gz", "barcodes.tsv.gz", "matrix.mtx.gz",

molecule: protein

source_name: salivary gland (submandibular)

growth_protocol: Epithelial cells were purified from primary SG tissues (sub-mandibular glands) of adult female mice (strain: C57BL/6J; source: The Jackson Laboratory, stock #000664). In the specific case of the scRNAseq experiment performed on irradiated SGs, the specimens were collected 90 days after selective stereotactic irradiation (30 Gy) of the left SMG.

extract_protocol:
Single cells were loaded into a 10x Genomics Chromium Single Cell Controller and encapsulated in Gel-Beads-in-emulsion (GEMs).
Single-cell RNA-seq libraries were generated using a Chromium Single Cell 3' GEM Library & Gel Bead Kit (with v3 chemistry) and sequenced on an Illumina NovaSeq 6000 machine (paired-end) at the J.P. Sulzberger Columbia Genome Center (Columbia University)

treatment_protocol: Mouse sub-mandibular glands were surgically dissected, mechanically disaggregated by mincing into small fragments and then dissociated into single-cell suspensions by incubation with DNAse-I (100 units/ml), Collagenase-III (200 units/ml), Hyaluronidase (100 units/ml) for 2 hours, followed by a brief digestion (5 minutes) with Trypsin (0.25%). Single-cell suspensions were stained first with monoclonal antibodies (anti-Epcam, clone G8.8, BioLegend; anti-Cd49f, clone GoH3; BioLegend; anti-Cd3, clone 17A2, BioLegend; anti-Cd16/Cd32-biotin, clone 93, BioLegend; anti-Cd31-biotin, clone 390, BioLegend; anti-Cd45-biotin, clone 30F-11, BioLegend) and secondarily with Streptavidin-PE/Cy5 (BioLegend). Target epithelial populations were sorted by FACS, after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-W profiles) and cells of non-epithelial lineages (Cd3+, Cd16/Cd32+, Cd31+, Cd45+). Finally, cells sorted from independent biological replicates were tagged by labeling with 3 distinct anti-mouse antibodies for "cellular hashing" (TotalSeq™ B0301, B0302, B0303; BioLegend) before pooling into a single experimental sample.

value: salivary gland (submandibular)

value: C57BL/6J - The Jackson Laboratory [stock #000664]

value: wild-type (wt)

value: female

tag: age

value: 8-10 weeks

tag: cell phenotype

value: EpCAM+

value: whole epithelium

value: irradiated (30 Gy)

tag: library type

value: HTO

tag: hto

value: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody


title: BJ-5ta exposed to an accumulated dose off 100 J/cm2, rep4

description: Library name: BJ-5ta_UVA_rep4

tag: cell line

value: hTERT-immortalized fibroblast cell

value: wild type


title: Koshihikari-R1-1

value: Koshihikari


title: MprA_pBAD_Ctr_R1

description:
Library name: MprA_pBAD_Ctr_R1
The mprA-deleted E.coli strain carrying the empty pBAD plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 1.0. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 1 of the control group.


title: Mouse, H3K27ac,6-OHDA, rep2

description: Library name: Mouse_CR_6_R2

tag: tissue

value: Brain

value: CNS

value: ICR

value: WT


title: BJ-5ta exposed to an accumulated dose off 100 J/cm2, rep3

description: Library name: BJ-5ta_UVA_rep3

tag: cell type

tag: treatment

value: UVA 100 J/cm2


title: mSG, whole epithelium (Epcam+), irradiated [scRNAseq], GEX

description:
polyA RNA
GEX (3' mRNA) library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
PS056_mRNA

value: salivary gland (submandibular)

value: C57BL/6J - The Jackson Laboratory [stock #000664]

tag: genotype

value: mRNA


title: Mouse, H3K27ac,sham, rep2

description: Library name: Mouse_CR_CTRL_R2

value: Sham-control


title: BJ-5ta exposed to an accumulated dose off 100 J/cm2, rep2

description: Library name: BJ-5ta_UVA_rep2


title: EC_UhpTU_G6P_R1

description:
Library name: EC_UhpTU_G6P_R1
E. coli ΔUhpTU strain was grown in M9CA + 0.1% Glucose-6-phosphate medium at 37°C until the culture reached an OD₆₀₀ of approximately 0.4. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 1.

value: Escherichia coli str. K-12 substr. MG1655


title: mSG, whole epithelium (Epcam+), wild-type [scRNAseq], GEX

description:
polyA RNA
GEX (3' mRNA) library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
PS050_mRNA

value: wild-type (wt)

value: female

value: 8-10 weeks

value: EpCAM+

value: whole epithelium

value: untreated


title: Mouse, H3K27ac,6-OHDA, rep1

description: Library name: Mouse_CR_6_R1


title: BJ-5ta exposed to an accumulated dose off 100 J/cm2, rep1

description: Library name: BJ-5ta_UVA_rep1

value: hTERT-immortalized fibroblast cell

value: wild type


title: Mouse, H3K27ac, sham, rep1

description: Library name: Mouse_CR_CTRL_R1

value: Brain

value: CNS


title: mSG, basal compartment (Epcam+, Cd49f-high), wild-type [scRNAseq], HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read 1 file contains cell barcode and UMI; read 2 file contains Hashtag Antibody Derived Tag reads
PS018_barcodes.tsv.gz
PS018_features.tsv.gz
PS018_matrix.mtx.gz
PS018_HTO

value: EpCAM+, Cd49f-high

value: basal compartment

value: HTO

value: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody, TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody


title: mSG, whole epithelium (Epcam+), wild-type [scRNAseq], HTO

description:
Hashtag-derived oligonucleotide (HTO)
HTO library: read 1 file contains cell barcode and UMI; read 2 file contains Hashtag Antibody Derived Tag reads
PS050_barcodes.tsv.gz
PS050_features.tsv.gz
PS050_matrix.mtx.gz
PS050_HTO

value: salivary gland (submandibular)

value: C57BL/6J - The Jackson Laboratory [stock #000664]


title: Mouse, 6-OHDA+NDST3, rep2

description: Library name: Mouse_6N_R2

value: ICR

value: WT

value: 6-OHDA with NDST3 treatment


title: EC_WT_G6P_R2

description:
Library name: EC_WT_G6P_R2
Wild-type E. coli strain was grown in M9CA + 0.1% Glucose-6-phosphate medium at 37°C until the culture reached an OD₆₀₀ of approximately 0.4. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 2

value: Escherichia coli str. K-12 substr. MG1655


first: Scott

last: Armstrong

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
Library name: Sample 6
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_VTP_0_1pct_chow_4w_REP2_RNAseq_210521_GTGATC_S16

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Assembly: GRCh38/hg38
Supplementary files format and content: Signal pileup in BigWig (.bw) format; mutation detail in Excel .xlsx format

source_name: PDX model

growth_protocol: The patient derived xenograft (PDX) CPCT-0024 was thawed from cryovials and transplanted into immunodeficient mice. Upon engraftment, mice were randomized to vehicle (n = 2), VTP-50469 0.03% chow (n = 2), or VTP-50469 0.1% chow (n = 2). After four weeks of treatment, bone marrow samples were obtains from crushing tibia, fibula, femur, pelvice, and vertebral bones.

extract_protocol:
PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny)
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).

treatment_protocol: Treatment of PDX CPCT-0024 occurred after engraftment of CD45+ cells and treatment was with VTP-50469 at 0.03% and 0.1% chow.

value: PDX model

value: 4 weeks


description:
Library name: Sample 5
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_VTP_0_1pct_chow_4w_REP1_RNAseq_210521_CTATAC_S15


title: Mouse, H3K27ac,6-OHDA+NDST3, rep1

description: Library name: Mouse_CR_6N_R1


title: EC_WT_G6P_R1

description:
Library name: EC_WT_G6P_R1
Wild-type E. coli strain was grown in M9CA + 0.1% Glucose-6-phosphate medium at 37°C until the culture reached an OD₆₀₀ of approximately 0.4. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 1


title: SCC7-BMDM treated SCC7-3

first: Yu

last: Zhang

address: No.150  Rd. Fenglin

institute: Zhongshan Hospital, Fudan University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: murine squamous carcinoma cell

value: CM from SCC7-BMDM


title: Mouse, 6-OHDA+NDST3, rep1

description: Library name: Mouse_6N_R1


title: MprA_pBAD_MprA_R2

description:
Library name: MprA_pBAD_MprA_R2
The mprA-deleted E.coli strain carrying the pBAD-MprA plasmid was cultured in LB miller medium at 37°C until reaching an OD₆₀₀ of approximately 1.0. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression. Cultures were incubated for an additional 10 minutes before total RNA was extracted. This sample represents biological replicate 2 of the control group.


title: SCC7-BMDM treated SCC7-2


title: CITE-seq - Non-Granuloma Monkey 1 - ADT library

city: Ithaca

first: Davide

last: Pisu

state: NY

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description:
Library name: U2_ADT
Antibody-derived Oligonucleotide (ADT)

data_processing:
Sequencing data derived from each run were processed using software tailored to the library type. mRNA libraries were processed using CellRanger software (v. 6.0) (10X Genomics), utilizing a custom reference genome combining the M. fascicularis 5.0 assembly (GCF_000364345.1) and the Mtb Erdman genome (GCA_00668235.1). ADT libraries were processed using CITE-Seq-Count (v. 1.4.3), available at https://hoohm.github.io/CITE-seq-Count/. This processing yielded raw count matrices for both mRNA and proteins. Downstream data analysis was conducted in Seurat (v. 4.3) [34]. To ensure robust data, cells with fewer than 700 unique genes as well as cells with a high proportion (>5%) of ribosomal protein genes (RPS and RPL) were identified and removed.
In our scRNA-seq analysis, we processed individual samples’ datasets using Seurat’s regularized negative binomial regression, regressing out the number of counts, as in Hafemeister and Satija. Metadata columns such as ‘Batch,’ ‘Type,’ and ‘Infection’ were then added to each dataset. Next, we combined all datasets into a single Seurat object. The raw counts from the RNA slot of this merged object served as input for Harmony integration. Raw counts underwent log-normalization, followed by the identification of the top 5,000 variable genes. These genes were then scaled and centered. Subsequently, we performed Principal Component Analysis (PCA) on these values. Finally, we performed integration with Harmony, using ‘Batch,’ ‘Infection,’ and ‘Type’ as covariates
Using the Harmony-aligned embeddings, graph-based cluster detection was achieved utilizing principal components (PCs) that had been marked statistically significant by the jackstraw method [37]. For community detection, we employed the Louvain algorithm]. Both reference-based approaches and canonical markers gene analysis were used to annotate the cell type of each identified cluster.
Assembly: macfas5 GCA_000364345.1
Supplementary files format and content: CellRanger Output files:barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cite-seq Output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

organism: Macaca fascicularis

source_name: Lung

extract_protocol:
Immune cells and macrophages were sorted from Mtb-infected NHP lungs at 5 wpi.Cells have been incapsulated in Gel-beads-in-emulsion (GEMs) using the 10X controller with a chromium single cell 3' GEM Library and Gel bead kit (Cornell University).
The CITE-seq and hashing protocol described by Stoeckius et al was used to generate an antibody-derived tag (ADT) library and a 3' Gene Expression library. (Stoeckius et al 2017).https://cite-seq.com/wp-content/uploads/2019/02/cite-seq_and_hashing_protocol_190213.pdf

value: Lung

value: Macrophages + Immune cells

value: Infected with M.Tuberculosis


description:
Library name: Sample 3
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_VTP_0_03pct_chow_4w_REP1_RNAseq_210521_CGGAAT_S13


title: CITE-seq - Non-Granuloma Monkey 1 - mRNA library

description:
Library name: U2_mRNA
polyA RNA


title: Mouse, 6-OHDA, rep1

description: Library name: Mouse_6_R1

value: Brain

value: CNS


description:
Library name: Sample 4
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_VTP_0_03pct_chow_4w_REP2_RNAseq_210521_CTAGCT_S14


title: EC_UhpTU_G6P_R2

description:
Library name: EC_UhpTU_G6P_R2
E. coli ΔUhpTU strain was grown in M9CA + 0.1% Glucose-6-phosphate medium at 37°C until the culture reached an OD₆₀₀ of approximately 0.4. Total RNA was extracted for sequencing. This sample corresponds to biological replicate 2.


title: SCC7-BMDM treated SCC7-1


title: Mouse, sham, rep1

description: Library name: Mouse_CTRL_R1

value: Sham-control


title: CPCT0024_RNA_control_4w_REP1_RNAseq

description:
Library name: Sample 1
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_control_4w_REP1_RNAseq_210521_CATTTT_S11

value: Vehicle control


title: CPCT0024_RNA_control_4w_REP2_RNAseq

description:
Library name: Sample 2
Bone marrow specimens from tibia, fibula, femur, pelvic, and vertebral body bones
CPCT0024_RNA_control_4w_REP2_RNAseq_210521_CCAACA_S12


title: mSG, basal compartment (Epcam+, Cd49f-high), wild-type [scRNAseq], GEX

description:
polyA RNA
GEX (3' mRNA) library: read 1 file contains cell barcode and UMI; read 2 file contains transcript
PS018_mRNA

value: salivary gland (submandibular)

value: wild-type (wt)

value: female

value: 8-10 weeks

value: EpCAM+, Cd49f-high

value: basal compartment

value: untreated

value: mRNA


title: M2-BMDM treated SCC7-3

value: murine melanoma

value: WT

value: CM from M2-BMDM


title: CITE-seq - Non-Granuloma Monkey 3 - ADT library - Infected cells

description:
Library name: 4I_ADT
Antibody-derived Oligonucleotide (ADT)

value: Lung

value: Macrophages + Immune cells


title: Galectin-9 siRNA_3

city: Nijmegen

first: Guido

last: van Mierlo

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboudumc

description: Column name: RC_LQC_32_A65_S17

data_processing:
The resulting library was sequenced paired-end on an Illumina Nextseq 500 platform. Reads were aligned to the hg38 human genome using the seq2science pipelinewith STAR used as aligner. Reads that mapped equally well to multiple locations were discarded.
Assembly: Hg38
Supplementary files format and content: Unnormalized count matrix

source_name: Primary moDCs

growth_protocol: Monocytes isolated from healthy blood donors (informed consent obtained) were cultured for up to five days in RPMI 1640 medium (Life Technologies, Bleiswijk, Netherlands) containing 10 % foetal bovine serum (FBS, Greiner Bio-one, Alphen aan den Rijn, Netherlands), 1 mM ultra-glutamine (BioWhittaker), antibiotics (100 U/ml penicillin, 100 µg/ml streptomycin and 0.25 µg/ml amphotericin B, Life Technologies), IL-4 (500 U/ml, Miltenyi Biotec) and GM-CSF (800 U/ml, #130-093-868, MiltenyiBiotec ) in a humidified, 5 % CO2. On day 3, medium was refreshed with new IL-4 (500 U/ml, Miltenyi Biotec) and GM-CSF (800 U/ml, Miltenyi Biotec). On day 6, moDCs were supplemented with a maturation cocktail: IL-6 (15 ng/ml, #130-093-933, Miltenyi Biotec), TNF‑α (10 ng/mg, #130-094-014 Miltenyi Biotec), IL‑1β (5 ng/ml, #130-093-898 Miltenyi Biotec) and PGE2 (10 ug/ml, Pfizer).

extract_protocol:
Total RNA was extracted from mature moDC using zymo quick-RNA miniprep kit R1055 according to manufacturer instructions
Libraries were prepared using a KAPA RNA HyperPrep Kit (#KR1351, KAPA BIOSYSTEMS)

treatment_protocol: DCs were transfected with non-targeting (NT) or galectin-9 siRNAs

value: Primary moDCs

value: Galectin-9 siRNA

tag: batch

value: Donor 3


title: WBC, TCR (CD45.1+)

city: New York

first: Omar

last: Abdel-Wahab

state: New York

address: 1275 York Ave

department: Molecular Pharmacology Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: WBC_TCR_VDJ
T cell receptor sequence

data_processing:
5’ single-cell RNA and ADT sequencing FASTQs were processed using the nf-core scRNA-seq pipeline v4.0.0 with 10x Genomics CellRanger Multi v8.0.0 and aligned to GRCm39 modified to include U5 snRNP200- and control-CAR constructs.
TCR-seq FASTQ files were processed using CellRanger V(D)J v8.0.0.
Assembly: GRCm39
Supplementary files format and content: Cellranger multi output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger VDJ: filtered_contig_annotations.csv
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
Bone marrow mononuclear cells isolated from recipient mice were incubated with mouse Fc receptor blocker (BioLegend; 101320) and then stained with FITC anti-mouse CD45.1 (BioLegend; 110706), PE anti-mouse CD45.2 (BioLegend; 109808), PE-Cy7 anti-mouse CD3 (BioLegend; 100220), and Brilliant Violet 711 anti-mouse CD11b (BioLegend; 101242) antibodies in PBS supplemented with 0.5% BSA. RN2 cells (CD45.2+ CD11b+), donor-derived T cells (CD45.2+ CD3+), and recipient-derived WBCs (CD45.1+) cells were sorted using an Aria cytometer (BD Biosciences). 500,000 sorted cells were incubated with Fc receptor blocker (BioLegend, 101320), stained with TotalSeq-C Mouse Universal Cocktail (BioLegend, 199903) in cell staining buffer (BioLegend, 420201) for 30 min at 4°C, and subsequently washed with PBS supplemented with 0.04% BSA.
Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification.  Between 20,000 and 60,000 cells were targeted for each sample, and several samples were multiplexed together on one lane of 10X Chromium X, following cell hashing protocol using TotalSeqC (BioLgened). The scRNA-seq and scTCR-seq libraries were prepared using the 10x Single Cell Immune Profiling Solution Kit, according to the manufacturer’s instructions. For gene expression library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected with SPRIselect beads, PCR-amplified with sample indexing primers (98 °C for 45 s; 14–16 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and double-sided size-selected with SPRIselect beads. For TCR library construction, TCR transcripts were enriched from 2 μl of amplified cDNA by PCR (primer sets 1 and 2: 98 °C for 45 s; 10 cycles of 98 °C for 20 s, 67 °C for 30 s, 72 °C for 1 min; 72 °C for 1 min). Following TCR enrichment, enriched PCR product was fragmented and end-repaired, size-selected with SPRIselect beads, PCR-amplified with sample-indexing primers (98 °C for 45 s; 9 cycles of 98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s; 72 °C for 1 min), and size-selected with SPRIselect beads. Final libraries (GEX, TCR and HTO) were sequenced on Illumina NovaSeq X platform (R1 – 26 cycles, i7 – 10 cycles, i5 – 10 cycles, R2 – 90 cycles).

value: Blood

value: WBC


title: M2-BMDM treated SCC7-1

value: murine squamous carcinoma cell


title: M2-BMDM treated SCC7-2


title: CITE-seq - Non-Granuloma Monkey 3 - mRNA library - Infected cells

description:
Library name: 4I_mRNA
polyA RNA

value: Infected with M.Tuberculosis


title: WBC, ADT/HTO (CD45.1+)

description:
Library name: WBC_ADT_HTO
antibody-derived oligonucleotide
WBC.filtered_feature_bc_matrix.barcodes.tsv.gz
WBC.filtered_feature_bc_matrix.features.tsv.gz
WBC.filtered_feature_bc_matrix.matrix.mtx.gz
WBC.raw_feature_bc_matrix.barcodes.tsv.gz
WBC.raw_feature_bc_matrix.features.tsv.gz
WBC.raw_feature_bc_matrix.matrix.mtx.gz

data_processing:
5’ single-cell RNA and ADT sequencing FASTQs were processed using the nf-core scRNA-seq pipeline v4.0.0 with 10x Genomics CellRanger Multi v8.0.0 and aligned to GRCm39 modified to include U5 snRNP200- and control-CAR constructs.
TCR-seq FASTQ files were processed using CellRanger V(D)J v8.0.0.
Assembly: GRCm39
Supplementary files format and content: Cellranger multi output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger VDJ: filtered_contig_annotations.csv
Library strategy: CITE-seq


title: WBC, GEX (CD45.1+)

description:
Library name: WBC_GEX
5' gene expression
WBC.filtered_feature_bc_matrix.barcodes.tsv.gz
WBC.filtered_feature_bc_matrix.features.tsv.gz
WBC.filtered_feature_bc_matrix.matrix.mtx.gz
WBC.raw_feature_bc_matrix.barcodes.tsv.gz
WBC.raw_feature_bc_matrix.features.tsv.gz
WBC.raw_feature_bc_matrix.matrix.mtx.gz


title: CITE-seq - Granuloma Monkey 1 - mRNA library - Infected cells

description:
Library name: I2_mRNA
polyA RNA


title: M1-BMDM treated SCC7-3

value: CM from M1-BMDM


title: CITE-seq - Non-Granuloma Monkey 2 - ADT library - Infected cells

description:
Library name: 3I_ADT
Antibody-derived Oligonucleotide (ADT)


title: Mouse, sham, rep2

description: Library name: Mouse_CTRL_R2

value: Brain

value: CNS

value: ICR

value: Sham-control


title: M1-BMDM treated SCC7-2


title: Recipient WBC from mice treated with U5 CAR T, TCR (CD45.1+)

description:
Library name: Treatment_RecipientWBC_TCR_VDJ
T cell receptor sequence

value: U5 SNRNP200 CAR


title: CITE-seq - Granuloma Monkey 1 - ADT library - Infected cells

description:
Library name: I2_ADT
Antibody-derived Oligonucleotide (ADT)


title: Non-targeting siRNA_2

description: Column name: RC_LQC_21_A61_S13

value: Non-targeting siRNA

value: Donor 2


title: Recipient WBC from mice treated with U5 CAR T, ADT/HTO (CD45.1+)

description:
Library name: Treatment_RecipientWBC_ADT_HTO
antibody-derived oligonucleotide
Treatment_RecipientWBC.filtered_feature_bc_matrix.barcodes.tsv.gz
Treatment_RecipientWBC.filtered_feature_bc_matrix.features.tsv.gz
Treatment_RecipientWBC.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.features.tsv.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.matrix.mtx.gz


title: Galectin-9 siRNA_1

description: Column name: RC_LQC_12_A59_S11

value: Donor 1


title: CITE-seq - Non-Granuloma Monkey 2 - mRNA library - Infected cells

description:
Library name: 3I_mRNA
polyA RNA

value: Lung

value: Macrophages + Immune cells


title: M0-BMDM treated SCC7-3

value: WT

value: CM from M0-BMDM


title: M1-BMDM treated SCC7-1


title: CITE-seq - Granuloma Monkey 3 - mRNA library - Infected cells

description:
Library name: I4_mRNA
polyA RNA


title: Recipient WBC from mice treated with U5 CAR T, GEX (CD45.1+)

description:
Library name: Treatment_RecipientWBC_GEX
5' gene expression
Treatment_RecipientWBC.filtered_feature_bc_matrix.barcodes.tsv.gz
Treatment_RecipientWBC.filtered_feature_bc_matrix.features.tsv.gz
Treatment_RecipientWBC.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.features.tsv.gz
Treatment_RecipientWBC.raw_feature_bc_matrix.matrix.mtx.gz

value: Blood


title: Non-targeting siRNA_3

description: Column name: RC_LQC_31_A64_S16

value: Primary moDCs

value: Donor 3


title: M0-BMDM treated SCC7-1

value: murine squamous carcinoma cell


title: Donor T cells from mice treated with U5 CAR T, TCR (CD45.2+/CD3+)

description:
Library name: Treatment_DonorT_TCR_VDJ
T cell receptor sequence

value: T cells


title: Non-targeting siRNA_1

description: Column name: RC_LQC_11_A58_S10


title: Donor T cells from mice treated with U5 CAR T, ADT/HTO (CD45.2+/CD3+)

description:
Library name: Treatment_DonorT_ADT_HTO
antibody-derived oligonucleotide
Treatment_DonorT.filtered_feature_bc_matrix.features.tsv.gz
Treatment_DonorT.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_DonorT.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_DonorT.raw_feature_bc_matrix.features.tsv.gz
Treatment_DonorT.raw_feature_bc_matrix.matrix.mtx.gz


title: serk1-1 wild type NaCl treated, biological replicate #1

first: DAMI

last: YANG

address: Cheonpa-ro 47 gil 100, Yongsan-gu

department: Department of Biological Sciences

institute: Sookmyung Women's University

data_processing:
Tuxedo protocol (https://doi.org/10.1038/nprot.2016.095)
Filtering : The quality of the reads were checked using fastQC (v.0.10.1), helping the understanding for the basic quality for sequence quality score, GC content, N content, length distribution and duplication level. Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Sequence alignment : Filtered reads were mapped to the Arabidopsis thaliana reference genome (Ensembl release 23) using the aligner Tophat2.
Gene expression estimation : Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of Ensembl release 23. Non-coding gene region was removed with –mask option. To improve the accuracy of measurement, multi-read-correction and fragbias-correct options were applied. All other options were set to default values.
Assembly: TAIR10
Supplementary files format and content: Exel file including FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 24hour imbibed Seeds

growth_protocol: Seeds were sterilized with 75% ethanol containing 0.05% Tween-20 for 15 min, washed twice in 95% ethanol and once in 100% ethanol, and then placed in 1/2 Murashige & Skoog (MS; Duchefa Biochemie) liquid medium.

extract_protocol:
Total RNA was extracted from 24hours imbibed seeds using TRI Reagent® (SIGMA according to the manufacturer’s protocol)
The libraries were prepared for 100bp paired-end sequencing using TruSeq RNA Sample Preparation Kit (Illumina, CA, USA). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×100bp) using Illumina HiSeq2500 (Illumina, CA, USA).

treatment_protocol: No treatment or 200mM NaCl treatment

value: 24hour imbibed Seeds

tag: ecotype

value: Columbia-0 (Col-0)

value: 200mM NaCl treatment


title: serk1-1 wild type NaCl treated, biological replicate #2


title: Donor T cells from mice treated with U5 CAR T, GEX  (CD45.2+/CD3+)

description:
Library name: Treatment_DonorT_GEX
5' gene expression
Treatment_RN2.filtered_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.features.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_RN2.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.features.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.matrix.mtx.gz


title: CITE-seq - Granuloma Monkey 3 - mRNA library

description:
Library name: B4_mRNA
polyA RNA

value: Infected with M.Tuberculosis


title: B16F10-BMDM treated  B16F10-3

value: murine melanoma cell

value: CM from B16F10-BMDM


title: serk1-1 wild type, biological replicate #2

value: No treatment


title: CITE-seq - Non-Granuloma Monkey 3 - ADT library

description:
Library name: U4_ADT
Antibody-derived Oligonucleotide (ADT)


title: CITE-seq - Granuloma Monkey 3 - ADT library

description:
Library name: B4_ADT
Antibody-derived Oligonucleotide (ADT)


title: B16F107-BMDM treated  B16F10-2


title: CITE-seq - Granuloma Monkey 3 - ADT library - Infected cells

description:
Library name: I4_ADT
Antibody-derived Oligonucleotide (ADT)


title: RN2 cells from mice treated with U5 CAR T, ADT/HTO (CD45.2+/CD11b+)

description:
Library name: Treatment_RN2_ADT_HTO
antibody-derived oligonucleotide
Treatment_RN2.filtered_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.features.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_RN2.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.features.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.matrix.mtx.gz

value: RN2 AML

value: U5 SNRNP200 CAR


title: B16F10-BMDM treated  B16F10-1


title: RN2 cells from mice treated with U5 CAR T, GEX (CD45.2+/CD11b+)

description:
Library name: Treatment_RN2_GEX
5' gene expression
Treatment_RN2.filtered_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.features.tsv.gz
Treatment_RN2.filtered_feature_bc_matrix.matrix.mtx.gz
Treatment_RN2.raw_feature_bc_matrix.barcodes.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.features.tsv.gz
Treatment_RN2.raw_feature_bc_matrix.matrix.mtx.gz


title: CITE-seq - Granuloma Monkey 2 - ADT library - infected cells

description:
Library name: I3_ADT
Antibody-derived Oligonucleotide (ADT)

value: Lung

value: Macrophages + Immune cells


title: Col-0 wild type NaCl treated, biological replicate #2

value: wildtype


title: M0-BMDM treated SCC7-2

value: WT

value: CM from M0-BMDM


title: Recipient WBC from mice treated with control CAR T, TCR (CD45.1+)

description:
Library name: Control_RecipientWBC_TCR_VDJ
T cell receptor sequence

value: Blood

value: WBC

value: Control CAR


title: CITE-seq - Granuloma Monkey 2 - mRNA library - infected cells

description:
Library name: I3_mRNA
polyA RNA


title: Col-0 wild type NaCl treated, biological replicate #1

value: 24hour imbibed Seeds


title: Col-0 wild type, biological replicate #2

value: Columbia-0 (Col-0)


title: CITE-seq - Non-Granuloma Monkey 3 - mRNA library

description:
Library name: U4_mRNA
polyA RNA


title: CITE-seq - Granuloma Monkey 2 - ADT library

description:
Library name: B3_ADT
Antibody-derived Oligonucleotide (ADT)


title: Recipient WBC from mice treated with control CAR T, GEX (CD45.1+)

description:
Library name: Control_RecipientWBC_GEX
5' gene expression
Control_RecipientWBC.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_RecipientWBC.filtered_feature_bc_matrix.features.tsv.gz
Control_RecipientWBC.filtered_feature_bc_matrix.matrix.mtx.gz
Control_RecipientWBC.raw_feature_bc_matrix.barcodes.tsv.gz
Control_RecipientWBC.raw_feature_bc_matrix.features.tsv.gz
Control_RecipientWBC.raw_feature_bc_matrix.matrix.mtx.gz


title: M2-BMDM treated B16F10-1

value: CM from M2-BMDM


title: Galectin-9 siRNA_2

description: Column name: RC_LQC_22_A62_S14

value: Primary moDCs

value: Galectin-9 siRNA

value: Donor 2


title: M2-BMDM treated B16F10-3

value: murine melanoma cell


title: Col-0 wild type, biological replicate #1

value: No treatment


title: M1-BMDM treated B16F10-3

value: CM from M1-BMDM


title: CITE-seq - Non-granuloma Monkey 2 - ADT library

description:
Library name: U3_ADT
Antibody-derived Oligonucleotide (ADT)

value: Lung

value: Infected with M.Tuberculosis


title: Donor T cells from mice treated with control CAR T, ADT/HTO (CD45.2+/CD3+)

description:
Library name: Control_DonorT_ADT_HTO
antibody-derived oligonucleotide
Control_DonorT.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_DonorT.filtered_feature_bc_matrix.features.tsv.gz
Control_DonorT.filtered_feature_bc_matrix.matrix.mtx.gz
Control_DonorT.raw_feature_bc_matrix.barcodes.tsv.gz
Control_DonorT.raw_feature_bc_matrix.features.tsv.gz
Control_DonorT.raw_feature_bc_matrix.matrix.mtx.gz

value: T cells


title: CITE-seq - Non-granuloma Monkey 2 - mRNA library

description:
Library name: U3_mRNA
polyA RNA

value: Macrophages + Immune cells


title: Donor T cells from mice treated with control CAR T, TCR  (CD45.2+/CD3+)

description:
Library name: Control_DonorT_TCR_VDJ
T cell receptor sequence


title: M1-BMDM treated B16F10-1

value: WT


title: M1-BMDM treated B16F10-2


title: serk1-1 wild type, biological replicate #1


title: CITE-seq - Granuloma Monkey 1 - ADT library

description:
Library name: B2_ADT
Antibody-derived Oligonucleotide (ADT)


title: Donor T cells from mice treated with control CAR T, GEX (CD45.2+/CD3+)

description:
Library name: Control_DonorT_GEX
5' gene expression
Control_DonorT.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_DonorT.filtered_feature_bc_matrix.features.tsv.gz
Control_DonorT.filtered_feature_bc_matrix.matrix.mtx.gz
Control_DonorT.raw_feature_bc_matrix.barcodes.tsv.gz
Control_DonorT.raw_feature_bc_matrix.features.tsv.gz
Control_DonorT.raw_feature_bc_matrix.matrix.mtx.gz

value: Blood


title: M0-BMDM treated B16F10-3

value: CM from M0-BMDM


title: Tbx5 KO, Left ventricle, Replicate 3

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago

description: Library name: Sample 6

data_processing:
Dataset was processed  with the UCSC mm10 genome assembly through nf-core/rnaseq v3.13.2. The pipeline employed reproducible environments from the Bioconda and Biocontainers projects, using STAR v2.6.1d for read alignment, Samtools v1.10 for file processing, and Salmon v1.10.1 for transcript quantification. Pipeline execution was coordinated with Nextflow v23.10.0.
Assembly: mm10
Supplementary files format and content: Salmon quant files

source_name: Heart, left ventricle

growth_protocol: Mice were raised according to university protocols (protocol # 71737).

extract_protocol:
Tissues were mechanically homogenized in TRIzol Reagent (Invitrogen), chloroform was added, aqueous phase was isolated, ethanol was added, and then RNA was isolated using RNeasy Mini Columns. Overall, 12μg of total RNA for each sample was treated with the mouse GlobinClear kit (Ambion) to remove the majority of globin RNA
Total RNA was prepared with a TRIzol-based extraction and isolated using a Qiagen RNeasy Mini Column

treatment_protocol: A tamoxifen inducible cre recombinase driven by the ubiquitous R26 promoter was used to excise exon 3 of TBX5 as previously described (Arnolds et al JCI 2012). Excision of TBX5 was induced by IP tamoxifen for 3 days, 0.167mg tamoxifen/day. Mice were sacrificed at 1 week post tamoxifen and right and left atrial appendage were dissected.

value: Heart, left ventricle


title: RN2 cells from mice treated with control CAR T, ADT/HTO (CD45.2+/CD11b+)

description:
Library name: Control_RN2_ADT_HTO
antibody-derived oligonucleotide
Control_RN2.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_RN2.filtered_feature_bc_matrix.features.tsv.gz
Control_RN2.filtered_feature_bc_matrix.matrix.mtx.gz
Control_RN2.raw_feature_bc_matrix.barcodes.tsv.gz
Control_RN2.raw_feature_bc_matrix.features.tsv.gz
Control_RN2.raw_feature_bc_matrix.matrix.mtx.gz

value: RN2 AML

value: Control CAR


title: Tbx5 KO, Left ventricle, Replicate 1

description: Library name: Sample 4


title: CITE-seq - Granuloma Monkey 1 - mRNA library

description:
Library name: B2_mRNA
polyA RNA


title: RN2 cells from mice treated with control CAR T, GEX (CD45.2+/CD11b+)

description:
Library name: Control_RN2_GEX
5' gene expression
Control_RN2.filtered_feature_bc_matrix.barcodes.tsv.gz
Control_RN2.filtered_feature_bc_matrix.features.tsv.gz
Control_RN2.filtered_feature_bc_matrix.matrix.mtx.gz
Control_RN2.raw_feature_bc_matrix.barcodes.tsv.gz
Control_RN2.raw_feature_bc_matrix.features.tsv.gz
Control_RN2.raw_feature_bc_matrix.matrix.mtx.gz


title: M0-BMDM treated B16F10-2

city: Shanghai


title: Control, Left ventricle, Replicate 2

description: Library name: Sample 2


title: S. Typhimurium ΔcspE, bile treatment, replicate 3

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Rockhopper
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trimgalore
Trimmed sequence reads were processed using Rockhopper Pipeline
Read count extraction and normalization were performed using featureCounts
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium
Supplementary files format and content: Read_Count_Data_All_Samples.xLSX

source_name: Bacteria

growth_protocol: Salmonella Typhimurium wild type and ΔcspE strains were grown in Luria Broth (LB) (Miller) with or without 3% bile (Sigma) at 37 °C, 180 rpm.

extract_protocol:
RNA was isolated using Trizol (Ambion)-chloroform (Sigma) extraction method.
As per Illumina recommended protocol

treatment_protocol: Cells were grown to O.D. 0.3 and then treated with 3% bile for 90 minutes.

value: Bacteria

value: cspE knockout

value: Bile stress


title: Control, Left ventricle, Replicate 1

description: Library name: Sample 1


title: p53-defective feeders

city: 沈阳市

first: Zonghua

last: Ma

state: 辽宁省

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

institute: Northeastern University

description: Library name: DNp53_feeder

data_processing:
3 million paired-end reads suffice for nucleosome modifications, even for the mouse genome. For maximum economy, up to 96 barcoded samples per 2-lane flow cell can be pooled for 25 × 25 bp sequencing. For peak calling, parameters used were macs2 callpeak—t input_file –p 1e-5 –f BEDPE/BED(Paired End vs. Single End sequencing data) –keep-dup all –n out_name.
Assembly: Ensembl mouse (mm10/GRCm38) reference genomes
Library strategy: CUT&Tag

source_name: Embryonic fibroblasts

extract_protocol:
In brief, about 50,000 cells were bound to activated Concanavalin A beads. Cells-beads complex were incubated with the p53 antibody and homologous secondary antibody. Hyperactive pG-Tn5 adapter complex with a concentration of 0.04 μM was added to the cells with gentle vortexing and incubated at RT for 1 h.
21 µL DNA was mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. Post-PCR clean-up was performed by adding 1.1× volume of Ampure XP beads (Beckman Counter), and libraries were incubated with beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 µL 10 mM Tris pH 8.0.

value: Embryonic fibroblasts

value: paired-end


title: M0-BMDM treated B16F10-1

value: murine melanoma cell


title: CITE-seq - Granuloma Monkey 2 - mRNA library

description:
Library name: B3_mRNA
polyA RNA


title: S. Typhimurium ΔcspE, bile treatment, replicate 2

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: Control feeders

address: 辽宁省沈阳市东北大学浑南校区生命科学与健康学院

description: Library name: primarary_feede


title: S. Typhimurium ΔcspE, bile treatment, replicate 1


title: Tbx5 KO, Left ventricle, Replicate 2

description: Library name: Sample 5


title: S. Typhimurium WT, bile treatment, replicate 3

value: Wild type


title: MVT2

city: shanghai

first: dan

last: zhou

address: shanghai

department: Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine

institute: Tongji University

description:
Library name: sample 7
vitrified blastocyst with 10-10 M melatonin added to vitrification and thawing media, replicate biosample 2

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

source_name: Blastocyst

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Blastocyst

tag: group

value: melatonin treated vitrification


title: Calu-3SAMHD1knockout2_20hours_2

city: Iowa City

first: Pak Hin Hinson

last: Cheung

state: Iowa

address: 51 Newton Raod

department: Department of Microbiology and Immunology

institute: University of Iowa

description:
Library name: KO2-2
Column name in raw count.xlsx: S_8_KO25

data_processing:
Gene expression profiling using RNA-Seq was performed by the University of Iowa Genomics Division using manufacturer recommended protocols. Briefly, at least 500 ng of DNase I-treated total RNA was used to prepare sequencing libraries using the Illumina stranded mRNA library preparation kit (Cat. #20040534, Illumina, Inc., San Diego, CA). Barcoded libraries were quantified using a Qubit fluorometer (ThermoFisher Scientific) and pooled together to give the same molar concentration per sample. The pooled libraries were sequenced on the Element AVITI24 sequencing platform (Element Biosciences, San Diego, CA) on a Cloudbreak FS 150 cycle (2x75 bp) medium output sequencing flow cell (Cat. #:  860-00014) to generate at least 30M paired-end sequencing reads per sample. The raw base files were converted to fastq files using the Bases2fastq v2.1 tool.
Assembly: GRCh38
Supplementary files format and content: Excel

growth_protocol: Calu-3 Ctrl, KO1 and KO2 cells were grown in DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin

extract_protocol:
8 x 105 Calu-3 Ctrl, KO1 and KO2 cells were seeded in 6 well plates in biological triplicate. Cells were cultured in 2mL DMEM/F12 with 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. At 20 hours after seeding, cells were washed once with DPBS and lysed with RLT plus lysis buffer. Cellular RNA was purified with RNeasy Plus kit following manufacturer’s instructions. All RNA samples got RNA integrity Number (RIN) scores equal to or more than 9.9 as determined by Agilent BioAnalyzer by Genomics Division of Iowa Institute of Human Genetics (University of Iowa). RNA samples were processed through Illumina Stranded mRNA Prep (illumina) and sequenced by Element Aviti24 using Cloudbreak FS-High output flow cell at 150 cycle (2x75) by the Genomics Division.
The RNA samples were processed through Illumina Stranded mRNA Prep following manufacturer's protocol.

treatment_protocol: No additional treatment

value: Human bronciolar epithelial cells

value: SAMHD1 knockout by exon 4 frameshifting

value: 20 hours culturing in DMEM/F12 20% FBS, 1xP/S


title: Calu-3SAMHD1knockout2_20hours_1

description:
Library name: KO2-1
Column name in raw count.xlsx: S_7_KO24


title: MVT1

description:
Library name: sample 6
vitrified blastocyst with 10-10 M melatonin added to vitrification and thawing media, replicate biosample 1


title: Calu-3SAMHD1knockout1_20hours_3

description:
Library name: KO1-3
Column name in raw count.xlsx: S_6_KO16

value: SAMHD1 knockout by exon 1 frameshifting


title: Calu-3SAMHD1knockout1_20hours_1

description:
Library name: KO1-1
Column name in raw count.xlsx: S_4_KO14


title: Control, Left ventricle, Replicate 3

description: Library name: Sample 3


title: S. Typhimurium WT, bile treatment, replicate 2


title: Calu-3SAMHD1knockout2_20hours_3

description:
Library name: KO2-3
Column name in raw count.xlsx: S_9_KO26


title: S. Typhimurium WT, bile treatment, replicate 1