title: prf3_treat_6h, rep3

city: Coventry

first: Andrew

middle: James

last: Bowman

state: West Midlands

address: Gibbet Hill, Gibbet Hill Campus, The University of Warwick

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description: Gene expression after 6hr post-infiltration  with P. syringae DC3000

hyb_protocol: 1.65 µg of linearly amplified and labelled cDNA was hybridized for 17 h at 65oC on 4 x180k format 60-mer oligonucleotide probes designed against the S.lycopersicum cv. Heinz 1706 build 2.4 (annotation 2.5) genome (Agilent design ID = 069672; GEO record GPL21602).

scan_protocol: Arrays were imaged using an MS200 microarray scanner with only the 480 nm laser and using the autogain feature of the NimbleScan software. Image (tiff) files were imported into the Agilent Feature Extraction software for quality control assessment, grid alignment and expression value extraction at the probe and transcript level with the RMA algorithm.

data_processing:
Linear Models for Microarray Data (package limma in R) was then used to correct background with backgroundCorrect function, method normexp and normalized between arrays using normalizeBetweenArrays method scale. Then linear models was fit to pairs of samples, identifying genes that contrasted the most between the experimental pairs. Transcripts were termed to be differentially expressed if they showed a Benjamini-Hochberg adjusted P-value ≤ 0.05 in the comparison between treatment and control.
ProcessedData.txt - supplementary file linked to Series record.  The data provided in the ProcessedData.txt file has been further processed to avoid false positive differentially expressed genes in downstream analysis. From the Feature Extraction files Linear Models for Microarray Data (package limma in R) was used to correct background with backgroundCorrect function, method normexp and normalized between arrays using normalizeBetweenArrays method scale. The function avereps was applied to average replicated spots (ID = ProbeName), producing the Matrix template (separate .txt file). From these data, the function averep was used again to average genes with several probes according to GPL21602 (ID = SPOT_ID). Then Spike probes, and genes with values consistently below the lowest spike or consistently above highest spike were removed to produce the ProcessedData.txt datafile. These data was then used to fit linear models to pairs of samples, identifying genes that contrasted the most between the experimental pairs. Transcripts were termed to be differentially expressed if they showed a Benjamini-Hochberg adjusted P-value less than or equal to 0.05 in the comparison between treatment and control.

organism: Solanum lycopersicum

label_protocol: First-strand cDNA synthesis was performed from 2 µg of total RNA using RevertAid reverse transcriptase (Invitrogen). 200 ng of RNA was used for cDNA synthesis and Cy3-labelling using the Low Input Quick Amp Labeling Kit for One-Color Microarray-Based Gene Expression Agilent analysis.

growth_protocol: Tomato Rio Grande prf3, Prf-SBP-FLAG and tft3 2-2 lines were grown in the greenhouse with 16 h of light and average temperature of 24 °C.

extract_protocol: After tissue harvesting and grinding in liquid nitrogen, RNA extraction was performed using a RNeasy kit (QIAGEN) and quality checked using Bioanalyzer analysis.

treatment_protocol: Leaves of four-week-old tomato prf3, Prf-SBP-FLAG and tft3 2-2 lines were vacuum infiltrated with Pseudomonas syringae DC3000 (OD=0.1) for 6 h; 10 mM MgCl2 infiltration served as control. All infiltrations were carried out in biological triplicate and three technical replicates were used.

tag: strain

value: Rio Grande

value: Leaves

tag: developmental stage

value: P. syringae DC3000


title: Cap_16

status: Public on Mar 28 2023

type: SRA

city: Yantai

first: Xicheng

last: Song

address: No.20, Yuhuangding East Road, Zhifu District, Yantai City, Shandong Province

department: Department of Otorhinolaryngology, Head and Neck Surgery

country: China

institute: Qingdao University Affiliated Yantai Yuhuangding Hospital

library_source: transcriptomic

data_processing:
The sequenced data are called raw reads. first, we filter out the rRNA, low quality, junctional contamination and high content of unknown base N reads, and the filtered data are called clean reads. then the clean reads are compared to the reference genome and transcriptome respectively. In this project, we used UW's self-developed filtering software SOAPnuke for filtering, HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) software for genome comparison, and Bowtie2 to align the clean reads to the reference genes. Reference genome version: GCF_000001405.39_GRCh38.p13.
Supplementary files format and content: Processed data are formatted for Microsoft Excel (.xls extension). Files contain Transcript per Kilobase per Million mapped reads (TPM) reads of samples of interest.

molecule: total RNA

organism: Homo sapiens

source_name: Paraneoplastic tissue of laryngeal squamous cell carcinoma

extract_protocol: The extracted total RNA was first removed from the ribosomal rRNA using the MGIEasy rRNA removal kit. after purification, the RNA was fragmented at a certain temperature and ionic environment. The cDNA first strand is then synthesized using random primers and reverse transcriptase from the MGIEasy RNA Directional Library Preparation Kit, followed by the synthesis of double-stranded cDNA using DNA polymerase I and RNaseH. During cDNA second-strand synthesis, the RNA template is removed and dTTP is replaced by dUTP. dUTP involvement prevents the cDNA second strand from being amplified in subsequent processes amplified in subsequent processes because the polymerase is unable to cross the dUTP site on the template during extension. The double-stranded cDNA product is then ligated with an "A" base and a splice. The ligated product is amplified, the PCR product is heat denatured to a single strand, and a bridge primer is used to loop the single stranded DNA to obtain a single stranded circular DNA library for sequencing.

tag: tissue

tag: cell type

value: Normal human epithelial tissue


title: Cap_15

value: Paraneoplastic tissue of laryngeal squamous cell carcinoma


title: Tft3_2-2treat_6h, rep3

type: RNA

tag: genotype

tag: treatment


title: Tft3_2-2treat_6h, rep2


title: Ca_9

source_name: Laryngeal squamous cell carcinoma tissue

value: Squamous cell carcinoma


title: M_i_36

city: nanjing

first: Xiangyu

last: Ma

state: JIANGSU

address: No. 2, Sipai Building, Dashiqiao Community, Xinjiekou Street, Xuanwu District, Nanjing

institute: Southeast University

description:
M_i_36
This sample represents a single cell.

data_processing:
Sample quality and yield were determined with a Bioanalyzer (Agilent). The DNA was sequenced from the 43 bp-end with both i5 and i7 indices (6 bp each) using an Illumina HiSeq 2500. And then, raw reads were filtered with Trimmomatic software and aligned to the GRCm38 mm10 assembly reference genome with hisat2 . Reads mapped to the mouse transcriptome were counted using the featureCounts program in the Subread package (v 1.4.6).
Genome_build: mm10

organism: Mus musculus

source_name: cochlea

extract_protocol:
Sample quality and yield were determined with a Bioanalyzer (Agilent). The DNA was sequenced from the 43 bp-end with both i5 and i7 indices (6 bp each) using an Illumina HiSeq 2500
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cochlea

tag: region

value: inner hair cells/middle

tag: age


title: Tft3_2-2treat_6h, rep1


title: M_i_35

description:
M_i_35
This sample represents a single cell.


title: M_i_38

description:
M_i_38
This sample represents a single cell.


title: prf3_treat_6h, rep2


title: Prfc_treat_6h, rep3

value: Prfc


title: prf3_treat_6h, rep1


title: Tft3_2-2control, rep3

description: Gene expression after 6hr post-infiltration (MgCl2, control)

value: control


title: M_i_31

description:
M_i_31
This sample represents a single cell.


title: Ca_15

value: Laryngeal squamous cell carcinoma tissue


title: M_i_30

description:
M_i_30
This sample represents a single cell.


title: Ca_16


title: Ca_14

source_name: Hypopharyngeal carcinoma tissue

value: Hypopharyngeal carcinoma tissue


title: Prfc_treat_6h, rep1


title: prf3_control, rep1


title: prf3_control, rep3


title: Prfc_treat_6h, rep2


title: M_i_29

description:
M_i_29
This sample represents a single cell.


title: M_i_117

description:
M_i_117
This sample represents a single cell.


title: Ca_11


title: Prfc_control, rep3


title: M_i_118

description:
M_i_118
This sample represents a single cell.


title: Prfc_control, rep1


title: cyaA_2

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

country: USA

institute: The University of Maryland, College Park

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 then mapped to the e_coli_MG1655_NCBI reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6.
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 locus_tag feature in the annotation file. Only unique reads that fell within gene regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: e_coli_MG1655_NCBI reference genome available on ENSEMBL
Supplementary files format and content: counts

organism: Escherichia coli BW25113

source_name: Escherichia coli K-12 BW25113

growth_protocol: Growth in LB at 37 °C to mid-log phase

extract_protocol:
Total RNA extraction using QiaGen RNAeasy kit according to manufacture's protocol
rRNA depletion and library preperation by Genewiz according to standard protocol
RNA-seq by Genewiz

value: Bacterial cell

value: {delta}cyaA


title: M_i_37

description:
M_i_37
This sample represents a single cell.


title: cyaA_1


title: M_i_116

description:
M_i_116
This sample represents a single cell.


title: BW_2

value: Wild-type


title: Tft3_2-2control, rep2


title: M_i_112

description:
M_i_112
This sample represents a single cell.


title: BW_1


title: M_i_110

description:
M_i_110
This sample represents a single cell.


title: Tft3_2-2control, rep1


title: M_i_108

description:
M_i_108
This sample represents a single cell.


title: prf3_control, rep2


title: M_i_109

description:
M_i_109
This sample represents a single cell.


title: Prfc_control, rep2


title: M_i_106

description:
M_i_106
This sample represents a single cell.


title: M_i_28

description:
M_i_28
This sample represents a single cell.


title: M_i_107

description:
M_i_107
This sample represents a single cell.


title: M_i_105

description:
M_i_105
This sample represents a single cell.


title: M_i_104

description:
M_i_104
This sample represents a single cell.


title: M_i_102

description:
M_i_102
This sample represents a single cell.


title: B_o_52

description:
B_o_52
This sample represents a single cell.

value: outer hair cells/base


title: M_i_103

description:
M_i_103
This sample represents a single cell.


title: B_o_50

description:
B_o_50
This sample represents a single cell.


title: B_o_51

description:
B_o_51
This sample represents a single cell.


title: B_o_49

description:
B_o_49
This sample represents a single cell.


title: B_o_41

description:
B_o_41
This sample represents a single cell.


title: B_o_48

description:
B_o_48
This sample represents a single cell.


title: B_o_106

description:
B_o_106
This sample represents a single cell.


title: B_i_76

description:
B_i_76
This sample represents a single cell.

value: inner hair cells/base


title: B_i_75

description:
B_i_75
This sample represents a single cell.


title: B_o_103

description:
B_o_103
This sample represents a single cell.


title: B_i_74

description:
B_i_74
This sample represents a single cell.


title: B_i_77

description:
B_i_77
This sample represents a single cell.


title: B_i_73

description:
B_i_73
This sample represents a single cell.


title: B_i_68

description:
B_i_68
This sample represents a single cell.


title: B_i_66

description:
B_i_66
This sample represents a single cell.


title: B_i_62

description:
B_i_62
This sample represents a single cell.


title: B_i_64

description:
B_i_64
This sample represents a single cell.


title: B_i_109

description:
B_i_109
This sample represents a single cell.


title: B_i_61

description:
B_i_61
This sample represents a single cell.


title: B_i_114

description:
B_i_114
This sample represents a single cell.


title: B_i_65

description:
B_i_65
This sample represents a single cell.


title: B_i_115

description:
B_i_115
This sample represents a single cell.


title: B_i_63

description:
B_i_63
This sample represents a single cell.


title: B_i_106

description:
B_i_106
This sample represents a single cell.


title: B_i_117

description:
B_i_117
This sample represents a single cell.


title: B_i_102

description:
B_i_102
This sample represents a single cell.


title: A_o_20

description:
A_o_20
This sample represents a single cell.

value: outer hair cell /apex


title: B_i_101

description:
B_i_101
This sample represents a single cell.


title: A_o_19

description:
A_o_19
This sample represents a single cell.


title: A_o_22

description:
A_o_22
This sample represents a single cell.


title: A_o_18

description:
A_o_18
This sample represents a single cell.


title: A_o_14

description:
A_o_14
This sample represents a single cell.


title: A_o_120

description:
A_o_120
This sample represents a single cell.


title: A_o_13

description:
A_o_13
This sample represents a single cell.


title: A_o_11

description:
A_o_11
This sample represents a single cell.


title: A_o_12

description:
A_o_12
This sample represents a single cell.


title: A_o_119

description:
A_o_119
This sample represents a single cell.


title: A_o_116

description:
A_o_116
This sample represents a single cell.


title: A_o_118

description:
A_o_118
This sample represents a single cell.


title: B cells transfected with CD40-encoding mRNA and NK cells transfected with CD40L-encoding mRNA

city: Stanford

first: Aaron

last: Wilk

state: California

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
mRNA reads in read 2 FASTQ files tagged with cell barcode and UMI from read 1 file with dropTag (dropEst)
Tagged reads aligned with STAR using GRCh37 including the complete sequences of exogenous transfected GFP-, CD40-, and CD40L-encoding mRNAs
Count matrices built from BAM files using dropEst
Assembly: GRCh37 including the complete sequences of exogenous transfected GFP-, CD40-, and CD40L-encoding mRNAs
Supplementary files format and content: .rds files containing exonic, intronic, and spanning count matrices

molecule: polyA RNA

source_name: Peripheral blood mononuclear cells

growth_protocol: No growth or treatment performed

extract_protocol:
Immediately after Ficoll separation, 50,000 PBMCs were resuspended in RPMI + 10% FCS at a concentration of 75,000 cells/mL. 200 μL of this cell suspension (15,000 cells) was then loaded onto Seq-Well arrays pre-loaded with mRNA capture beads (ChemGenes). Following four washes with DPBS to remove serum, the arrays were sealed with a polycarbonate membrane (pore size of 0.01 µm) for 30 minutes at 37°C and then frozen at -80°C for no less than 24 hours and no more than 14 days to allow batching of samples processed at irregular hours. Next, arrays were thawed, cells lysed, transcripts hybridized to the mRNA capture beads, and beads recovered from the arrays and pooled for downstream processing.
Library preparation was performed with a Nextera XT DNA library preparation kit (Illumina FC-131-1096) with 1 ng of pooled library using dual-index primers. Tagmented and amplified libraries were again purified by Agencourt AMPure XP beads with a 0.6x volume wash followed by a 1.0x volume wash, and quality and concentration determined by Fragment Analysis. Libraries between 400-1000bp with no primer peaks were considered successful and pooled for sequencing. Sequencing was performed on a NovaSeq S2 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with read 1 beginning from a custom read 1 primer11 containing a 12bp cell barcode and an 8 bp unique molecular identifier (UMI), and with read 2 containing 50bp of mRNA sequence.

treatment_protocol: No growth or treatment performed

value: PBMCs

tag: sample origin

value: Healthy patient consented for release of genomic information

tag: transfection


title: B cells transfected with GFP-encoding mRNA and NK cells transfected with CD40L-encoding mRNA


title: A_o_113

description:
A_o_113
This sample represents a single cell.


title: A_o_112

description:
A_o_112
This sample represents a single cell.


title: B cells and NK cells transfected with GFP-encoding mRNA


title: A_o_110

description:
A_o_110
This sample represents a single cell.


title: A_o_21

description:
A_o_21
This sample represents a single cell.


title: A_o_108

description:
A_o_108
This sample represents a single cell.


title: A_o_107

description:
A_o_107
This sample represents a single cell.


title: A_i_27

description:
A_i_27
This sample represents a single cell.

value: inner hair cell /apex


title: A_o_105

description:
A_o_105
This sample represents a single cell.


title: A_i_8

description:
A_i_8
This sample represents a single cell.


title: H295R_RIP_IP_Rep1

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Salmon (Patro et al. 2017) was used for quantifying transcript levels from all libraries using Gencode v26 (parameters -l A --allowDovetail --validateMappings).
Assembly: Gencode GRCh38 v26
Supplementary files format and content: Comma separated text files with raw transcript counts quantified using salmon

growth_protocol: H295R cells were cultured in complete media (DMEM/F12 media, 10% Cosmic Calf Serum, 1% Insulin-Transferrin-Selenium) at 37°C, 5% CO2. For all ELISA assays, cells were cultured in low sera media (DMEM/F12 media, 0.1% Cosmic Calf Serum, 1% Insulin-Transferrin-Selenium).

extract_protocol:
Beads were resuspended in TRIZOL to release RNPs. RNA isolation was performed using ZYMO Research Direct-zol RNA Microprep kit with on-column DNaseI treatment.
Ribosomal RNA was depleted from the samples as described in Baldwin et. al., 2021 (PMID: 34165268). Library was prepared using KAPA RNA Hyper kit and KAPA Dual index adapters.

treatment_protocol: RIP-Seq was performed as described in Wessels et al., 2016 (PMID: 26463382). Briefly H295R cells were lysed in NT2 buffer and incubated with Dyna beads coated with 5 µg anti-MSI2 antibody (Abcam ab-76148) for 20 min in RT. Beads were washed 5x with 1ml of NT2 buffer and resuspended in 100 µl of NT2 buffer.

value: IP


title: H295R_RIP_IP_Rep2


title: H295R_RIP_input_Rep2

value: input


title: M2, co-cultured with Adipocyte, biol rep 3

city: Berkeley

first: Yuchen

last: He

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

data_processing:
FASTQ file generation was performed by Novogene using Illumina NovaSeq 6000
Original image data file from the high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
STAR 2.7.2b  alignment software was used to accomplish the mapping.
Assembly: Ensembl Homo_sapiens.GRCh38.96
Supplementary files format and content: Tab-delimited text files include RPKM values of all Samples

source_name: WTC11 iPSC

growth_protocol: The human M1 and M2 iMACs were generated using methods detailed in our previous publication. Briefly, iPSCs from the WTC-11 human iPSC line were induced to hematopoietic stem cells using commercial media (STEMdiffTM Hematopoietic Kit, Stemcell Technologies). Floating HSCs were collected and further differentiated toward the human monocyte lineages in RPMI 1640 medium with 10% fetal bovine serum (Avantor Seradigm), 1% penicillin/streptomycin, and 100 ng/mL macrophage-colony stimulating factors (M-CSF). We previously showed that these iMACs were more M2 like, and so these cells were used directly as M2 iMACs.  M1 macrophages were obtained by polarizing the M2-like macrophages in culture medium supplemented with 10ng/mL LPS and 20 ng/mL IFN for one day prior to use. Differentiation efficiency was approximate 70%. On the day of use, the cells were washed in fresh medium with M-CSF and then magnetically sorted using anti-CD45 coated beads (Miltenyi Biotec) before loading into our coculture system or MPS. Fidelity of iMACs was examined by cytokine profiles. Trace of LPS carryover was also examined by endotoxin assay (E-TOXATE Kit, Sigma Aldrich) to avoid unintended LPS-adipocyte interaction.    Differentiation of iADIPOs were described in our previous study. Briefly, all iPSCs were firstly differentiated into mesenchymal level (iPSC-MSCs) then transfected with exogeneous PPAR. The iPSC-MSCs were thus chemically inducible for overexpressing PPARgamma to enhance adipogenesis. The fidelity and mesenchymal potency of WTC11 iPSC-MSCs was verified previously. For proliferation, iPSC-MSCs were cultivated in a commercial medium (MesenCult-ACF Plus, Stem Cell Technologies) with 30~70% of confluency. For differentiation, cells were grown to confluent with 2 days post-confluent culture. Differentiation was initiated in complete medium (DMEM/F12 containing 1% HEPES, 1% penicillin/streptomycin (all from Gibco) and 10% fetal bovine serum (Equafetal)) with supplements of 0.25 M dexamethasone, 0.25 mM 3-isobutyl-1-methylxanthine (Sigma-Aldrich), 100 nM rosiglitazone (all from Sigma-Aldrich), 500 nM insulin (Humulin R, Eli Lilly) for 4 days (Day 0 to 3). The rest differentiation was in the complete medium with supplements of insulin and rosiglitazone at the same concentration (Day 4 to the end). Exogeneous PPAR was expressed by addition of 1 g/mL doxycycline from Day 0 till the end. A TGF- pathway inhibitor, SB431542 (abcam), was added into media from Day -2 to Day 14  to prevent chondrogenesis. Final differentiation efficiency is competent to primary adipocytes collected from human biopsy, verified by lipid coverage and gene expression.

extract_protocol:
Cells were lysed with TRI reagent, RNA was extracted by Applied biosystems PicoPure RNA isolation kit
Library construction was performed by Novogene. ThepolyA enrichment library preparationprocedure was used and resulted in the construction of 250-300 bp insert cDNA library.

treatment_protocol: Macrophages and adipocytes were monocultured in 24-well plate or cocultured in 24-well trans-well settings with 0.3 mL medium per well with supply of 50 ng/mL M-CSF for 2 days.

tag: cell line

value: WTC11 iPSC

value: Macrophage

value: WT

value: HSC and monocyte differentiation

tag: condition


title: M2, co-cultured with Adipocyte, biol rep 1


title: A_i_25

description:
A_i_25
This sample represents a single cell.

value: cochlea


title: M2, co-cultured with Adipocyte, biol rep 2


title: A_o_114

description:
A_o_114
This sample represents a single cell.


title: M1, co-cultured with Adipocyte, biol rep 2


title: M1, co-cultured with Adipocyte, biol rep 3


title: A_i_23

description:
A_i_23
This sample represents a single cell.


title: A_o_115

description:
A_o_115
This sample represents a single cell.


title: A_i_24

description:
A_i_24
This sample represents a single cell.


title: B cells transfected with CD40-encoding mRNA and NK cells transfected with GFP-encoding mRNA


title: A_i_22

description:
A_i_22
This sample represents a single cell.


title: M2, monoculture control, biol rep 3


title: M2, monoculture control, biol rep 2


title: M1, co-cultured with Adipocyte, biol rep 1


title: A_i_21

description:
A_i_21
This sample represents a single cell.


title: A_i_20

description:
A_i_20
This sample represents a single cell.


title: A_i_19

description:
A_i_19
This sample represents a single cell.


title: H295R_RIP_input_Rep1


title: M1, monoculture control, biol rep 2


title: M2, monoculture control, biol rep 1


title: M1, monoculture control, biol rep 1


title: A_i_18

description:
A_i_18
This sample represents a single cell.


title: A_i_17_2

description:
A_i_17_2
This sample represents a single cell.


title: A_i_26

description:
A_i_26
This sample represents a single cell.


title: A_i_17

description:
A_i_17
This sample represents a single cell.


title: Adipocyte, co-cultured with M2, biol rep 1

value: Adipocyte

value: MSC and adipogenic differentiation, PPARG lentivius transduction


title: Adipocyte, co-cultured with M2, biol rep 2


title: Adipocyte, co-cultured with M2, biol rep 3


title: Adipocyte, co-cultured with M1, biol rep 3


title: A_i_14

description:
A_i_14
This sample represents a single cell.


title: Adiopicyte, monoculture control, biol rep 2

value: Acontrol


title: A_i_12

description:
A_i_12
This sample represents a single cell.


title: Adipocyte, co-cultured with M1, biol rep 2


title: A_i_115

description:
A_i_115
This sample represents a single cell.


title: C666_1

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

description:
C666_1
tpm.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: MGC 803

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: MGC 803

value: mixed origins of the MGC 803 cell line


title: Adiopicyte, monoculture control, biol rep 1


title: A_i_120

description:
A_i_120
This sample represents a single cell.


title: Acox1-/- rep2

city: Dijon

first: Stéphane

last: Savary

address: 6 Bd Gabriel

country: France

institute: University of Bourgogne

data_processing:
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the mm10 assembly of human genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 91.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: BV-2 microglial cells (KO Acox1)

growth_protocol: WT and mutant BV-2 cells were grown in DMEM supplemented with 10% heat-inactivated FBS (Corning), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco). Cultures were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from 3 independent batches of BV-2 cells for each genotype (WT, Abcd1-/-, Abcd2-/-, Abcd1-/-/Abcd2-/-, and Acox1-/-) using RNeasy kit (Qiagen).
RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: A treatment with 0.01% ethanol and 0.5 mM α-cyclodextrine (vehicle) was applied.


title: Acox1-/- rep3


title: A_i_116

description:
A_i_116
This sample represents a single cell.


title: A_i_118

description:
A_i_118
This sample represents a single cell.


title: A_i_117

description:
A_i_117
This sample represents a single cell.


title: A_i_11

description:
A_i_11
This sample represents a single cell.


title: CNE_2

description:
CNE_2
tpm.txt


title: Adiopicyte, monoculture control, biol rep 3


title: A_i_114

description:
A_i_114
This sample represents a single cell.


title: A_i_113

description:
A_i_113
This sample represents a single cell.


title: Adipocyte, co-cultured with M1, biol rep 1


title: scRNA-seq of Homo sapiens: 382-01 preboost d201 blood IgDlo, bio rep 1

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description:
10x Genomics
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
aggregation.csv.gz

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v6.0.1
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.
Supplementary files format and content: aggregation.csv contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: blood

extract_protocol:
PBMCs were isolated from blood and sorted for either plasmablasts or IgDlo B cells. Fine-needle aspiration was performed on draining ipsilateral axillary lymph nodes.
Libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' gene expression workflow

value: blood

value: IgDlo B cell

tag: isolate

tag: timepoint

value: pre-boost d201


title: scRNA-seq of Homo sapiens: 382-13 preboost d201 blood IgDlo, bio rep 2


title: scRNA-seq of Homo sapiens: 382-08 preboost d201 blood IgDlo, bio rep 1


title: scRNA-seq of Homo sapiens: 382-01 preboost d201 blood IgDlo, bio rep 2


title: scRNA-seq of Homo sapiens: 382-13 preboost d201 blood IgDlo, bio rep 1


title: scRNA-seq of Homo sapiens: 382-15 d57 lymph node, bio rep 2

source_name: lymph node

value: lymph node

value: various

value: post-boost d57


title: A_i_111

description:
A_i_111
This sample represents a single cell.

value: inner hair cell /apex


title: Abcd1-/-Abcd2-/- BV-2 rep2

source_name: BV-2 microglial cells (KO Abcd1/Abcd2)


title: scRNA-seq of Homo sapiens: 382-15 d15 lymph node, bio rep 2

value: post-boost d15


title: Abcd1-/-Abcd2-/- BV-2 rep1


title: scRNA-seq of Homo sapiens: 382-15 d15 lymph node, bio rep 1


title: A_i_110

description:
A_i_110
This sample represents a single cell.


title: A_i_9

description:
A_i_9
This sample represents a single cell.


title: Abcd2-/- BV-2 rep3

source_name: BV-2 microglial cells (KO Abcd2)


title: Abcd2-/- BV-2 rep2


title: Acox1-/- rep1


title: scRNA-seq of Homo sapiens: 382-13 d57 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-13 d15 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-01 d57 lymph node, bio rep 4


title: A_i_107

description:
A_i_107
This sample represents a single cell.


title: A_i_112

description:
A_i_112
This sample represents a single cell.


title: scRNA-seq of Homo sapiens: 382-08 preboost d201 blood IgDlo, bio rep 2


title: Abcd1-/-Abcd2-/- BV-2 rep3


title: Abcd2-/- BV-2 rep1


title: scRNA-seq of Homo sapiens: 382-13 d57 lymph node, bio rep 2


title: A_i_106

description:
A_i_106
This sample represents a single cell.


title: Abcd1-/- BV-2 rep3

source_name: BV-2 microglial cells (KO Abcd1)


title: scRNA-seq of Homo sapiens: 382-15 d57 lymph node, bio rep 1


title: A_i_105

description:
A_i_105
This sample represents a single cell.


title: scRNA-seq of Homo sapiens: 382-01 d57 lymph node, bio rep 1


title: A_i_109

description:
A_i_109
This sample represents a single cell.


title: scRNA-seq of Homo sapiens: 382-01 d15 lymph node, bio rep 4


title: scRNA-seq of Homo sapiens: 382-01 d15 lymph node, bio rep 3


title: A_i_104

description:
A_i_104
This sample represents a single cell.


title: scRNA-seq of Homo sapiens: 382-01 d15 lymph node, bio rep 2


title: A_i_103

description:
A_i_103
This sample represents a single cell.


title: scRNA-seq of Homo sapiens: 382-01 d15 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-07 d57 lymph node, bio rep 2


title: WT BV-2 rep3

source_name: BV-2 microglial cells (WT)


title: A_i_102

description:
A_i_102
This sample represents a single cell.


title: WT BV-2 rep2


title: Abcd1-/- BV-2 rep2


title: scRNA-seq of Homo sapiens: 382-07 d57 lymph node, bio rep 1


title: WT BV-2 rep1


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 6

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Base calling was perfromed using bcl2fastq (v2.20.0.422).
RNA-seq analysis was performed in R (v3.6.1). The scPipe package (v1.8.0) was employed to process and de-multiplex the data. A combined multiplexed FASTQ file was created from the R1 and R2 FASTQ files, by trimming the sample index and UMI sequences and storing them in the read header, using the sc_trim_barcode function (with bs2 = 0, bl2 = 8, us = 8, ul = 10).
Additionally, the original multiplexed R1 and R2 FASTQ files were de-multiplexed using cutadapt v3.0 (with error rate 1 and action none).
Read alignment was performed using the RSubread package (v2.0.0). An index was built using the human (GRCh38) and mouse (GRCm38) Ensembl primary assembly genome files and alignment performed with nBestLocations = 2, so that the first two locations for multi-mapping reads were reported, and keepReadOrder = TRUE. The second-best multi-mapping reads were removed using samtools (v1.7) and grep, by excluding reads with the “HI:i:2” tag. Species-specific reads were obtained using xenomapper (v1.0.2) with the cigar_scores option. The multi-mapping reads were kept in order to ensure that xenomapper could correctly compare reads that mapped uniquely in one species to reads mapping to multiple places in the second species. Any species-specific reads that were multi-mapping were removed using samtools and grep, by excluding reads with the “NH:i:2” tag.
Aligned reads were mapped to exons using the sc_exon_mapping function with the Ensembl Homo sapiens GRCh38 v99 GFF3 genome annotation file. The resulting BAM file was de-multiplexed and reads mapping to exons were associated with each individual sample using the sc_demultiplex function, taking the UMI into account, and an overall count for each gene for each was sample was generated using the sc_gene_counting function (with UMI_cor = 1).
UMI gene counts were processed using the edgeR package (v3.28.0). Two samples with low counts were excluded, lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method.
Differential gene expression analyses were performed using the limma package (v3.42.0), with the voomWithQualityWeights, lmFit, contrasts.fit and treat functions.
Assembly: hg38
Supplementary files format and content: Matrix table with UMI gene counts for every gene and every sample

source_name: Peritoneal exudate cells

extract_protocol:
Frozen peritoneal lavage cells were thawed briefly prior to RNA extraction. Total cellular RNA was extracted using QIAGEN RNeasy Mini columns as per manufacturer’s instructions (QIAGEN, Germany), including an on-column DNase digestion using the QIAGEN RNase-free DNase Set according to manufacturer’s instructions. RNA samples with an RNA integrity number (RIN) ≥ 7.0 by Bioanalyzer assessment were of an acceptable quality for RNA-seq analysis.
Libraries were generated using an in-house multiplex RNA-seq method (MHTP, Medical Genomics Facility) and were prepared using 10 ng of total RNA input. An 8 bp sample index and a 10 bp unique molecular identifier (UMI) were added during initial poly(A) priming and pooled samples were amplified using a template switching oligonucleotide. The Illumina P5 and P7 sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilised a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) used the standard R2 primer to sequence the cDNA in the sense direction for transcript identification. Paired-end sequencing (R1 19 bp; R2 72 bp) was performed on the NextSeq 550 (Illumina), using the v2.5 High Output Kit.

treatment_protocol: NSG mice bearing two different PDX were treated with i.p. recombinant human interferon epsilon (300 IU), recombinant human interferon beta (300 IU), recombinant mouse interferon epsilon  (3 IU, equivalent to 300 IU of human interferon epsilon), or PBS thrice weekly for 6 weeks after first detectable evidence of tumour growth in sentinel mice.

value: mIFNE


title: scRNA-seq of Homo sapiens: 382-02 d57 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-02 d15 lymph node


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 5


title: scRNA-seq of Homo sapiens: 382-08 d57 lymph node, bio rep 2


title: scRNA-seq of Homo sapiens: 382-02 d57 lymph node, bio rep 2


title: scRNA-seq of Homo sapiens: 382-01 d57 lymph node, bio rep 2


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 4


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 3


title: KGN-T5

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

description: KGN, ceramide

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: KGN

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: KGN

value: granulosa cell

value: ceramide


title: scRNA-seq of Homo sapiens: 382-08 d8 blood plasmablast, bio rep 2

value: plasmablast

value: post-boost d8


title: scRNA-seq of Homo sapiens: 382-08 d15 lymph node, bio rep 2


title: scRNA-seq of Homo sapiens: 382-08 d57 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-08 d15 lymph node, bio rep 1


title: scRNA-seq of Homo sapiens: 382-08 d8 blood plasmablast, bio rep 1


title: Abcd1-/- BV-2 rep1


title: scRNA-seq of Homo sapiens: 382-15 d8 blood plasmablast


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 2


title: KGN-T2

description: KGN, ceramide


title: scRNA-seq of Homo sapiens: 382-07 d15 lymph node


title: Peritoneal exudate cells – PDX134183, mIFNE replicate 1


title: KGN-T1

description: KGN, ceramide


title: scRNA-seq of Homo sapiens: 382-07 d8 blood plasmablast


title: scRNA-seq of Homo sapiens: 382-01 d8 blood plasmablast


title: KGN-C5

description: KGN, control

value: control


title: scRNA-seq of Homo sapiens: 382-02 d8 blood plasmablast


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 6

value: hIFNB


title: KGN-C4

description: KGN, control


title: KGN-T3

description: KGN, ceramide


title: EPR-overexpressing SW480 cells replica 2

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

data_processing:
demultiplexing: bcl2fastq v2.20.0.422
trimming: with BBDuk v38.49 from BBTools suite (sourceforge.net/projects/bbmap/).
alignment: STAR v2.5.3a
R v3.5.1 and Bioconductor v3.8 were used for secondary analysis
counts: featureCounts function from Rsubread v1.6.4 package was used to assign read counts to the genes of the Ensembl GRCm38.97
Assembly: hg38
Supplementary files format and content: bigwig files generated using bamCoverage (deeptools) with defaults parameters
Supplementary files format and content: CPM (counts per million) table matrix.

source_name: colon

growth_protocol: Colon adenocarcinoma cell lines SW480 cells (ICLC HTL99017), HCT116 (ICLC HTL95025), HCT-15 (ICLC HTL00001), CACO-2 (ICLC HTL97023), and HT-29 (ICLC HTL99026) were obtained from the Interlab Cell Line Collection at the Ospedale Policlinico San Martino IRCCS (Genova, Italy). SW480 cells stably over-expressing either full-length EPR (from nucleotide 1 to 1487 of murine BC030870 (10), named SW480-EPR) or EPRSTOPM (EPR mutated as described in ref. 10., named SW480-EPRSTOPM) as well as cells stably transfected with the empty vector (mock) were maintained in selective medium containing 1000 μg/ml G418 (Sigma-Aldrich). Transfections were performed using Lipofectamine 3000 (ThermoFisher).

extract_protocol:
cytoplasmic and nucleoplasmic RNAs were precipitated and washed with ice-cold 70% (vol/vol) ethanol prior to be dissolved in TriPure reagent (Roche) while the chromatin pellets were immediately dissolved in TriPure. Ten microliters of 0.5 M EDTA was added to all the samples in TriPure that were heated to 65 °C with vortexing until dissolved (~10 min).
paired-end

value: colon

value: epithelial

tag: build

value: EPR


title: EPR-overexpressing SW480 cells replica 3


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 4


title: EPR-overexpressing SW480 cells replica 1


title: mock SW480 cells replica 3

value: MOCK


title: KGN-C3

description: KGN, control


title: mock SW480 cells replica 2


title: scRNA-seq of Homo sapiens: 382-13 d15 lymph node, bio rep 2

value: lymph node


title: mock SW480 cells replica 1


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 2


title: neutrophil, unstimulated, donor4

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

description:
unstim_4b_D5
rsubread_featureCounts.csv
IFNg_all.csv
IL13_all.csv
IL4_all.csv

data_processing:
Sequencing was performed using Illumina NovoSeq 6000 S4 V1.5 and 2 x 100 bp read lengths.
The quality of the sequenced reads was assessed using FastQ (v.0.11.8) and MultiQC (v.1.10) software with default parameters.
Reads were aligned to the human genome with Rsubread (v.2.0.0) aligner
Statistical analysis of differential gene expression was assessed by DESeq2 algorithms
Data was analyzed in pairs, comparing read counts of cytokine stimulated cells to their unstimulated counterparts.
Assembly: hg38
Supplementary files format and content: rsubread_featureCounts.csv is a tab-delimited text file containing gene-wise read counts across the samples (rows with zero counts in all samples are omitted)
Supplementary files format and content: IFNg_all.csv is a tab-delimited text file containing the results of DESeq analysis of IFNg-stimulated versus unstimulated cells.
Supplementary files format and content: IL4_all.csv is a tab-delimited text file containing the results of DESeq analysis of IL-4-stimulated versus unstimulated cells.
Supplementary files format and content: IL13_all.csv is a tab-delimited text file containing the results of DESeq analysis of IL13-stimulated versus unstimulated cells.

source_name: peripheral blood

growth_protocol: Human neutrophils were purified from the peripheral blood of healthy donors using a discontinuous Percoll-gradient method followed by sorting

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Hilden, Germany) following the manufacturer's protocol.
Illumina Stranded mRNA Preparation kit (San Diego, CA, US) protocol 1000000124518 using Human Brain Total RNA AM7962 (ThermoFisher Scientific, Waltham, MA, US) as a positive control

treatment_protocol: After the isolation, neutrophils were resuspended to a concentration of 1-4x106 cells/ml into RPMI 1640 with 10 % FBS, L-glutamine and penicillin/streptomycin and stimulated with 100 ng/ml IL-4, IL-13 or IFN-γ at 37˚C for 1 h.

value: peripheral blood

value: neutrophil

value: unstimulated


title: scRNA-seq of Homo sapiens: 382-13 d8 blood plasmablast

value: blood


title: neutrophil, unstimulated, donor3

description:
unstim_3_D3
rsubread_featureCounts.csv
IFNg_all.csv
IL13_all.csv
IL4_all.csv


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 1

description:
C37
Excluded from final analysis due to low UMI counts.


title: neutrophil, unstimulated, donor2

description:
unstim_2_D2
rsubread_featureCounts.csv
IFNg_all.csv
IL13_all.csv
IL4_all.csv


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 5


title: neutrophil, IL4, 60 min, donor4

description:
IL_4_8b_D5
rsubread_featureCounts.csv
IL4_all.csv

value: IL4 100 ng/ml


title: neutrophil, unstimulated, donor1

description:
unstim_1_D1
rsubread_featureCounts.csv
IFNg_all.csv
IL13_all.csv
IL4_all.csv


title: neutrophil, IL4, 60 min, donor2

description:
IL_4_6_D2
rsubread_featureCounts.csv
IL4_all.csv


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 6

value: hIFNE


title: neutrophil, IL4, 60 min, donor3

description:
IL_4_7_D3
rsubread_featureCounts.csv
IL4_all.csv


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 5


title: RNA-seq of 3xTg mice treated by 1-month administration [T3]

city: Nanjing

first: Shang

last: Li

state: Jiangsu

address: Tongjia Valley No. 24

institute: China Pharmaceutical University

data_processing:
RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After purification, the double stranded PCR library was unzipped and then looped to form single stranded circular DNA.
The rolling circle amplification (RCA) technology is used to form DNA nanoball (DNB).
The DNB is loaded into the chip, which was then put into DNBSEQ-T7 for sequencing, and 150bp double ended sequencing reads was obtained.
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each Sample.

source_name: hippocampus

extract_protocol:
Total RNA of postmortem hippocampus from WT or 3xTg mice was extracted with TRIzol and chloroform, purified by the RNeasy mini kit (Qiagen).300 ng of RNA was used to prepare RNA sequencing library.
High-quality RNA was used to prepare RNA sequencing library with MGIEasy RNA library preparation kit V3.0 (96 RXN).

value: hippocampus

tag: Sex

value: female

value: 10 mg/kg of LP-10d, p.o. four times per week.


title: RNA-seq of 3xTg mice treated by 1-month administration [T2]


title: neutrophil, IL13, 60 min, donor3

description:
IL_13_11_D3
rsubread_featureCounts.csv
IL13_all.csv

value: IL13 100 ng/ml


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 4


title: neutrophil, IL4, 60 min, donor1

description:
IL_4_5_D1
rsubread_featureCounts.csv
IL4_all.csv


title: neutrophil, IL13, 60 min, donor2

description:
IL_13_10_D2
rsubread_featureCounts.csv
IL13_all.csv


title: RNA-seq of 3xTg mice [Model3]

value: Blank solvent, p.o. four times per week.


title: Peritoneal exudate cells – PDX134183, hIFNB replicate 3

value: hIFNB


title: RNA-seq of 3xTg mice treated by 1-month administration [T1]


title: neutrophil, IL13, 60 min, donor4

description:
IL_13_10b_D5
rsubread_featureCounts.csv
IL13_all.csv


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 3


title: RNA-seq of 3xTg mice [Model2]


title: KGN-C1

description: KGN, control

value: KGN

value: granulosa cell

value: control


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 2


title: RNA-seq of 3xTg mice [Model1]


title: Ythdc1-NC-2

first: Juan

last: Meng

address: Yueyang Road Street

institute: Center for Excellence in Brain Science and Intelligence Technology, Chineses Academy of Sciences

data_processing:
Sequence reads were processed with Trimmomatic to remove low quality sequences and adaptors (LEADING:3 TRAILING:3 MINLEN:50).
Qualified reads were quantified at transcript level with kallisto for SLIM-seq data.
Qualified reads were mapped to the reference genome (GRCm38.99) by Hisat2 and the read counts for each transcript were quantified by featureCounts.
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include counts values for each Sample

source_name: embryo

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen). Anti-m6A antibody (0.5 μg per sample) (ab15320, Abcam) was pre-bound to Protein A magnetic beads (Thermo Fisher Scientific) in IP buffer (10mM Tris-HCl pH 7.4, 100mM NaCl,0.1% NP40, 0.4 U/μl RNasin) with head-to-tail mixing at 4°C for 2 h. Total RNA (100 ng per sample) was added and incubated at 4°C for another 2 h. Beads were washed twice with 200 μL IP buffer, twice with 200 μL low-salt buffer (10 mM Tris-HCl pH 7.4, 50 mM NaCl, 0.1% NP-40, 0.4 U/μL RNasin), twice with 200 μL high-salt buffer (10 mM Tris-HCl (pH 7.4), 500 mM NaCl, 0.1% NP40, 0.4 U/μL RNasin) and once with 200 μL 1 × IP buffer. Captured RNA was eluted by heating beads for 2 min at 94°C in 10 μL DEPC H2O.
Total RNA-seq libraries were prepared using the SMART-Seq Stranded Kit (Vazyme) following the manufacturer’s instructions.

value: embryo

tag: time

tag: library type

value: low-input RNA-seq


title: Ythdc1-NC-3


title: neutrophil, IL13, 60 min, donor1

description:
IL_13_9_D1
rsubread_featureCounts.csv
IL13_all.csv

value: peripheral blood


title: Peritoneal exudate cells – PDX134183, hIFNE replicate 1

description:
B31
Excluded from final analysis due to low UMI counts.


title: neutrophil, IFNg, 60 min, donor4

description:
IFNg_16b_D5
rsubread_featureCounts.csv
IFNg_all.csv

value: neutrophil

value: IFNg 100 ng/ml


title: KGN-C2

description: KGN, control


title: neutrophil, IFNg, 60 min, donor3

description:
IFNg_15_D3
rsubread_featureCounts.csv
IFNg_all.csv


title: Ythdc1-NC-1


title: Peritoneal exudate cells – PDX134183, PBS replicate 6

value: PBS


title: Ythdc1-KD-3


title: neutrophil, IFNg, 60 min, donor2

description:
IFNg_14_D2
rsubread_featureCounts.csv
IFNg_all.csv


title: KGN-T4

description: KGN, ceramide

value: ceramide


title: RNA-seq of WT mice [Control2]


title: Ythdc1-KD-2


title: Peritoneal exudate cells – PDX134183, PBS replicate 4


title: neutrophil, IFNg, 60 min, donor1

description:
IFNg_13_D1
rsubread_featureCounts.csv
IFNg_all.csv


title: RNA-seq of WT mice [Control1]


title: Ythdc1-KD-1


title: Peritoneal exudate cells – PDX134183, PBS replicate 3


title: IP-L2C-3


title: SHARESeq_ATAC_T128_8

city: Cambridge

first: Jason

last: Buenrostro

state: MA

address: 7 Divinity Ave

institute: Harvard University

description:
human_BMMC.fragments.tsv.gz
human_BMMC_peaks.bed.gz
human_BMMC_ATAC_cell_meta.tsv.gz
human_BMMC_ATAC_count_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Processed using SHARE-Seq-v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2/)
Assembly: hg38
Supplementary files format and content: human_BMMC.fragments.tsv.gz
Supplementary files format and content: human_BMMC_peaks.bed.gz
Supplementary files format and content: human_BMMC_ATAC_cell_meta.tsv.gz
Supplementary files format and content: human_BMMC_ATAC_count_matrix.mtx.gz
Supplementary files format and content: File for ATAC fragments. Tab-delimited table with 4 columns: Chromosome, start coordinate, end coordinate, cell barcode.
Supplementary files format and content: Bed file for ATAC peak ranges. Tab-delimited table with 3 columns: Chromosome, start coordinate, end coordinate.
Supplementary files format and content: Tab-delimited text file of cell metadata. Each row corresponds to a cell and each column is a metadata feature.
Supplementary files format and content: Table of single cell ATAC read counts. Can be read into R using the readMM() function from the package "Matrix". Each row corresponds to an ATAC peak and each column is a cell.

molecule: genomic DNA

source_name: Bone marrow

extract_protocol:
Frozen human Bone Marrow Mononuclear Cells (BMMCs, Allcells) were thawed in a 37 °C water bath for 1 min and transferred to a 15 mL centrifuge tube. 10 mL of pre-warmed DMEM with 10% FBS was added to cells drop-wisely. The cells were spun at 400g for 3 min at room temperature. After removing supernatant, the cells were washed twice in 0.5 mL PBS with 0.04% BSA. To deplete neutrophils, the cells were resuspended in 100 μl chilled DPBS with 0.2% BSA and 10 μl of human TrueStain FcX (BioLegend, 422302) and incubated on ice for 10 min to reduce non-specific labeling. The cells were then incubated on ice for another 30 min after adding 0.5 μl of biotin anti-human CD15 antibody (BioLegend, 301913). After immunostaining, 25 μl of MyOne T1 beads were added to the sample to capture the neutrophils for 5 min at room temperature. We then added 900 μl of DPBS with 0.2% BSA to dilute the sample. The sample was placed on a magnet for 3 min and 1 ml of the sample was transferred to a new tube while the sample was on the magnet. The cells were ready for fixation and SHARE-seq experiment.
Cells were centrifuged at 300g for 5 minutes and resuspended to 1 million cells/ml in PBSI. Cells were fixed by adding formaldehyde (28906, ThermoFisher) to a final concentration of 1% and incubated at room temperature for 5 minutes. The fixation was stopped by adding 56.1 μl of 2.5M glycine, 50 μl of 1M Tris-HCl pH 8.0, and 13.3 μl of 7.5% BSA on ice. The sample was incubated at room temperature for 5 minutes and then centrifuged at 500g for 5 minutes to remove supernatant. All centrifugations were performed on a swing bucket centrifuge. The cell pellet was washed twice with 1ml of PBSI, and centrifuged at 500g for 5 minutes between washings. The cells were resuspended in PBS with 0.1U/μl Enzymatics RNase Inhibitor and aliquoted for transposition. Following fixation SHARE-seq was performed as previously described in the original SHARE-Seq paper, with the following modifications. To improve transposition, transposition was performed using pre-assembled Tn5 (seqWell, Tagify(TM) SHARE-Seq Reagent). To improve RNA capture, we added polyA to transcripts prior to reverse transcription. To do this, transposed cells (60 μl) were mixed 240 μl of poly(A) mix (final concentration of 1× Maxima RT buffer, 0.25 U/μl Enzymatics RNase Inhibitor, 0.25 U/μl SUPERase RI, 0.018 U/μl E.coli poly-A enzyme (M0276L), 1 mM rATP). The sample was aliquoted to 50 μl per PCR tube and incubated at 37 °C for 15 minutes.

value: Bone marrow

value: Bone marrow mononuclear cells


title: Peritoneal exudate cells – PDX134183, PBS replicate 2


title: Peritoneal exudate cells – PDX134183, PBS replicate 1


title: RNA-seq of WT mice [Control3]

value: hippocampus

value: female


title: SHARESeq_ATAC_T128_6


title: IP-L2C-1


title: IP-L2C-2


title: SHARESeq_ATAC_T128_5


title: SHARESeq_ATAC_T128_4


title: Input-L2C-2


title: Peritoneal exudate cells – PDX134183, PBS replicate 5


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 6

value: mIFNE


title: SHARESeq_ATAC_T128_3


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 4


title: Input-L2C-3


title: ID8_UT_R2_2

description: UT_R2 technical replicate

hyb_protocol: 600 ng Cy3-labelled cRNA was fragmented using Agilent fragmentation and blocking reagents following the manufacturer's instructions. On completion, the preparation was hybridised to Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarrays for 17 hours at 67°C and washed following the manufacturer's instructions.

scan_protocol: Slides were scanned on Agilent DNA Microarray Scanner (G2505C) using one-colour scan setting for 8x60K array slides.

data_processing:
The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially de-trended processed signal intensities. Features flagged in feature extraction as “feature non-uniform” outliers were excluded.
Raw data were imported into R (v3.6.1) using the read.maimages function from the limma package (v3.42.0). Microarray probe annotation was obtained using the GEOquery package (v2.54.1) from the accession GPL21810 and additional annotation was obtained using the biomaRt package (v2.42.1). Normexp background correction and quantile normalisation were performed on the raw data.

source_name: ID8 cells, no IFN, replicate 2

label_protocol: 100 ng total RNA was labelled with cyanine-3 (Cy3) using the One-Color Low RNA Input Quick Amp Labelling Kit (Agilent v6.6) and purified by RNeasy column purification (QIAGEN).

growth_protocol: ID8 murine ovarian cancer cells (Roby KF et al., Carcinogenesis 2000) were cultured in RPMI 1640 (GibcoBRL, Ontario, Canada) supplemented with 4% heat-inactivated foetal calf serum (FCS; GibcoBRL).

extract_protocol: RNA was extracted using a QIAGEN RNeasy mini-kit (QIAGEN, Germany)  as per the manufacturer’s protocol. Cells were harvested in 1% betamercaptoethanol in RLT buffer and homogenised using a 1 mL syringe and a 23-gauge needle. RNA was on-column DNase treated using the QIAGEN RNase-free DNase Set according to manufacturer’s instructions. RNA yield and quality were then assessed using a NanoDrop ND-1000 spectrophotometer and stored at −80°C.

treatment_protocol: Cell lines were plated (150,000 cells/well) in a 12-well plate 24 hours prior to stimulation with recombinant murine IFN epsilon or IFN beta at 10, 100 or 1000 IU/ml or PBS, as a vehicle control. Cells were then incubated at 37°C for 3 hours prior to mRNA extraction.

value: UT

tag: replicate


title: ID8_10IU_IFNB_R3

description: Excluded from final analysis due to anomalously high induction of interferon-stimulated genes.

source_name: ID8 cells, 10 IU IFN beta, replicate 3


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 3


title: SHARESeq_ATAC_T128_7

tag: tissue


title: SHARESeq_ATAC_T128_2

tag: cell type


title: IP-L1C-3


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 2


title: Input-L2C-1


title: ID8_UT_R3_2

description: UT_R3 technical replicate

source_name: ID8 cells, no IFN, replicate 3


title: SHARESeq_ATAC_T128_1


title: IP-L1C-2


title: SHARESeq_ATAC_T124_1


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 1


title: Peritoneal exudate cells – PDX134111, mIFNE replicate 5


title: ID8_100IU_IFNB_R3

source_name: ID8 cells, 100 IU IFN beta, replicate 3


title: Input-L1C-3


title: ID8_1000IU_IFNB_R3

source_name: ID8 cells, 1000 IU IFN beta, replicate 3


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 5

value: hIFNB


title: Input-L1C-2


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 4


title: SHARESeq_RNA_T128_6

data_processing:
Processed using SHARE-Seq-v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2/)
Assembly: hg38
Supplementary files format and content: human_BMMC_gene_names.tsv.gz
Supplementary files format and content: human_BMMC_cell_meta.tsv.gz
Supplementary files format and content: human_BMMC_count_matrix.tsv.gz
Supplementary files format and content: Plain text file of gene names. Table of a single column.
Supplementary files format and content: Tab-delimited text file of cell metadata. Each row corresponds to a cell and each column is a metadata feature.
Supplementary files format and content: Table of single cell RNA read counts. Can be read into R using the readMM() function from the package "Matrix". Each row corresponds to a genek and each column is a cell.


title: ID8_UT_R1_2

description: UT_R1 technical replicate

source_name: ID8 cells, no IFN, replicate 1


title: ID8_100IU_IFNE_R3

source_name: ID8 cells, 100 IU IFN epsilon, replicate 3


title: SHARESeq_RNA_T128_8


title: SHARESeq_RNA_T128_7


title: Input-L1C-1


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 3


title: ID8_10IU_IFNE_R3

source_name: ID8 cells, 10 IU IFN epsilon, replicate 3


title: ID8_1000IU_IFNE_R3

source_name: ID8 cells, 1000 IU IFN epsilon, replicate 3


title: ID8_UT_R3_1

description: UT_R3 technical replicate


title: SHARESeq_RNA_T128_5


title: IP-MII-3

value: MII


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 2


title: IP-L1C-1


title: scRNA-seq of Homo sapiens: 382-01 d57 lymph node, bio rep 3

description:
10x Genomics
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz
aggregation.csv.gz

source_name: lymph node

value: lymph node

value: various

value: post-boost d57


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 6

source_name: Peritoneal exudate cells


title: SHARESeq_RNA_T128_3


title: SHARESeq_RNA_T128_4


title: Peritoneal exudate cells – PDX134111, hIFNB replicate 1


title: IP-MII-2

value: embryo


title: SHARESeq_RNA_T128_2


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 6

value: hIFNE


title: IP-MII-1


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 5


title: Input-MII-3

value: low-input RNA-seq


title: Input-MII-2


title: SHARESeq_RNA_T128_1


title: ID8_10IU_IFNE_R2

source_name: ID8 cells, 10 IU IFN epsilon, replicate 2


title: SHARESeq_RNA_T124_1


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 4


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 3


title: Input-MII-1


title: ID8_1000IU_IFNB_R2

source_name: ID8 cells, 1000 IU IFN beta, replicate 2


title: ID8_10IU_IFNB_R2

source_name: ID8 cells, 10 IU IFN beta, replicate 2


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 2


title: ID8_100IU_IFNB_R2

source_name: ID8 cells, 100 IU IFN beta, replicate 2


title: Peritoneal exudate cells – PDX134111, hIFNE replicate 1


title: Crypts, EPR cKO, 43A

library_source: genomic

data_processing:
Arima Mouse Promoter Panel Design The Arima Mouse Promoter Panel was designed to the promoters of 25,752 genes from the Mouse GRCm38 Ensemble database, version 94, including: 21,088 protein-coding genes, 207 antisense RNA’s, 544 lincRNA’s, 1,015 miRNA’s, 1,494 snoRNA’s, and 1,383 snRNA’s.
bigwig files generated using bamCoverage (deeptools) with defaults parameters
Assembly: mm10
Supplementary files format and content: bigwig

source_name: colon

growth_protocol: Hi-C was performed in crypts from mouse proximal colon using the Arima-HiC Kit according to the manufacturer?s instructions (Arima Genomics). Briefly, crypts were isolated from two distinct EPR fl/fl and two EPR cKO mice, snap-frozen and weighted (100-130 ?g/sample). Hundred ?g crypts were resuspended in PBS and crosslinked in 2% formaldehyde for 10 min. at room temperature, digested with a restriction enzyme cocktail, end-labeled with Biotin-14-dATP and then ligated. The ligated chromatin was reverse cross-linked and fragmented using Bioruptor (Diagenode) to obtain an average fragment size of 400bp. Fragmented DNA was then size-selected to have a size distribution between 200-600 bp, and finally subjected to biotin enrichment. Then, DNA libraries were prepared according to the procedure detailed in the Arima Capture-HiC Kit User Guide for mammalian cells (https://arimagenomics.com/wp-content/files/User-Guide-Arima-Capture-HiC-for-Mammalian-Cell-Lines.pdf). The Arima Mouse Promoter Panel was designed to the promoters of 25,752 genes from the Mouse GRCm38 Ensemble database, version 94, including: 21,088 protein-coding genes, 207 antisense RNAs, 544 lincRNAs, 1,015 miRNAs, 1,494 snoRNAs, and 1,383 snRNAs. Capture probes were designed to the restriction fragment of each of the promoters. The probes were manufactured using 1x tiling with repeat masking and balance boosting. Arima Capture-HiC libraries were sequenced via Illumina sequencers in ?paired-end? mode and sequence analyzed according to the Arima Capture-HiC Analysis Pipeline. Data were pre-processed using HiCUP and loops called using CHiCAGO at Arima Genomics.

extract_protocol:
chromatin from crypts was crosslinked and digested using a restriction enzyme cocktail. The 5’-overhangs are then filled in, causing the digested ends to be labeled with a biotinylated nucleotide. Next, spatially proximal digested ends of DNA are ligated, capturing the sequence and structure of the genome. The ligated DNA is then purified, producing pure proximally-ligated DNA. The proximally-ligated DNA is then fragmented, and the biotinylated fragments are enriched. The enriched fragments are then subjected to a custom library preparation protocol utilizing the Arima Library Prep Module . Following Library prep we perform shallow sequencing (500k-2M paired-end reads) to assess the libraries’ quality in terms of library complexity and long-range interaction information prior to proceeding with the capture. Once Hi-C is complete, the sample is pre-cleared to remove carry over biotinylated Hi-C molecules. The interactions of interest are then enriched using biotinylated RNA probes from the Arima Mouse Promoter Panel
paired-end

treatment_protocol: Crypts were isolated from 12-16-week-old mice

value: colon

tag: strain

value: epithelial

tag: genotype

value: EPR cKO


title: Crypts, EPR cKO, 43


title: Crypts, EPR fl/fl, 42A

value: EPR fl/fl


title: BAC rep5

data_processing:
The sequencing data was processed the same way as SHARE-seq ATAC-seq data.
Assembly: hg38
Supplementary files format and content: BAC.fragments.tsv.gz
Supplementary files format and content: File for ATAC fragments. Tab-delimited table with 4 columns: Chromosome, start coordinate, end coordinate, replicade index
Supplementary files format and content: selectedBACs.tsv.gz
Supplementary files format and content: Tab-delimited text file with 4 columns: BAC ID, chromosome, start, end

source_name: BAC clone

growth_protocol: We selected 25 chromatin regions based on overlap with a manually selected set of key transcription factors and differentiation related genes. The BAC clones (BACPAC Resources) were cultured in LB for 14 hours

extract_protocol:
The BAC DNA was extracted using ZR BAC DNA Miniprep Kit (Zymo, D4048) following manufacturer’s instructions. The purified DNA was quantified using Qibit (ThermoFisher)
The BAC DNA were tagmented similar to SHARE-seq ATAC-seq experiment. Briefly, 50 ng of BAC DNA from multiple clones were pooled for tagmentation following the SHARE-seq transposition condition. The tagmented DNA was purified using a Qiagen Minelute PCR clean up kit and then amplified for 7 cycles by PCR. To minimize batch effect, we generated 5 replicates and pooled all the materials for sequencing. The library was sequenced on a Nova platform (Illumina) using a 100-cycle kit (Read 1: 50 cycles, Index 1: 8 cycles, Index 2: 8 cycles, Read 2: 50 cycles).
Transposition into naked DNA

value: BAC clone


title: HepG2_SHARESeq_ATAC

data_processing:
Processed using SHARE-Seq-v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2/)
Assembly: hg38
Supplementary files format and content: HepG2.fragments.tsv.gz
Supplementary files format and content: File for ATAC fragments. Tab-delimited table with 4 columns: Chromosome, start coordinate, end coordinate, cell barcode.
Supplementary files format and content: HepG2_peaks.bed.gz
Supplementary files format and content: Bed file for ATAC peak ranges. Tab-delimited table with 3 columns: Chromosome, start coordinate, end coordinate.
Supplementary files format and content: HepG2_cell_meta.tsv.gz
Supplementary files format and content: Tab-delimited text file of cell metadata. Each row corresponds to a cell and each column is a metadata feature.
Supplementary files format and content: HepG2_count_matrix.mtx.gz
Supplementary files format and content: Table of single cell ATAC read counts. Can be read into R using the readMM() function from the package "Matrix". Each row corresponds to an ATAC peak and each column is a cell.
Library strategy: HARE-Seq

growth_protocol: HepG2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, 11965092, ThermoFisher) with the addition of 10% FBS and 1% of penicillin-streptomycin. Cells were incubated at 37°C in 5% CO2 and maintained at the exponential phase. Cells were digested with TrypLE express (12604013, ThermoFisher) for preparing single-cell suspension.

extract_protocol: Cells were centrifuged at 300g for 5 minutes and resuspended to 1 million cells/ml in PBSI. Cells were fixed by adding formaldehyde (28906, ThermoFisher) to a final concentration of 1% and incubated at room temperature for 5 minutes. The fixation was stopped by adding 56.1 μl of 2.5M glycine, 50 μl of 1M Tris-HCl pH 8.0, and 13.3 μl of 7.5% BSA on ice. The sample was incubated at room temperature for 5 minutes and then centrifuged at 500g for 5 minutes to remove supernatant. All centrifugations were performed on a swing bucket centrifuge. The cell pellet was washed twice with 1ml of PBSI, and centrifuged at 500g for 5 minutes between washings. The cells were resuspended in PBS with 0.1U/μl Enzymatics RNase Inhibitor and aliquoted for transposition. Following fixation SHARE-seq was performed as previously described in the original SHARE-Seq paper, with the following modifications. To improve transposition, transposition was performed using pre-assembled Tn5 (seqWell, Tagify(TM) SHARE-Seq Reagent). To improve RNA capture, we added polyA to transcripts prior to reverse transcription. To do this, transposed cells (60 μl) were mixed 240 μl of poly(A) mix (final concentration of 1× Maxima RT buffer, 0.25 U/μl Enzymatics RNase Inhibitor, 0.25 U/μl SUPERase RI, 0.018 U/μl E.coli poly-A enzyme (M0276L), 1 mM rATP). The sample was aliquoted to 50 μl per PCR tube and incubated at 37 °C for 15 minutes.

value: hepatocellular carcinoma


title: ID8_UT_R2_1

description: UT_R2 technical replicate

source_name: ID8 cells, no IFN, replicate 2

tag: treatment


title: ID8_1000IU_IFNE_R2

source_name: ID8 cells, 1000 IU IFN epsilon, replicate 2


title: ID8_100IU_IFNE_R2

source_name: ID8 cells, 100 IU IFN epsilon, replicate 2


title: BAC rep4


title: BAC rep3


title: Peritoneal exudate cells – PDX134111, PBS replicate 6

value: PBS


title: ID8_10IU_IFNB_R1

source_name: ID8 cells, 10 IU IFN beta, replicate 1


title: Crypts, EPR fl/fl, 41


title: BAC rep2


title: BAC rep1


title: ID8_100IU_IFNB_R1

source_name: ID8 cells, 100 IU IFN beta, replicate 1


title: KO6

data_processing:
demultiplexing: bcl2fastq v2.20.0.422
trimming: with BBDuk v38.49 from BBTools suite (sourceforge.net/projects/bbmap/).
alignment: STAR v2.5.3a
R v3.5.1 and Bioconductor v3.8 were used for secondary analysis
counts: featureCounts function from Rsubread v1.6.4 package was used to assign read counts to the genes of the Ensembl GRCm38.97
Assembly: mm10
Supplementary files format and content: bigwig files generated using bamCoverage (deeptools) with defaults parameters
Supplementary files format and content: CPM (counts per million) table matrix.

extract_protocol:
We followed the protocol published by Corey and coworkers (20) starting from isolated large intestine crypts. Both cytoplasmic and nucleoplasmic RNAs were precipitated and washed with ice-cold 70% (vol/vol) ethanol prior to be dissolved in TriPure reagent (Roche) while the chromatin pellets were immediately dissolved in TriPure. Ten microliters of 0.5 M EDTA was added to all the samples in TriPure that were heated to 65 °C with vortexing until dissolved (~10 min).
Colon was isolated from either six EPR fl/fl or six EPR cKO 12-week-old mice and flushed with ice-cold PBS. The proximal third of each colon was excised and immediately frozen in dry ice. Then, the organ fragments were homogenized using a motorized pestle (Sigma-Aldrich) in the presence of TriPure reagent and high-quality RNA was extracted. A total of twelve libraries were prepared using standard Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol and sequenced on Illumina NovaSeq 6000. Image analysis and base calling were performed using the Illumina NovaSeq Control Software.

value: ko

tag: replica


title: ID8_10IU_IFNE_R1

source_name: ID8 cells, 10 IU IFN epsilon, replicate 1


title: Peritoneal exudate cells – PDX134111, PBS replicate 4


title: KO5


title: Peritoneal exudate cells – PDX134111, PBS replicate 3


title: N4

city: Chengdu

first: Xin

last: Huang

address: Chenglongdadao

institute: West China Second University Hospital

data_processing:
We use fastp to perform basic statistics on the quality of the raw reads.
For each gene and each cell barcode, unique molecule identifiers were counted to construct digital expression matrices.
Filtration by Seurat :A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Assembly: hg38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: uterus

extract_protocol: The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X  Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and  sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s  instructions.

value: Endometirum

tag: disease

value: Control

tag: cycle phase

value: proliferative


title: N3


title: ID8_100IU_IFNE_R1

source_name: ID8 cells, 100 IU IFN epsilon, replicate 1


title: KO4


title: ID8_1000IU_IFNB_R1

source_name: ID8 cells, 1000 IU IFN beta, replicate 1


title: Peritoneal exudate cells – PDX134111, PBS replicate 2

tag: cell line


title: Chitin treated 5

city: Waedenswil

first: Moritz

last: Kaufmann

state: Zurich

address: Einsiedlerstrasse 29

department: Institute of Natural Resource Sciences

country: Switzerland

institute: ZHAW

data_processing:
Sequence reads quality of the raw files obtained from BGI was assessed using FastQC v0.11.9 (Andrew, 2015).
Reads were then aligned with STAR v2.7.10 (Dobin et al., 2013) against the genome of L. sativa cv. ‘Salinas’. The genome version for the fasta and the gtf file was v7 downloaded from https://www.ncbi.nlm.nih.gov/assembly/GCF_002870075.2.
The alignment quality was checked with Qualimap v2.2.1 (Okonechnikov et al., 2015).
Read counting was performed using featureCounts v2.0.1 (Liao et al., 2014).
To analyze the different gene expression the featureCounts output was analyzed with R v4.2.1 (R. C. Team, 2020) using the DESeq2 package v1.30.1 (Love et al., 2017) in RStudio v1.3.959 (R. Team, 2020).
Assembly: GCA_002870075.2
Supplementary files format and content: raw read counts

organism: Lactuca sativa var. capitata

source_name: Lettuce grown in chitin amended potting soil

growth_protocol: Lettuce seedlings were germinated from pelletized butterhead lettuce seeds (L. sativa L. var. capitata ‘Alexandria’) obtained from Rijk Zwaan Distribution B.V. (De Lier, the Netherlands). First, peat-based sowing soil (Saniflor, Potground voor zaaien en stekken) was used to fill 77-well germination trays, then, one pelleted seed was gently pressed down with tweezers in the center of each well and covered with another thin layer of sowing soil. Every two days the soil was watered to 40 % WFPS. Seedlings were transplanted at three to four true leaf stage in 1.3 L pots filled with 1 L potting soil, with or without chitin addition, and grown in the greenhouse at ILVO. Temperature, humidity, photoperiod and light intensity were not strictly controlled and varied along the local weather (Belgium, January – March 2021).

extract_protocol:
Lettuce roots from each treatment (PS, PS+CH) were sampled at 72 hpt. Five biological replicates per treatment/timepoint combination were randomly selected. The soil on the roots was washed off and roots were pooled, flash frozen in liquid nitrogen and stored at -80°C before further processing. Total RNA was extracted using the CTAB method as described in detail by Luypaert et al. (2017). Contaminating DNA was removed using DNA-free DNA removal kit (AM1906, Invitrogen; Thermo Fisher Scientific, Inc., Waltham, USA, Massachusetts) according to the manufacturer’s protocol.
To study the overall transcriptional reprogramming in lettuce upon chitin treatment, in total five RNA samples per treatment sampled at 72 hpt were shipped to BGI Tech Solutions Co. Ltd. (Hong Kong, China) for cDNA synthesis, library preparation, and sequencing.

value: Root

tag: cultivar

value: Alexandria

value: wt

value: Chitin


title: Chitin treated 4


title: KO3


title: Chitin treated 3


title: N2

value: secretory


title: Chitin treated 2


title: N1


title: KO1


title: Chitin treated 1


title: Peritoneal exudate cells – PDX134111, PBS replicate 1

source_name: Peritoneal exudate cells


title: EMS6

value: endometriosis


title: KO2


title: WT osteocytes (209_13) (biol. repl. 2)

city: Jupiter, FL 33458

first: Gogce

middle: Ceren

last: Crynen

state: Florida

address: 130 Scripps Way

department: Bioinformatics and Statistics Core

institute: UF Scripps Biomedical Research

data_processing:
In house pipeline managed by Bioinformatics and Statistics Core (RRID:SCR_023048)
Sequence reads were trimmed trimmomatic version 0.35
Trimmed sequence reads were mapped to M.musculus-UCSC-mm10 using Star version 2.5.2a
Tools used to count gene features were  python version 2.7.11, and htseq version 0.9.1.
Tool used to test for diff gene exprression were R version 3.4.0, and deseq2 version 1.16.1
Assembly: mm10
Supplementary files format and content: Excel sheet includes raw counts, DESeq2 normalized counts, and TPM normalized counts
Supplementary files format and content: Excel sheet includes Deseq2 results  such as fold change, pvalue and adjpvalue

source_name: femur bone

growth_protocol: Cell fraction enriched in osteocytes was isolated by sequential collagenase digestion of femora bone and grown  ex vivo on collagenase coated plates for 6 days in the presence of aMEM supplemented with 5% FBS and 5% CS.

extract_protocol: RNA extraction with Tri Reagent

treatment_protocol: No treatment

value: femur bone

value: osteocyte

tag: age

value: 5 months

value: PPARa WT

value: 6 days ex vivo growth


title: WT osteocytes (209_9) (biol. repl. 1)


title: ID8_UT_R1_1

description: UT_R1 technical replicate

source_name: ID8 cells, no IFN, replicate 1

value: UT


title: flfl6


title: ID8_1000IU_IFNE_R1

source_name: ID8 cells, 1000 IU IFN epsilon, replicate 1


title: KO osteocytes (209_5) (biol. repl. 2)

value: PPARa KO


title: Control 5

source_name: Lettuce grown in potting soil


title: EMS5


title: EMS4


title: Peritoneal exudate cells – PDX134111, PBS replicate 5

value: PBS


title: flfl4

source_name: colon


title: EMS3

value: Endometirum


title: flfl3


title: Control 2


title: Control 4


title: flfl2


title: EMS2


title: KO osteocytes (209_1) (biol. repl. 1)


title: Control 1


title: flfl1


title: Young_LinNeg_RNA

data_processing:
Data processing was performed using CellRanger pipeline
Assembly: mm10
Supplementary files format and content: mouse_HSC_aging_gene_names.txt.gz
Supplementary files format and content: mouse_HSC_aging_RNA_cell_meta.txt.gz
Supplementary files format and content: mouse_HSC_aging_RNA_count_matrix.txt.gz
Supplementary files format and content: Plain text file of gene names. Table of a single column.
Supplementary files format and content: Tab-delimited text file of cell metadata. Each row corresponds to a cell and each column is a metadata feature.
Supplementary files format and content: Tab-delimited text file of single cell RNA read counts. Each row corresponds to a gene and each column is a cell.

source_name: Bone marrow

growth_protocol: Mouse experiments were approved and performed in compliance with Harvard University’s Institutional Animal Care and Use Committee. C57BL6 mice were obtained from either Jackson Laboratory or the National Institute on Aging Aged Rodent Colony (Charles River Laboratory), and housed at a density of 2-5 mice per cage in standard ventilated racks and provided food and water ad libitum in a pathogen-specific free facility accredited by the Association and Accreditation of Laboratory Animal Committee (AALAC). Mouse cages contained Anderson’s Bed o Cob bedding (The Anderson, Inc), two nestlets (Ancare, 2x2” compressed cotton square), and a red mouse hut (Bioserv)

extract_protocol: 10x Multiomic sequencing

treatment_protocol: For HSC isolation and flow cytometry. Cells from the bone marrow of long bones (2 femurs and 2 tibias per mouse) from young (n=10; 11 weeks old) and aged (n=5; 24 mo. old) male C57BL/6 mice were flushed with a 21-gauge needle into staining media (HBSS/2% fetal bovine serum), pelleted, and resuspended in ACK lysis buffer for 5 min on ice. Cells were then washed with staining media, filtered through a 40mm cell strainer, pelleted, and incubated with the following cocktail of  rat anti-mouse, biotin conjugated lineage antibodies on ice for 30 min: CD3 clone C145-2c11 (Biolegend, 1000304; 1:100), CD4 clone GK15 (Biolegend, 1000404; 1:400), CD5 clone 53-7.3 (eBioscience, 13-0051-85; 1:400), CD8 clone 53-6.7 (Biolegend, 100704; 1:400), CD19 clone 6D5 (Biolgend, 115504; 1:400), B220 clone RA3-6B2 (Biolegend, 103204; 1:200), GR1 (Ly6-G/Ly6-C) clone RB6-8C5 (eBioscience, 13-5931-82; 1:400), Mac1/CD11b clone M1/70 (Biolegend, 101204; 1:800), and Terr119 clone TERR-119 (Biolegend, 116204; 1:100). Cells were then washed in staining media, with a small aliquot reserved for each sample to serve as a non-depleted control, and lineage depleted using sheep anti-rat Dynabeads (Invitrogen, 1135) on a magnet. Cells were washed, pelleted, and incubated with the following cocktail of anti-mouse antibodies on ice for 45 min. to identify hematopoietic stem cells (HSC): Pacific Orange Streptavidin (Invitrogen, S32365; 1:500), PE/Cy7 Sca1(Ly-6a/E) clone D7 (eBioscience, 25-5981-82; 1:200), APC cKit clone 2B8 (BD Pharmingen, 553356; 1:200), FITC CD48 clone HM48-1 (Biolegend, 103403; 1:200), and PE CD150 clone Tc15-12F12.2 (Biolegend, 115904; 1:200). Following incubation, cells were washed and resuspended in staining media, and 7-AAD (BD Pharmingen, 559925; 1:50) added immediately prior to flow cytometry. Cell sorting of HSCs (Live Lin- Sca1+ cKit+ CD48- CD150+) was performed on a BD FACS Aria II, and data analysis performed using BD FACS Diva and FlowJo software

value: Bone marrow

value: Hematopoietic progenitors

value: male

value: 11 weeks


title: Tgfb_PFI3

first: Mary

last: Weiser-Evans

state: CO

address: 12700 East 19th Avenue, C281

department: Renal Diseases & Hypertension

institute: University of Colorado Anschutz Medical Campus

data_processing:
CUT&RUN reads were quality assessed by FastQC (v0.11.8), MultiQC (v1.8), FastQ Screen (v0.14.0) and quality filtered with BBDuk (v38.87).
Sequencing reads were aligned to the mm10 mouse using Bowtie2 (v2.3.4.3).
Samtools (v.1.11) was used to select the uniquely mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates (v2.21.1) tool.
The normalization ratio of each sample was calculated by dividing the total number of mapped reads mapping to the murine genome of each sample by the total number of mapped reads mapping to the murine genome of the sample with the lowest number of reads mapping to the murine genome. Using the normalization ratio, random sub-sampling of the reads was performed using samtools view -s.
Bedtools genomecov was used to create bedgraph files from the bam files.
Bigwig files were generated with DeepTools (v3.5.1) and visualized with IGV (v2.13.2).
Peaks were called using MACS2 (v2.1.2) with default parameters.
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Aorta and carotid artery

growth_protocol: AdvSca1-SM cells were maintained in alpha-MEM GlutaMAX media supplemented with 10% mesenchymal stem cell-qualified fetal bovine serum (FBS), 1ng/mL murine basic fibroblast growth factor, 5ng/mL murine epidermal growth factor, and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C. Prior to treatment, AdvSca1-SM cells were maintained in alpha-MEM GlutaMAX media supplemented with 0.1% mesenchymal stem cell-qualified fetal bovine serum (FBS), 1ng/mL murine basic fibroblast growth factor, 5ng/mL murine epidermal growth factor, and 1x penicillin/streptomycin for 24hrs to growth arrest cells

extract_protocol:
On the day of extract, cells were trypsinized with 0.25% trypsin and washed three times in wash buffer containing 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine supplemented with protease inhibitor cocktail. The cells were then adsorbed to Concanavalin A beads for 20 minutes at room temperature. Cells were then permeabilized with Antibody Buffer containing 0.1% digitonin and 2mM EDTA. Permeabilization was validated by Trypan Blue. Samples were incubated with 0.5μg of anti-Brg1, anti-H3K4me3, or IgG antibody overnight at 4°C. The following day, cells were washed twice in wash buffer plus 0.1% digitonin and incubated with pAG-micrococcal nuclease (pAG-MNase) for 20 minutes at room temperature and then cells were incubated with 1mM CaCl2 for 2 hours at 4°C to activate pAG-MNase digestion of chromatin fragments under target. The digest reaction was quenched using EpiCypher Stop Buffer and samples were incubated at 37°C for 30 minutes to liberate digested DNA. The enriched DNA was purified using the EpiCypher DNA column purification kit
Libraries were prepared with the Tecan/Nugen Ultralow DNA Input Kit for end repair and adapter ligation, Paired End 150 cycle 2x150 with 14 cycles of amplification and library distribution was evaluated using TapeStation.

treatment_protocol: On the day of treatment, growth-arrested AdvSca1-SM cells were switched to DMEM media supplemented with 0.1% FBS and 1x penicillin/streptomycin and treated with either 5ng/mL TGF-B by adding a 5ug/mL stock solution of TGFB at a 1:1000 dilution (diluted in serum-free DMEM) to the cells, or treated with 5ng/mL TGF-B + 50uM PFI-3. For cells treated with PFI-3, a 50mM stock was applied at a 1:1000 dilution in DMSO. All cells received 0.1% DMSO as vehicle control. Cells were incubated for 72 hours.

value: Aorta and carotid artery

value: AdvSca1-SM cells

value: Resident vascular progenitor

value: Tgfb and PFI-3


title: Young_HSC_RNA

value: Hematopoietic stem cells


title: Tgfb

value: Tgfb


title: flfl5

value: wt


title: BJ0847

city: Beijing

first: Feifei

last: Ma

address: Road 2 Yabao

institute: Capital Institue of Pediatrics

description: miRNAs expression in Peripheral Blood between obesity and lean of children

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section.

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US).

source_name: Peripheral Blood

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Normal environment

extract_protocol: Total RNA was extracted and purified using mirVanaTM PARISTM (Cat#AM1556, Ambion, Austin, TX, US) in accordance with the manufacturer’s instructions and checked for the RIN number to inspect RNA integration with an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Blood samples were centrifuged. Plasma and red blood cells were separated.

value: plasma

tag: gender

value: boy

tag: phenotype

value: lean


title: Stem

value: vehicle


title: EMS1

value: endometriosis

value: secretory


title: Old_LinNeg_RNA

value: Bone marrow

tag: Sex

value: 24 months


title: Control 3

value: Root

value: Alexandria


title: BJ0727


title: Old_HSC_RNA

value: male


title: BJ0717

value: girl


title: Tgfb_PFI3_rep2 [14_Both_B]

data_processing:
Paired-end RNA-Seq reads were obtained using Illumina analysis Pipeline.
Fastq files were preprocessed with Flexbar 3.5.0 to trim 12 bases at the left side of reads and remove adapter sequences.
The fastq files were were aligned to the Mus musculus GRCm39 reference genome (Ensembl, release 104) using HISAT2 version 2.2.1 with the following options: -p 8 --dta --rna-strandness RF
Samtools 1.13 were used to sort the aligned reads and HTSeq 0.11.3 were used to produce raw counts uniquely mapping to genes for each samples.
Assembly: GRCm39 (Ensembl release 104)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated from hepatic tissue using QIAshredders and RNeasy Plus mini kit (Qiagen). RNA quality and quantity were analyzed using TapeStation Systems (Agilent)
Ribo Depleted total RNA library preparation and sequencing (Paired end 150 cycle 2x150, using NovaSEQ 6000) were conducted at The Genomics Shared Resource at the University of Colorado Cancer Center.

value: Aorta and carotid artery

value: AdvSca1-SM cells

value: Resident vascular progenitor


title: Wound_Trem2+_Rep2

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
bedtools2.27.1 multicov to generate normalized counts
DESEQ2 used for differential peak calling
Assembly: hg38
Supplementary files format and content: bigwig

source_name: mouse wound

growth_protocol: 7-week old C57BL/6 female mice were used for the 'Normal' and 'Wound' samples. Ptch1+/-;p53f/f;K14CreER mice were induced to form tumors (Whitson et al., 2018; PMID: 29400712)

extract_protocol:
Samples were dissociated by first mincing into pieces smaller than 1 mm in diameter and then incubated in 40 mL of a 0.5% collagenase solution (Gibco; 25200056) for 1hrs with rotation at 37°C . 5 mL of 0.25% Trypsin was then added and incubated for an additional 15min with rotation at 37°C . Cells were then FACS sorted for Cd45+Trem2+ cells and then processed for bulk ATAC-Seq.
Bulk ATAC-Seq was performed using the Omni-ATAC protocol (Corces et al., 2017: 28846090)

treatment_protocol: For wound samples, two 6-mm punch wounds were made on the mouse back. The wounds were isolated 4 days after wounding.

value: mouse wound


title: BJ0679


title: BJ0646


title: Donor 75, 2D suspension HIV-1 infected i+ Vpx and Raltegravir

city: Heidelberg

first: Lara

last: Gallucci

address: Neuenheimer Feld

department: Department of Infectious Diseases, Integrative Virology

country: Germany

institute: University Hospital Heidelberg

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and Raltegravir and cultured for two days in 2D suspension

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

data_processing: The data were analyzed with GeneChip Command Console

label: Biotin

source_name: monocyte derived dendritic cells

label_protocol: Standard Affymetrix protocols

growth_protocol: Monocytes, isolated from PBMCs of healthy donors, were differentiated into iDCs for six days by the addition of IL-4/GM-CSF. Once differentiated, iDCs were cultured for two days either in 3D collagen matrix or in 2D suspension cultures under the respective conditions

extract_protocol: RNA was extracted using “Macherey-Nagel NucleoSpin RNA kit according to the manufacturer's instructions.

treatment_protocol: Two days post culturing iDCs were treated with collagenase I (100U Worthington) for 30-45 min at 37°C, were extensively washed in PBS and RNA was extracted.

value: monocyte derived dendritic cells

value: iDC spin-transduced with VLPs_Vpx, infected with HIV-1 and treated with raltegravir in 2D suspension

tag: donor


title: Donor 75, 2D suspension LPS treated

description: gene expression data from monocyte derived iDCs trated with LPS and cultured for two days in 2D suspension

value: LPS treated iDCs in 2D suspension


title: Tgfb_PFI3_rep1 [13_Both_A]

value: Tgfb and PFI-3


title: Wound_Trem2+_Rep1

city: Stanford


title: Tgfb_PFI3_rep3 [15_Both_C]

city: Aurora


title: Donor 75, 2D suspension HIV-1 infected

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5 and cultured for two days in 2D suspension

value: HIV-1 infected iDCs in 2D suspension


title: Tumor_Trem2+_Rep2

source_name: mouse BCC

value: Mouse tumor from Ptch1+/-;p53f/f;K14CreER model

value: mouse basal cell carcinoma (BCC) tumor


title: Tgfb_rep1 [10_TGF_A]

value: Tgfb


title: Tumor_Trem2+_Rep1


title: Tgfb_rep3 [12_TGF_C]


title: BJ0618

value: plasma

value: lean


title: Normal_Trem2+_Rep2

source_name: mouse back skin

value: mouse back skin


title: Normal_Trem2+_Rep1


title: Stem_rep3 [3_Stem_C]

value: vehicle


title: Stem_rep2 [2_Stem_B]


title: BJ0582

value: girl


title: Stem_rep1 [1_Stem_A]

value: Aorta and carotid artery


title: BJ0559


title: BJ0543

value: boy


title: Donor 75, 2D suspension Untreated

description: gene expression data from monocyte derived iDCs cultured for two days in 2D suspension

value: Untreated iDCs in 2D suspension


title: Fgf9 Null

city: San Francisco

first: Julie

middle: B

last: Sneddon

address: 500 Parnassus Ave.

institute: UCSF

description: 10x Genomics

data_processing:
FASTQ files were generated from raw sequencing data using bcl2fastq software.
The demultiplexing, barcode processing and gene counting were performed using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The resulting matrices were then analyzed with Seurat v3.2.3.
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: Pancreas

growth_protocol: Fgf9 LacZ mice were maintained on a C57BL/6J background.

extract_protocol:
Pancreata were minced into small pieces and dissociated into single cells using TrypLE Express dissociation reagent (Gibco, 12604013) at 37°C for 15 min. We neutralized dissociations with FACS buffer (10% FBS+ 2 mM EDTA in phenol-red free HBSS), and passed cell suspensions through 30 µm cell strainers. Single cells were stained with DAPI before loading to the sorter (BD FACSAria II). After size selection to remove doublets, all DAPI negative live cells were collected.
Libraries were prepared according to the manufacturer’s instructions (10x Genomics). Each resulting library was sequenced on the Novaseq 6000 platform (Illumina) using the S4 flowcell with the following parameters: Read 1 – 28 cycles, Index 1 i7 – 8 cycles, Index 2 i5 – 0 cycles, Read 2 – 91 cycles.

value: Pancreas

tag: developmental stage

value: Embryonic day 14.5


title: Donor 75, 2D suspension HIV-1 infected + Vpx

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and cultured for two days in 2D suspension

value: monocyte derived dendritic cells

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 2D suspension


title: Donor 75, 3D Collagen LPS treated

description: gene expression data from monocyte derived iDCs trated with LPS and cultured for two days in 3D collagen

value: LPS treated iDCs in 3D collagen


title: BJ0510


title: BJ0518


title: Fgf9 Control

description: 10x Genomics


title: BJ0535


title: Donor 75, 3D Collagen HIV-1 infected + Vpx

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5  in the presence of Vpx and cultured for two days in 3D collagen

value: iDC spin-transduced with VLPs_Vpx and infected with HIV-1 in 3D collagen


title: BJ0316


title: BJ0422


title: E14.5_Null_01

description:
E14_M1
Bulk RNA-Seq

data_processing:
Sequencing reads were mapped to the reference genome (mm10-2020-A) using TopHat.
Gene expression quantification was performed using HTSeq.
Differential gene expression analysis was performed using DESeq2.
Assembly: mm10-2020-A
Supplementary files format and content: E13.5_E14.5_Control_Null_Counts.xls: Excel processed data file contains a gene by sample matrix of counts.

extract_protocol:
Dissected pancreata were placed in TriZol reagent. Total RNA was extracted using Zymo Directzol Microprep (R2060) according to the manufacturer's instructions.
Libraries were constructed using the Illumina NEBNext Ultra II RNA library prep kit following manufacturer's instructions for the NEBNext Poly(A) mRNA magnetic isolation module.

tag: pancreata per sample


title: JW1911

tag: tissue

value: obesity


title: Donor 75, 3D Collagen HIV-1 infected

description: gene expression data from monocyte derived iDCs infected with HIV-1 R5 and cultured for two days in 3D collagen

value: HIV-1 infected iDCs in 3D collagen