title: Cornea,SF/HA,rep3

first: Yilin

last: Zhang

address: XueYuan Road No.37, HaiDian District

institute: Beihang University

description: Library name: SF3

data_processing:
Raw sequencing data were first demultiplexed and converted into FASTQ format using the Illumina bcl2fastq software. Low-quality reads and adapter sequences were removed using fastp. The clean reads were then aligned to the Rattus norvegicus reference genome using STAR aligner. Gene-level expression quantification was performed with featureCounts to generate the raw count matrix. Downstream analyses such as normalization and differential expression analysis were conducted using DESeq2 in R.
Assembly: The reference genome used for read alignment was Rattus norvegicus genome assembly mRatBN7.2 (GCF_015227675.2), and the corresponding gene annotation file was obtained from the NCBI RefSeq database.
Supplementary files format and content: All files are formatted in a standard tab-delimited (TXT) or comma-delimited (CSV) format for easy compatibility with analysis tools like R, Python, or bioinformatics pipelines. The files contain no headers for rows or columns unless specified, and each data file adheres to standard conventions for genomic data analysis.

organism: Rattus norvegicus

source_name: cornea

extract_protocol:
Total RNA was extracted from cells after treatment. Cells were washed with PBS and lysed using a lysis buffer according to the manufacturer's instructions. RNA was purified using a silica column-based kit, and the concentration and purity were assessed using a NanoDrop spectrophotometer and agarose gel electrophoresis. Only high-quality RNA (OD260/280 between 1.8–2.0) was used for downstream cDNA synthesis and library construction.
Reverse transcription was performed using cell lysates, with each well receiving a poly(dT) primer containing unique sample barcodes and molecular identifiers (UMIs) to synthesize first-strand full-length cDNA. The resulting cDNA from different samples was pooled and purified, followed by an enzymatic digestion step to remove excess primers. Double-stranded cDNA was then generated through PCR amplification. The concentration of double-stranded cDNA was quantified using a Qubit 4 fluorometer, and fragment size distribution was analyzed using the Agilent 4150 Bioanalyzer. Samples with concentrations greater than 1.6 ng/μL and major peaks between 750 and 1500 bp were considered qualified for subsequent library construction.

value: cornea


title: Ethanol extracts of JGT (20 ug/mL dose)_rep2

status: Public on Jun 25 2025

type: SRA

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: Library name: JGE03_L_rep2

library_source: transcriptomic

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation mm10 Gene Transfer Format (GTF) file from UCSC browser
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Muscle

growth_protocol: C2C12 murine myoblasts (ATCC CRL-1772) were purchased from the ATCC (Manassas, VA, USA). Myoblasts were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, CARLSBAD, CA, USA) containing 10% fetal bovine serum (FBS; Gibco Grand Island, NY, USA) and 1% penicillin/streptomycin (Invitrogen) at 37°C in an atmosphere of 5% CO2. For differentiation to C2C12 myotubes, myoblasts were cultured in DMEM containing 2% horse serum (HS; Gibco) for 5 days. We used differentiated C2C12 myotubes.

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

treatment_protocol: Freeze-dried JG-E powder was obtained from KOC Biotech Co. (Daejeon, Republic of Korea). JGT-E powder was dissolved in 2% DMSO and then sterilized through a 0.22 µm membrane. C2C12 myotubes were treated vehicle or indicated concentrations of JGT-E for 24 h in triplicate.

tag: tissue

value: Muscle

tag: cell line

tag: cell type

value: Myotube

tag: treatment

value: JGT-E, 20 ug/ml, 24 h


title: EL.LS1.m.005.Epithelium

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

country: USA

institute: University of Chicago

description: Library name: DSP-1001660005767-C-F01

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

organism: Homo sapiens

source_name: Epithelium

extract_protocol:
FFPE tissue sections (5 μm) sliced consecutively to Deep Viusal Proteomics samples were processed following the Nanostring GeoMx user manual (MAN-10132-04). In brief, tissue slides were deparaffinized and rehydrated, followed by protein target retrieval using antigen retrieval buffer (Tris-EDTA) for 20 min in a pressure cooker. RNA target retrieval was accomplished by a digest with proteinase K for 15 min at 37°C. Tissue was post-fixed in 10% NBF, followed by an overnight hybridization at 37°C with the RNA probes (Human Whole Transcriptome Atlas, 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Excess probes were removed the next day by washing the samples twice in stringent washes at 37°C, followed by an incubation period in blocking buffer W (Nanostring LOT#:2-23020032). Thereafter, tissue was stained using conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488, 1:100) and vimentin (mouse monoclonal IgG1κ, Santa Cruz sc-373717, 1:100) as well as the SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomics data acquisition, slides were placed on the GeoMx Digital Spatial Profiler (DSP) and scanned in 20x magnification. Based on immunofluorescence images, regions of interest (ROI) were collected under supervision of an experienced pathologist (AB) and matched to the regions selected in DVP. Upon ROI selection, oligonucleotide barcodes were collected into a 96-well plate by UV-ablation while precisely separating compartments in each region.
Sequencing libraries were prepared using the Illumina TruSeq technology for the ligation of sequencing adaptors and amplification. Amplified libraries were purified using two rounds of Ampure XP magnetic bead cleanup (ratio 1.2:1 (beads: library)) (HighPrep PCR from MAGBIO (Cat#: AC-60500). Purified libraries were sequenced in an Illumina NovaSeq flowcell PE50 at a depth of 100x /μm2.

value: Ovarian Cancer, Tumor

value: Epithelium

tag: cohort

value: LGSC-PT


title: LCMV-pancreas-BMS-7Day-mouse13rep2

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Fastq files were processed to dcc files using GeoMx NGS pipeline software. Using the dcc files, spatial transcriptomics analysis was conducted in R studio v4.2.1 using the GeomxTools 3.4.0 package
The GeoMx whole mouse transcriptome atlas was used as the probe assay metadata
Sequencing quality was assessed using the default quality control (QC) parameter cut-offs, namely: minimum number of reads (1000); minimum percentage of reads trimmed (80%), stitched (80%), and aligned (80%); sequencing saturation (50%); negative control counts (10); maximum counts observed in no treatment control (NTC) well (1000); minimum number of nuclei estimated (100); and minimum segment area (5000). Any ROI that did not satisfy the above criteria was removed as part of QC filtering.
Following segment QC, probe QC was also performed to remove any outlier either globally or locally before generating gene-level count data.
The limit of quantification was determined per segment using the value recommended in the workflow, and segments with less than 1-5% of genes detected were removed. Furthermore, only genes that were detected in at least 1% of segments were retained.
The data was normalized using the quartile 3 method and log transformed.
For each organ, a linear mixed model without random slope was used to identify differentially expressed genes between vehicle and treatment groups for both the 3- and 7-day timepoints. Genes with linear scale fold change ³ 1.5 and p-value < 0.05 were considered as differentially expressed.
Assembly: GeoMx mouse whole transcriptome assay v1
Supplementary files format and content: .dcc files = Digital count conversion file (dcc file)
Supplementary files format and content: Rawcounts_LCMV.txt = raw counts for LCMV mouse dataset
Supplementary files format and content: q3 normalized counts_LCMV.txt = q3 normalized and log transformed values for LCMV mouse dataset
Supplementary files format and content: Rawcounts_NOD.txt = raw counts for NOD mouse dataset
Supplementary files format and content: q3 normalized counts_NOD.txt = q3 normalized and log transformed values for NOD mouse dataset
Library strategy: Spatial transcriptomics

source_name: pancreas

growth_protocol: RIP-LCMV-GP mice were purchased from Jackson Laboratory and bred in-house. Five-week-old female NOD/ShiLT mice were purchased from Jackson Laboratory and acclimated at the IU Laboratory Animal Research Center (LARC) for at least one week prior to treatment.

extract_protocol:
Mouse pancreas sections (5 µm) were fixed, sectioned, and mounted on positively charged slides. The slideswere deparaffinized, heated in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 min, and treated with 1 µg/mL proteinase K at 37 °C for 15 min. Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (NanoString Technologies, GMX-RNA-NGS-MsWTA). An overnightin situhybridization was performed with a mouse WTA probe, and the next day, the slides were washed twice at 37 °C for 25 min with 50% formamide/2X SSC buffer to remove unbound probes. The slides were then washed twice with 2X SSC buffer for 2 minutes at RT and blocked with blocking buffer containing Buffer W (Nanostring) with 1% Fc-Receptor blocker (Milteny) and 5% Normal Donkey Serum (Jackson Laboratories) as described previously (98). The slides were incubated with guinea pig anti-insulin (Dako), 1:200 rabbit anti-CD3 (Abcam), mouse anti-CD68 (Santa Cruz).The slides were washed twice with 2xSSC and incubated with secondary antibodies (1:400 goat-anti-guinea pig Alexa-488; 1:200 goat-anti rabbit Alexa-594 and 1:200 goat-anti mouse Alexa-647) for 30 minutes. Then, the slides were washed four times with 2xSSC for 3 minutes and counter-stainedwith 1:20,000 Syto83 (Invitrogen) for 1 h at room temperature. Stained slides were loaded onto the GeoMx instrument and scanned. After visual inspection using the GeoMx Digital Spatial Profiler (DSP; NanoString Technologies), geometrical ROIs (100 μm diameter) with different histologies were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq500 sequencer (Illumina).
The GeoMx libraries were prepared according to the GeoMx DSP NGS Readout User Manual. Briefly, for each plate, 4 μl of a GeoMx DSP sample was used for amplification. Each GeoMx DSP sample in a well was uniquely indexed with dual indexes. 4 μL of each resulting PCR product, including the NTC negative control, were pooled and purified with AMPure XP beads (Beckman Coulter). The final libraries were qualified and quantified using TapeStation and Qubit, respectively. The libraries were sequenced on an Illumina NextSeq 500 to generate 27 bp paired-end sequence reads.

treatment_protocol: Eight-week-old maleRIP-LCMV-GPmice werepre-treated with TYK2i (BMS-986202, 30 mg/kg) or vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse) by oral gavage two days prior to inoculation with LCMV. Mice continued to receive TYK2i treatment daily until the study endpoint. Six-week-old female NOD mice were treated with BMS-986202 (30 mg/kg) or vehicle for 6 weeks by oral gavage.Themice from each group were euthanized after 6 weeks of TYK2i treatment (12-weeks of age), and the pancreas was harvested and fixed for downstream analysis as described previously(80).

tag: mouse number

value: pancreas

tag: sample collection_day_post_inoculation

tag: roi

tag: strain

value: RIP-LCMV-GP

tag: age

value: 8-week old

tag: Sex

value: Male


title: EL.LS1.m.002.Stroma

description: Library name: DSP-1001660005767-C-E08

source_name: Stroma

value: Stroma


title: LCMV-spleen-BMS-7Day-mouse12rep3

source_name: spleen

value: spleen


title: Cornea,SF/HA,rep2

city: Beijing

country: China

description: Library name: SF2


title: IN_MUT_4

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

description: Library name: sample 4

data_processing:
fastp v0.23.4, STAR v2.7.0, RSEM v1.3.3
Sequence reads were trimmed for adaptor sequence/sequence quality using fastp v0.23.4 (qualified_quality_phred=20, nqualified_percent_limit=30, average_qual=25, low_complexity_filter=True, complexity_threshold=30)
passing filter reads were mapped to the genome reference (Danio rerio GRCz11v110, Ensembl v110 ) using STAR v2.7.10 with standard parameters, except for the sjdbOverhang option set on read length
Genome and transcripts annotation provided as input were downloaded from Ensembl v112 repository. Alignments were then elaborated by RSEM v1.3.3, to estimate transcript and gene abundances. Subsequently, the sample-specific gene-level abundances were merged into a single raw expression matrix applying a dedicated RSEM command (rsem-generate-data-matrix).
Assembly: Danio rerio GRCz11v112, Ensembl v112
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

organism: Danio rerio

source_name: heart

growth_protocol: Wild-type (wt) fish AB (Oregon) and ankrd1abns502 (mut) were maintained under standard conditions, in a circulating water system, under 14 h light/10 h dark cycle, at 27.5-28 ◦C.

extract_protocol:
Heart ventricles dissected out from cryoinjured and sham-operated wt and ankrd1a mutant fish were homogenized in TRIzol Reagent (Invitorgen, Thermo Fisher Scientific, USA). Three ventricles were pooled as one sample. Total RNA was extracted using RNA Clean and concentrator kit (ZYMO Research, USA), according to the manufacturer instructions and eluted in 23 µl of RNase-free water and its quantity and purity were measured promptly after isolation, using BioSpec-nano (Shimadzu, Japan) and Qubit 4TM Fluorometer with ssRNA BR Assay KitTM (Thermo Scientific Fisher, USA).
cDNA libraries were constructed via poly A enrichment using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina, California, USA)

treatment_protocol: Before the procedure, adult zebrafish were anesthetized in system water containing 0.02% tricaine (ethyl 3-aminobenzoate methanesulfonate salt, MS-222, Sigma-Aldrich, SAD). A small incision was made in the chest area to expose the heart, followed by the application of a cryoprobe precooled in liquid nitrogen to the ventricular apex, maintaining contact for 25 sec. Subsequently, cryoinjured fish were transferred into fresh system water and allowed to recover for 7 days. The procedure was repeated for sham-operated fish, using a cryoprobe at room temperature.

value: heart

tag: genotype

value: ankrd1a mutant

value: cryioinjured


title: Ethanol extracts of JGT (100 ug/mL dose)_rep2

description: Library name: JGE03_M_rep2

value: JGT-E, 100 ug/ml, 24 h


title: EL.LS1.m.004.Epithelium

description: Library name: DSP-1001660005767-C-E11


title: Vehicle_rep2

description: Library name: Veh_rep2


title: LCMV-spleen-BMS-7Day-mouse12rep2


title: EL.LS1.m.002.Epithelium

description: Library name: DSP-1001660005767-C-E07


title: EL.LS1.m.001.Stroma

description: Library name: DSP-1001660005767-C-E06


title: Cornea,SF/HA,rep1

description: Library name: SF1

value: cornea


title: Vehicle_rep1

description: Library name: Veh_rep1

value: Muscle


title: LCMV-lymphnode-BMS-7Day-mouse12rep1

source_name: lymph node

value: lymph node


title: Ethanol extracts of JGT (100 ug/mL dose)_rep1

description: Library name: JGE03_M_rep1

value: Myotube


title: EL.LS1.m.001.Epithelium

description: Library name: DSP-1001660005767-C-E05

value: Ovarian Cancer, Tumor


title: LCMV-spleen-BMS-7Day-mouse12rep1


title: LCMV-pancreas-BMS-7Day-mouse12rep11


title: EL.MST6.m.020.Epithelium

description: Library name: DSP-1001660005767-C-E03

value: Epithelium

value: SBT-MP


title: LCMV-pancreas-BMS-7Day-mouse12rep10

value: pancreas


title: Cornea,SF/HA-HEP-PAM,rep1

description: Library name: H1


title: Healthy control9

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description: Library name: HC9.bam

data_processing:
RNA-seq data analysis was performed using the Ion Torrent Software Suite version 5.4. The Torrent Mapping Alignment Program (TMAP) was used to align the raw sequencing reads generated by the Ion Torrent sequencing data against the reference sequence derived from the hg19 (GRCh37) assembly. The raw read counts of the targeted genes were normalized using the Fragments Per Kilobase Million (FPKM) normalization method. Principal component analysis (PCA) was performed using the indicated samples with R statistical software. Differentially expressed gene (DEG) analysis was performed using the DESeq2 R/Bioconductor package with raw read counts from the RNA sequencing data to identify the differentially expressed genes (DEGs) in each comparison of cell lines with CARD11 transfected against cell lines with empty vector transfected as well as of the patients with low (CARD11-) and high (CARD11+) CARD11 expressions
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Healthy pulp tissue

extract_protocol:
For the whole human transcriptomics experiment, a total of 16 samples including 4 periapical abscesses, 4 radicular cysts, 4 periapical granulomas, and 4 healthy pulp tissues, were processed for RNA isolation using the RNeasy Kit (Qiagen, Germany) following the manufacturer’s instructions. The eluted RNA was quantified using a NanoDrop 2000 Spectrophotometer (ThermoFisher Scientific, USA) and stored at -80 °C for downstream transcriptomic analysis.
Genomic DNA removal from RNA samples was ensured by treating the RNA with Turbo DNase (ThermoFisher Scientific, USA). Next, whole transcriptome sequencing was performed using targeted RNA-Seq with Ion AmpliSeq whole transcriptome human gene expression kit (ThermoFisher Scientific, USA). cDNA was synthesized using a SuperScript VILO cDNA Synthesis kit (ThermoFisher Scientific, USA) and amplified using Ion AmpliSeq human gene expression core panel primers. The amplified products were subjected to enzymatic shearing to get amplicons of ~200 bp, then ligated with the adapter and the unique barcodes. Next, the constructed library was purified using Agencourt AMPure XP Beads (Beckman Coulter, USA), quantified using an Ion Library TaqMan™ quantitation kit (Applied Biosystems, USA), further diluted to 100 pM, and pooled equally with 16 individual samples. The diluted library was amplified and enriched in Ion Chef System (ThermoFisher Scientific) according to the manufacturer’s instructions. Ion 540 Chip was used to sequence the prepared template libraries using an Ion S5 XL Semiconductor sequencer (ThermoFisher Scientific).

value: Healthy pulp tissue


title: Healthy control10

description: Library name: HC10.bam


title: EL.MST6.m.019.Stroma

description: Library name: DSP-1001660005767-C-E02


title: Healthy control8

description: Library name: HC8.bam


title: EL.MST6.m.019.Epithelium

description: Library name: DSP-1001660005767-C-E01


title: LCMV-pancreas-BMS-7Day-mouse12rep9

value: RIP-LCMV-GP

value: 8-week old


title: Cornea,Control,rep2

description: Library name: C2


title: EL.MST6.m.020.Stroma

description: Library name: DSP-1001660005767-C-E04

value: Stroma


title: Cornea,Control,rep3

description: Library name: C3


title: LCMV-pancreas-BMS-7Day-mouse12rep8

value: Male


title: EL.MST6.m.018.Epithelium

description: Library name: DSP-1001660005767-C-D12


title: LCMV-pancreas-BMS-7Day-mouse12rep7


title: Granuloma11

description: Library name: G11.bam

source_name: Periapical granuloma

value: Periapical granuloma


title: Healthy control7

description: Library name: HC7.bam


title: Granuloma10

description: Library name: G10.bam


title: EL.MST6.m.017.Epithelium

description: Library name: DSP-1001660005767-C-D11


title: Cornea,SF/HA-HEP-PAM,rep3

description: Library name: H3


title: Granuloma9

description: Library name: G9.bam


title: Cornea,Control,rep1

description: Library name: C1


title: EL.MST6.m.016.Stroma

description: Library name: DSP-1001660005767-C-D10


title: Granuloma8

description: Library name: G8.bam


title: LCMV-pancreas-BMS-7Day-mouse12rep5


title: Cornea,Alkali-burned,rep2

description: Library name: A2


title: Cornea,SF/HA-HEP-PAM,rep2

description: Library name: H2


title: LCMV-pancreas-BMS-7Day-mouse12rep4


title: EL.MST6.m.016.Epithelium

description: Library name: DSP-1001660005767-C-D09


title: Cornea,Alkali-burned,rep1

description: Library name: A1


title: EL.MST6.m.015.Epithelium

description: Library name: DSP-1001660005767-C-D08


title: Cyst11

description: Library name: C11.bam

source_name: Radicular cyst

value: Radicular cyst


title: LCMV-pancreas-BMS-7Day-mouse12rep3


title: EL.MST6.m.014.Epithelium

description: Library name: DSP-1001660005767-C-D07


title: ircAE combined CTLA4/PD1 1

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

description: Library name: 20160420.B-HG13_931_PD1

data_processing:
STAR v2.7.8a used for reference alignment against human genome
Rsubread v2.4.3 used for gene expression quantification
R package RUVseq v1.38 used for batch correction
R package EdgeR v4.2 used for differential gene expression analysis
Assembly: GRCh38.p13
Supplementary files format and content: Batch corrected normalized gene count matrix

source_name: Skin

extract_protocol:
Samples were thawed, and RNA extraction was carried out using Trizol along with the Qiagen RNAeasy kit (Qiagen, Germany), adhering to the manufacturer's instructions.
For RNA sequencing, total RNA (100–1,000 ng per sample) underwent ribosomal RNA depletion, was reverse-transcribed into double-stranded cDNA, and then selectively enriched by polymerase chain reaction (PCR). The enriched libraries' quality and quantity were assessed using the Fragment Analyzer (Agilent, Santa Clara, California, USA). Libraries were then normalized to a concentration of 10 nM in Tris-Cl 10 mM, pH 8.5 with 0.1 % Tween 20. Sequencing and cluster generation were performed using the HiSeq2500 (Illumina, Inc, California, USA) following the standard protocol.

value: Skin

tag: batch


title: LCMV-pancreas-BMS-7Day-mouse12rep2


title: LCMV-pancreas-BMS-7Day-mouse12rep6


title: LCMV-pancreas-BMS-7Day-mouse12rep1


title: ircAE PD1-Monotherapy 2

description: Library name: 20160420.B-HG13_1689_PD1


title: Cornea,Alkali-burned,rep3

description: Library name: A3


title: EL.MST6.m.012.Epithelium

description: Library name: DSP-1001660005767-C-D05


title: LCMV-pancreas-BMS-7Day-mouse11rep1


title: Cyst8

description: Library name: C8.bam


title: Cyst10

description: Library name: C10.bam


title: maculopapular drug rash 7

description: Library name: 20160518.A-HG15_402_AME


title: Abscess14

description: Library name: A14.bam

source_name: Periapical abscess

value: Periapical abscess


title: Abscess13

description: Library name: A13.bam


title: EL.MST6.m.010.Epithelium

description: Library name: DSP-1001660005767-C-D03


title: maculopapular drug rash 6

description: Library name: 20160420.B-HG14_1085_AME


title: Abscess12

description: Library name: A12.bam


title: LCMV-spleen-BMS-7Day-mouse11rep3

value: spleen


title: LCMV-spleen-BMS-7Day-mouse11rep2


title: EL.MST6.m.009.Epithelium

description: Library name: DSP-1001660005767-C-D02


title: maculopapular drug rash 5

description: Library name: 20160420.B-HG14_974_AME


title: LCMV-spleen-BMS-7Day-mouse11rep1


title: EL.MST6.m.008.Epithelium

description: Library name: DSP-1001660005767-C-D01


title: EL.MST6.m.013.Epithelium

description: Library name: DSP-1001660005767-C-D06


title: Abscess11

description: Library name: A11.bam


title: ircAE PD1-Monotherapy 3

description: Library name: 20160420.B-HG14_527_PD1


title: Cyst9

description: Library name: C9.bam


title: ircAE PD1-Monotherapy 1

description: Library name: 20160420.B-HG13_306_PD1


title: maculopapular drug rash 4

description: Library name: 20160420.B-HG14_705_AME


title: LCMV-spleen-BMS-7Day-mouse10rep6


title: EL.MST6.m.007.Epithelium

description: Library name: DSP-1001660005767-C-C12


title: maculopapular drug rash 3

description: Library name: 20160420.B-HG14_587_AME


title: EL.MST6.m.006.Epithelium

description: Library name: DSP-1001660005767-C-C11


title: EL.MST6.m.011.Epithelium

description: Library name: DSP-1001660005767-C-D04


title: sham - 2

type: RNA

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

country: Canada

institute: McGill University

hyb_protocol: Vizgen provided protocols for requisite tissue type were utilized to conduct data acquisition

scan_protocol: The MERSCOPE instrument was used for imaging of samples.

data_processing:
Following initial processing my MERSCOPE instrument, pseudospots were generated and transcripts were assigned accordingly.
*_detected_transcripts.csv files: location and identity of detected RNA transcripts. *_scs_ep.csv files: TSV file describing if cells were spatially selected for as ependymal. *_scs_choroid.csv files: TSV file describing if cells were spatially selected for as choroidal. *_scs_choroid.csv files: TSV file containing per-observation metadata.*_exp.mtx files: MM format matrix files containing spot by gene expression values as determined via pseudo-spot creation. *_feats.txt files: newline separated names of features corresponding to columns in *_exp.mtx files.  *_obs.txt: newline separated names of observations corresponding to rows in *_exp.mtx files.

source_name: brain, ICV injected w/ DMEM, 8dpi

extract_protocol: Mice were euthanized at 8 dpi with isoflurane and brains immediately collected. Brains were cut at the midline; the contralateral side was used for the infected tissue and the ipsilateral side for the sham. Both hemispheres were frozen in OCT on dry ice and transferred to a -80 C freezer for storage.   Prior to cutting tissue, the OCT blocks were allowed to warm to -20 C in the cryostat. The tissue was cut in 10 μm sections for slides horizontally from [bregma distance] to [bregma] to include ventricles and choroid plexus. Several sections of tissue were also collected and processed for checking RNA quality. Slide tissue was fixed with 4% PFA, washed three times with 1x PBS, and stored in 70% ethanol until processing. Sections for RNA quality were purified using Trizol and subsequent phenol/chloroform extraction, then resuspended in 20 μL RNAse free water.

treatment_protocol: Mice were anesthetized with ketamine/xylazine and infected intracerebroventricularly (icv) with 1 x 107 PFU/mL MuPyV. Sham mice were injected with the equivalent volume of DMEM. The strain of MuPyV used was the wild-type strain A2.

value: female


title: infected - 2

source_name: brain, polyomavirus infected via ICV injection, 8dpi

label_protocol: Vizgen provided protocols for requisite tissue type were utilized to conduct data acquisition


title: maculopapular drug rash 2

description: Library name: 20160420.B-HG14_254_AME


title: LCMV-spleen-BMS-7Day-mouse10rep5


title: EL.MST6.m.004.Epithelium

description: Library name: DSP-1001660005767-C-C09


title: infected - 1


title: maculopapular drug rash 1

description: Library name: 20160518.A-HG12_1113_AME


title: EL.MST6.m.005.Epithelium

description: Library name: DSP-1001660005767-C-C10


title: toxic epidermal necrolysis 3

description: Library name: 20160518.A-HG13_1720_Ly


title: sham - 1


title: LCMV-spleen-BMS-7Day-mouse10rep2


title: EL.MST6.m.003.Stroma

description: Library name: DSP-1001660005767-C-C08


title: LCMV-spleen-BMS-7Day-mouse11rep4


title: LCMV-spleen-BMS-7Day-mouse10rep3


title: 2RR, 4R,1N,2L | 016 | Full ROI

city: London

first: Jun

last: Ishihara

address: 86 Wood Lane

department: Bioengineering

country: United Kingdom

institute: Imperial College London

description:
Library name: IL-12 ROI-12
FFPE spatial transcriptome sequencing

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq software.
Sequenced samples were aligned and quantified by GeoMX NGS Pipeline and filtered by GeoMX DSP software according to NanoString’s guidelines. Normalization using Third quartile (Q3) normalization with all targets was performed according to NanoString instructions.
Count matrix files were used to perform differential gene expression analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: 5 percent target Q3 Norm Read Counts_DESeq 2.xlsx: Segment properties, target properties, Q3 normalized read counts, bioprobe properties and dataset summary
Library strategy: Spatial Transcriptomics

source_name: RM9-human STEAP1 prostate cancer

extract_protocol:
FFPE tissue blocks were sectioned by UCLA Translational Pathology Core Laboratory (TPCL). RNA was extracted from mouse FFPE samples with Qiagen RNeasy FFPE Kit.
Slides were stained using NanoString GeoMx (v1.0) Mouse NGS Whole Transcriptome Atlas RNApanel according to manufacturer instructions. ROIs were selected based on Anti-PanCK, Anti-CD45, and DNA staining as morphological markers. Oligo barcodes were collected from ROI into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. GeoMx Seq Code Pack were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeq X Plus for PE 2x50 runs.

value: RM9-human STEAP1 prostate cancer

value: mouse prostate


title: 2RR, 4R,1N,2L | 015 | Full ROI

description:
Library name: IL-12 ROI-11
FFPE spatial transcriptome sequencing


title: EL.MST6.m.003.Epithelium

description: Library name: DSP-1001660005767-C-C07

value: Ovarian Cancer, Tumor


title: toxic epidermal necrolysis 2

description: Library name: 20160518.A-HG12_394_Ly


title: toxic epidermal necrolysis 1

description: Library name: 20160518.A-HG11_1189_Ly


title: LCMV-spleen-BMS-3Day-mouse3rep6


title: 2RR, 4R,1N,2L | 014 | Full ROI

description:
Library name: IL-12 ROI-10
FFPE spatial transcriptome sequencing


title: EL.MST6.m.002.Epithelium

description: Library name: DSP-1001660005767-C-C06

value: Epithelium


title: LCMV-spleen-BMS-7Day-mouse10rep1


title: 2RR, 4R,1N,2L | 012 | Full ROI

description:
Library name: IL-12 ROI-9
FFPE spatial transcriptome sequencing


title: CN-no.12

city: Obu

first: Risa

last: Mitsumori

state: Aichi

address: 7-430, Morioka-cho

department: Research Institute

country: Japan

institute: National Center for Geriatrics and Gerontology

library_source: genomic

data_processing:
Raw sequence data were converted from bcl file to fastq file using Illumina bcl2fastq2 Conversion software v2.17.
Sequencing data were aligned to the reference sequence (GRCh37/ UCSChg19) using an application, MethylSeq, which is provided by Illumina, inc. through the cloud service named BaseSpace.
Counting the numbers of methylated and unmethylated cytosines at each CpG site, that is methylation call, was performed by MethylKit, another application available through BaseSpace.
The methylation call data was then used to detect differential DNA methylation between AD subjects and CN by the same application.
We set the condition of MethylKit for differentially methylated CpG sites to be identified as follows:  ≥ 10 coverage with independent reads, ≥15% methylation differences with q-value ≤ 0.01.
Assembly: GRCh37/ UCSChg19
Supplementary files format and content: The csv-table indicates the differential methylation CpG sites between AD cases and CNs that followed ≥ 10 coverage with independent reads and ≥15% methylation differences with q-value ≤ 0.01.

molecule: genomic DNA

source_name: Whole blood

extract_protocol:
Genomic DNA (gDNA) was extracted from peripheral blood by using a Maxwell RSC Instrument (Promega, USA) with Maxwell RSC Buffy Coat DNA Kit (Promega, USA).
Comprehensive methylation analysis of the 1st cohort was conducted by the target enrichment system, TruSeq methyl capture EPIC Kit (Illumina, Inc., San Diego, CA, USA), which was followed by next generation sequencing as follows: gDNA was fragmented to a few hundred base pairs (bps) by Covaris M220, followed by blunting, phosphorylation, addition of 3’-dA, and ligation of indexed adaptors to both ends of DNA.  DNA was mixed and hybridized to capture oligos, and hybridized DNA was recovered by streptavidin-conjugated magnetic beads.  Eluted DNA was treated with sodium bisulfite and amplified by PCR to construct a sequencing library, which was sequenced by using the Illumina HiSeq 2500 platform with paired-end reads of 100 bp by following the manufacturer’s instructions.  Library construction and sequencing were conducted by Takara bio, inc. (Shiga, Japan).

value: Whole blood

tag: disease state

value: normal


title: LCMV-spleen-BMS-7Day-mouse10rep4


title: 2RR, 4R,1N,2L | 011 | Full ROI

description:
Library name: IL-12 ROI-8
FFPE spatial transcriptome sequencing


title: EL.MST6.m.001.Epithelium

description: Library name: DSP-1001660005767-C-C05

value: SBT-MP


title: CN-no.10


title: EL.MST4.m.015.Stroma

description: Library name: DSP-1001660005767-C-C04


title: LCMV-spleen-BMS-3Day-mouse3rep5

value: RIP-LCMV-GP


title: CN-no.11


title: 2RR, 4R,1N,2L | 010 | Full ROI

description:
Library name: IL-12 ROI-7
FFPE spatial transcriptome sequencing


title: EL.MST4.m.015.Epithelium

description: Library name: DSP-1001660005767-C-C03


title: LCMV-spleen-BMS-3Day-mouse3rep3

value: 8-week old


title: CN-no.9


title: 2RR, 4R,1N,2L | 008 | Full ROI

description:
Library name: IL-12 ROI-6
FFPE spatial transcriptome sequencing


title: LCMV-spleen-BMS-3Day-mouse3rep4


title: LCMV-spleen-BMS-3Day-mouse3rep2


title: EL.MST4.m.013.Stroma

description: Library name: DSP-1001660005767-C-C01

value: Stroma


title: CN-no.8


title: EL.MST4.m.013.Epithelium

description: Library name: DSP-1001660005767-C-B12


title: LCMV-spleen-BMS-3Day-mouse3rep1

value: Male


title: 2RR, 4R,1N,2L | 007 | Full ROI

description:
Library name: IL-12 ROI-5
FFPE spatial transcriptome sequencing


title: CN-no.7


title: 2RR, 4R,1N,2L | 006 | Full ROI

description:
Library name: IL-12 ROI-4
FFPE spatial transcriptome sequencing


title: LCMV-pancreas-BMS-3Day-mouse3rep7

value: pancreas


title: EL.MST4.m.012.Stroma

description: Library name: DSP-1001660005767-C-B11


title: CN-no.6


title: EL.MST4.m.011.Epithelium

description: Library name: DSP-1001660005767-C-B09


title: 2RR, 4R,1N,2L | 004 | Full ROI

description:
Library name: IL-12 ROI-3
FFPE spatial transcriptome sequencing


title: LCMV-pancreas-BMS-3Day-mouse3rep6


title: EL.MST4.m.010.Stroma

description: Library name: DSP-1001660005767-C-B08


title: LCMV-pancreas-BMS-3Day-mouse3rep5


title: CN-no.4


title: 2RR, 4R,1N,2L | 002 | Full ROI

description:
Library name: IL-12 ROI-1
FFPE spatial transcriptome sequencing


title: CN-no.3


title: LCMV-pancreas-BMS-3Day-mouse3rep4


title: CBDIL12-CART | 012 | Full ROI

description:
Library name: CBD-12
FFPE spatial transcriptome sequencing


title: EL.MST4.m.010.Epithelium

description: Library name: DSP-1001660005767-C-B07


title: LCMV-pancreas-BMS-3Day-mouse3rep3


title: EL.MST4.m.009.Stroma

description: Library name: DSP-1001660005767-C-B06


title: EL.MST4.m.009.Epithelium

description: Library name: DSP-1001660005767-C-B05


title: CN-no.2


title: CBDIL12-CART | 010 | Full ROI

description:
Library name: CBD-10
FFPE spatial transcriptome sequencing


title: CN-no.1


title: EL.MST4.m.008.Stroma

description: Library name: DSP-1001660005767-C-B04


title: LCMV-pancreas-BMS-3Day-mouse3rep2


title: CBDIL12-CART | 009 | Full ROI

description:
Library name: CBD-9
FFPE spatial transcriptome sequencing


title: AD+no.12

value: Alzheimer


title: EL.MST4.m.008.Epithelium

description: Library name: DSP-1001660005767-C-B03


title: LCMV-pancreas-BMS-3Day-mouse3rep1


title: AD+no.11


title: CN-no.5


title: EL.MST4.m.007.Epithelium

description: Library name: DSP-1001660005767-C-B01


title: 2RR, 4R,1N,2L | 003 | Full ROI

description:
Library name: IL-12 ROI-2
FFPE spatial transcriptome sequencing


title: AD+no.10


title: LCMV-spleen-BMS-3Day-mouse2rep6


title: CBDIL12-CART | 008 | Full ROI

description:
Library name: CBD-8
FFPE spatial transcriptome sequencing


title: LCMV-spleen-BMS-3Day-mouse2rep5


title: CBDIL12-CART | 007 | Full ROI

description:
Library name: CBD-7
FFPE spatial transcriptome sequencing


title: EL.MST4.m.006.Epithelium

description: Library name: DSP-1001660005767-C-A11


title: LCMV-spleen-BMS-3Day-mouse2rep4


title: AD+no.9


title: CBDIL12-CART | 011 | Full ROI

description:
Library name: CBD-11
FFPE spatial transcriptome sequencing


title: CBDIL12-CART | 005 | Full ROI

description:
Library name: CBD-5
FFPE spatial transcriptome sequencing


title: CBDIL12-CART | 006 | Full ROI

description:
Library name: CBD-6
FFPE spatial transcriptome sequencing


title: EL.MST4.m.004.Epithelium

description: Library name: DSP-1001660005767-C-A08


title: LCMV-spleen-BMS-3Day-mouse2rep3


title: AD+no.7


title: AD+no.8


title: EL.MST4.m.005.Epithelium

description: Library name: DSP-1001660005767-C-A09


title: EL.MST4.m.003.Stroma

description: Library name: DSP-1001660005767-C-A07


title: LCMV-spleen-BMS-3Day-mouse2rep2


title: LCMV-spleen-BMS-3Day-mouse2rep7


title: LCMV-spleen-BMS-3Day-mouse2rep1


title: AD+no.6


title: EL.MST4.m.003.Epithelium

description: Library name: DSP-1001660005767-C-A06


title: AD+no.5


title: CBDIL12-CART | 004 | Full ROI

description:
Library name: CBD-4
FFPE spatial transcriptome sequencing


title: CBDIL12-CART | 002 | Full ROI

description:
Library name: CBD-2
FFPE spatial transcriptome sequencing


title: EL.MST4.m.002.Stroma

description: Library name: DSP-1001660005767-C-A05


title: LCMV-lymhpnode-BMS-3Day-mouse2rep10

value: lymph node


title: EL.MST4.m.002.Epithelium

description: Library name: DSP-1001660005767-C-A04


title: AD+no.4


title: AD+no.3


title: CBDIL12-CART | 001 | Full ROI

description:
Library name: CBD-1
FFPE spatial transcriptome sequencing


title: LCMV-lymhpnode-BMS-3Day-mouse2rep9


title: CAR-T | 012 | Full ROI

description:
Library name: S1-12
FFPE spatial transcriptome sequencing


title: LCMV-lymhpnode-BMS-3Day-mouse2rep8


title: AD+no.2


title: LCMV-lymhpnode-BMS-3Day-mouse2rep7


title: EL.MST4.m.001.Epithelium

description: Library name: DSP-1001660005767-C-A02


title: AD+no.1


title: EL.MST1.m.015.Epithelium

description: Library name: DSP-1001660009341-B-F10


title: CAR-T | 010 | Full ROI

description:
Library name: S1-10
FFPE spatial transcriptome sequencing


title: CBDIL12-CART | 003 | Full ROI

description:
Library name: CBD-3
FFPE spatial transcriptome sequencing


title: CAR-T | 009 | Full ROI

description:
Library name: S1-9
FFPE spatial transcriptome sequencing


title: LCMV-lymhpnode-BMS-3Day-mouse2rep6


title: EL.MST1.m.014.Stroma

description: Library name: DSP-1001660009341-B-F09


title: BnaC3.LFY_DAP_input

city: Hangzhou

first: Mengjie

last: Gong

address: Yuhangtang Road-866

institute: Zhejiang University

description: Library name: BnaC3.LFY_DAP_input

data_processing:
Raw sequencing data were processed using fastp with default parameters to generate high-quality clean reads for downstream analyses. Clean reads were then aligned to the Westar genome using bowtie2, and alignments with a mapping quality score (MAPQ) > 30 were retained using Samtools. Peak calling was conducted using MACS2, followed by motif identification and analysis using HOMER.
Assembly: Brassica napus Westar
Supplementary files format and content: narrowPeak

organism: Brassica napus

source_name: shoot apices

extract_protocol:
Genomic DNA (gDNA) was isolated from Brassica napus inflorescence tissue using the CTAB method.
Libraries were constructed using the MICH TLX DNA-Seq Kit (Cat# NGS0602, Bluescape Hebei Biotech Co., Ltd, Baoding, 071000, People’s Republic of China) according to the manufacturer’s instructions.

value: shoot apices


title: LCMV-lymhpnode-BMS-3Day-mouse2rep5


title: CAR-T | 008 | Full ROI

description:
Library name: S1-8
FFPE spatial transcriptome sequencing


title: EL.MST1.m.012.Epithelium

description: Library name: DSP-1001660009341-B-F04


title: BnaC3.LFY_DAP_rep2

description: Library name: BnaC3.LFY_DAP_rep2


title: LCMV-lymhpnode-BMS-3Day-mouse2rep4


title: CAR-T | 007 | Full ROI

description:
Library name: S1-7
FFPE spatial transcriptome sequencing


title: BnaC3.LFY_DAP_rep1

description: Library name: BnaC3.LFY_DAP_rep1


title: EL.MST1.m.008.Epithelium

description: Library name: DSP-1001660009341-B-E08


title: CAR-T | 006 | Full ROI

description:
Library name: S1-6
FFPE spatial transcriptome sequencing


title: LCMV-lymhpnode-BMS-3Day-mouse2rep3


title: EL.MST1.m.007.Epithelium

description: Library name: DSP-1001660009341-B-E07


title: EL.MST4.m.001.Stroma

description: Library name: DSP-1001660005767-C-A03


title: Testis_Saline_m68

city: Valencia

first: Jose Vicente

last: Roig Genovés

address: Calle Moratín 17

country: Spain

institute: Rara Avis Biotec S.L.

data_processing:
The resulting reads were processed for image analysis, base calling, and quality scoring using the manufacturer’s software, Real Time Analysis (RTA 1.18.66.3), followed by the generation of FASTQ sequence files by CASAVA 1.8.
The RNA-seq raw reads were pre-processed for trimming adapters and quality filtering (reads below a Q30 Phred score were discarded) using Cutadapt software v3.4. Read quality was assessed before and after adapter/quality trimming using FastQC software v0.11.9
Reads were aligned against the Solea senegalensis reference genome (GCF_019176455.1) using Subread software v2.0.1, with all samples showing > 70% of successfully assigned reads. Annotation of aligned reads was performed via R software (v4.0.4) and the RSubread package v2.2.6 at the gene level using the GCA_019176455.1 gff file with default parameters
Assembly: GCF_019176455.1
Supplementary files format and content: Comma-separated value file containing raw counts for each sample

organism: Solea senegalensis

source_name: Biopsy

growth_protocol: Two-year-old male Senegalese sole, F1 generation offspring from wild-caught parents, were acquired from the commercial supplier Stolt Sea Farm S.A. (Spain) and transferred to the IRTA fish research center in Sant Carles de la Ràpita (Spain). The fish were housed in 10 m³ fiberglass tanks with a recirculating system (IRTAmar1) and were fed five times a week with 0.75% of wet feed (mussels and polychaetes) and 0.55% of dry feed (balanced diet) based on total biomass. They were maintained for three months before the experiments under natural light cycles and regulated simulated natural temperatures. The experiment was conducted over six weeks from November to January to examine the specific impact of recombinant Fsh and Lh (rFsh and rLh) on testicular development.

extract_protocol:
Total RNA from was extracted using the RNeasy Plus Mini Kit (Qiagen). The extracted RNA's purity and concentration were assessed using the NanoDropVC 2000, and RNA size distribution profiles were analysed using the Agilent 2100 Bioanalyzer. RIN values were comprised between 8.7 and 9.8.
For library construction (n = 4 for each group: control, rFsh and rLh), the SMARTseq2 protocol was employed, with some modifications. The libraries were sequenced on a NovaSeq 6000 S1 sequencing system (Illumina) in paired-end mode with 100 bp paired-end reads length.

treatment_protocol: Males (347±9 gr) received intramuscular injections once a week with saline (control, n=8), rFsh (18 μg/kg, n=8) or rLh (18 μg/kg, n=8). The animal care and sample collection procedures were conducted in compliance with protocols approved by the Ethics Committee (EC) of the Institut de Recerca i Tecnologìa Agroalimentàries (IRTA) following the European Union Council Guidelines (86/609/EU). The study received specific approval from the IRTA EC.

value: Testis

value: Saline


title: Testis_Saline_m67


title: LCMV-lymhpnode-BMS-3Day-mouse2rep2


title: CAR-T | 005 | Full ROI

description:
Library name: S1-5
FFPE spatial transcriptome sequencing

value: RM9-human STEAP1 prostate cancer


title: CAR-T | 011 | Full ROI

description:
Library name: S1-11
FFPE spatial transcriptome sequencing

value: mouse prostate


title: LCMV-lymhpnode-BMS-3Day-mouse2rep1


title: EL.MST1.m.006.Epithelium

description: Library name: DSP-1001660009341-B-E06

source_name: Epithelium

value: Ovarian Cancer, Tumor


title: Testis_Saline_m66


title: CAR-T | 003 | Full ROI

description:
Library name: S1-3
FFPE spatial transcriptome sequencing


title: CAR-T | 004 | Full ROI

description:
Library name: S1-4
FFPE spatial transcriptome sequencing


title: LCMV-pancreas-BMS-3Day-mouse2rep8

source_name: pancreas


title: Testis_Saline_m64


title: EL.MST1.m.005.Epithelium

description: Library name: DSP-1001660009341-B-E05

value: Epithelium


title: LCMV-pancreas-BMS-3Day-mouse2rep7


title: EL.MF3.m.012.Epithelium

description: Library name: DSP-1001660009341-B-D12


title: Testis_Saline_m63


title: CAR-T | 002 | Full ROI

description:
Library name: S1-2
FFPE spatial transcriptome sequencing


title: LCMV-pancreas-BMS-3Day-mouse2rep6


title: EL.MF3.m.010.Epithelium

description: Library name: DSP-1001660009341-B-D08


title: CAR-T | 001 | Full ROI

description:
Library name: S1-1
FFPE spatial transcriptome sequencing


title: LCMV-pancreas-BMS-3Day-mouse2rep5


title: Testis_LH_m68

value: rssLH


title: EL.MF3.m.006.Epithelium

description: Library name: DSP-1001660009341-B-D02


title: EL.MF3.m.005.Epithelium

description: Library name: DSP-1001660009341-B-D01


title: LCMV-pancreas-BMS-3Day-mouse2rep4


title: Testis_LH_m67


title: Testis_LH_m66


title: EL.MF3.m.004.Epithelium

description: Library name: DSP-1001660009341-B-C12


title: Testis_LH_m64


title: WT CFA TMJ, scRNAseq

city: Los Angeles

first: Ziying

last: Lin

state: CA

address: 2250 Alcazar St. CSA Clinical Sciences Annex

institute: University of Southern California

description:
Library name: Sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: TMJ

extract_protocol:
Freshly collected TMJ were dissected on ice-cold HBSS. Next, The TMJs were incubated in digestion buffer (α-MEM with 3 mg/ml collagenase type I and 4 mg/ml Dispase II) at 37 ℃ for 30 min. Single cell suspension was filtered through 70um filter.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: TMJ

value: 8-10 weeks old

value: WT

value: CFA


title: LCMV-pancreas-BMS-3Day-mouse2rep3

value: RIP-LCMV-GP

value: 8-week old


title: EL.MF3.m.003.Epithelium

description: Library name: DSP-1001660009341-B-C11

value: SBT-MP


title: Testis_LH_m63

value: Male


title: LCMV-pancreas-BMS-3Day-mouse2rep2

value: pancreas


title: Pnma4 KO replicate 2

city: New York

first: Luke

last: Berchowitz

state: NY

department: Genetics & Development

institute: Columbia University

description: Library name: P4_KO_2

data_processing:
The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS).
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.
Sequence reads were trimmed and mapped to the Mus musculus GRCm38 genome using the STAR aligner v2.5.2b to generate .bam files. Unique hit counts were calculated using featureCounts from the Subread package v.1.5.254. Features with fewer than 10 total reads across all samples were filtered out. Enrichment analysis was done using the DEseq2 package comparing wild type to controls lacking Pnma4 with p-value cutoff of 10e-4 and fold change cutoff of > 2.
Assembly: GRCm38
Supplementary files format and content: featureCounts from the Subread package v.1.5.254 was used. Csv file includes raw counts for each feature

source_name: Testis

extract_protocol:
Lysate preparation: 8 snap-frozen testes from wild type (C57BL/6J) mice were ground by mortar and pestle into a fine powder under liquid nitrogen. 1 ml lysis buffer (150 mM NaCl, 50 mM Tris [pH 7.5], 0.25% NP-40, 1 mM PMSF, 1x Halt Protease Inhibitor Cocktail (Pierce)) was added. The lysate was clarified by centrifugation at 20,000 g for 20 minutes, collected to a new tube, and re-clarified by centrifugation at 20,000 g for 20 minutes and diluted to 8 ml in lysis buffer. Double sucrose gradient: 8 ml testis lysate was layered on top of a double sucrose cushion of 2 ml 25% (upper) and 2 ml 70% (lower) in an SW41 tube (Seton). The tubes were spun for 3 hr at 38,000 rpm 4˚ C in an SW41Ti rotor. After centrifugation, the following fractions were taken: lipids, lysate (from middle of 8 ml), meniscus of 25% sucrose, 25% sucrose, meniscus of 70% sucrose, 70% sucrose, and pellet. A sample of each fraction was taken for analysis by SDS-PAGE/immunoblot. Iodixanol step gradient: An iodixanol (Optiprep density gradient medium, supplied at 60% iodixanol) step gradient was prepared in an SW41 tube with the following steps: (top) 2 ml 15% (in 1 M NaCl), 3 ml 30%, 3 ml 40%, 3 ml 50% (bottom). The 70% meniscus fraction (~500 µL) was layered on top and the tube was spun at 41,000 rpm for 48 hours at 4˚ C in an SW41Ti rotor. Twelve 1 ml fractions were taken using a pipette. ~40 µL samples (20 µL 3x SDS loading buffer was added) from each fraction were taken for analysis by SDS-PAGE/immunoblot (30 µL load).  PNMA4 particle Immunoprecipitation 1 µg of PNMA4 antibody (Proteintech, 15325-1-AP) was added to PNMA4-containing iodixanol step gradient fractions from three wild type preparations and 3 control preparations (two Pnma4-/- and one Pnma1-/- Pnma4-/-). IPs were incubated with rotation at 4˚C overnight. Next, 50 µL of resuspended Protein A magnetic beads (Thermo Fisher, REF-88845) were added to each sample and incubated with rotation at 4˚C for four hours. After this incubation, the unbound sample was removed and saved. Beads were isolated using a DynaMag Spin magnet. Beads were washed three times with 500 µL of NP-40 buffer. After washing, beads were resuspended in 1 ml of lysis buffer (150 mM NaCl, 50 mM Tris [pH 7.5], 0.25% NP-40), snap frozen and stored at -80˚C. RNA was extracted from the beads using TES-acid phenol.
RNA library preparation, sequencing and data analysis were conducted at Azenta Life Sciences (South Plainfield, NJ, USA) as follows:  Total RNA samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared with no enrichment or fragmentation using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). cDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Pnma4 KO


title: LCMV-pancreas-BMS-3Day-mouse2rep1


title: Testis_FSH_m69

value: Testis

value: rssFSH


title: EL.MF1.m.010.Epithelium

description: Library name: DSP-1001660009341-B-C04


title: EL.MF3.m.002.Epithelium

description: Library name: DSP-1001660009341-B-C10


title: Testis_FSH_m68


title: LCMV-lymphnode-BMS-3Day-mouse1rep2

value: lymph node


title: LCMV-lymphnode-BMS-3Day-mouse1rep3


title: Wild type replicate 2

description: Library name: WT_2

value: wild type


title: Wild type replicate 3

description: Library name: WT_3


title: Testis_FSH_m64


title: Prox1 CFA TMJ, scRNAseq

description:
Library name: Sample2
10x Genomics

value: Prox1 mutant


title: EL.MF1.m.007.Epithelium

description: Library name: DSP-1001660009341-B-B12

value: Ovarian Cancer, Tumor

value: Epithelium


title: EL.MF1.m.008.Epithelium

description: Library name: DSP-1001660009341-B-C01


title: Pnma4 KO replicate 1

description: Library name: P4_KO_1


title: Wild type replicate 1

description: Library name: WT_1


title: LCMV-lymphnode-BMS-3Day-mouse1rep1


title: LCMV-pancreas-BMS-3Day-mouse1rep3


title: DKO replicate 1 (analyzed as replicate 3 of 'samples lacking PNMA4')

description: Library name: DKO

value: Pnma1, Pnma4 DKO


title: Testis_FSH_m61


title: EL.MF1.m.004.Epithelium

description: Library name: DSP-1001660009341-B-B09


title: EL.MF1.m.003.Epithelium

description: Library name: DSP-1001660009341-B-B08


title: LCMV-pancreas-BMS-3Day-mouse1rep1


title: Stk11f/f -1

city: 黄浦区

first: Lin

last: Hu

state: 上海市

address: 重庆南路280号

institute: 基础医学院

description: Library name: Sample 3

data_processing:
CLC genomics workbench v 11.0.1
Assembly: mm9
Supplementary files format and content: excel files include FPKM values for each sample

source_name: intestine

extract_protocol:
Sorting of ILC3 in the submucosal layer of the large intestine,then total RNA extracted by Trizol for sequencing libraries
RNA libraries for RNA-seq were prepared using Smart mRNA-seq library prep kit following manufacturer's protocols

value: intestine


title: LCMV-pancreas-BMS-3Day-mouse1rep2


title: Replicate 3, triple-KO + CREM WT

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

description: Library name: Sample 18

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 106). Transcript per million (TPM) and expected counts were generated by RSEM. Unless otherwise specified, the computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 106
Supplementary files format and content: CREB_family_rescue.txt

source_name: Kidney

growth_protocol: Cells were maintained in DMEM/F-12 media with 2% Fetal Bovine Serum and supplemented with 5 μg/mL insulin, 50 nM dexamethasone, 1 nM triiodothyronine, 10 ng/mL epidermal growth factor, 60 nM sodium selenite, 5 μg/mL transferrin; all from Sigma). In order to polarize cells, they were grown in permeable membrane supports (Transwell) and grown with complete media for 4 days, prior to changing to simple media (DMEM/F-12 media only supplemented with 50 nM dexamethasone, 60 nM sodium selenite and 5 μg/mL transferrin) for 3 days, with 0.1 nM dDAVP (1-desamino-8-D-arginine-vasopressin).

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMARTer V4 Ultra Low RNA Kit (Takara Bio). cDNA was generated with 8 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

treatment_protocol: dDAVP 0.1nM added for 72 hours

value: Kidney

value: mpkCCD

value: Immortalized mouse collecting duct

value: ATF1/CREB1/CREM-KO +CREM WT

value: dDAVP 0.1nM 72 hrs


title: EL.CS8.m.011.Epithelium

description: Library name: DSP-1001660009341-B-B04

value: SBT


title: Replicate 2, triple-KO + CREM WT

description: Library name: Sample 17


title: EL.CS8.m.009.Stroma

description: Library name: DSP-1001660009341-B-B01

source_name: Stroma

value: Stroma


title: RorccreStk11f/f -2

description: Library name: Sample 2


title: Replicate 1, triple-KO + CREM WT

description: Library name: Sample 16


title: RorccreStk11f/f -1

description: Library name: Sample 1


title: LCMV-spleen-vehicle-7Day-mouse6rep3

source_name: spleen

value: spleen

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: RIP-LCMV-GP

value: 8-week old

value: Male


title: Replicate 9, triple-KO control

description: Library name: Sample 15


title: EL.CS8.m.009.Epithelium

description: Library name: DSP-1001660009341-B-A12


title: LCMV-spleen-vehicle-7Day-mouse6rep4


title: EL.CS8.m.008.Stroma

description: Library name: DSP-1001660009341-B-A11


title: Testis_FSH_m62

value: Testis

value: rssFSH


title: LCMV-spleen-vehicle-7Day-mouse6rep2


title: LCMV-spleen-vehicle-7Day-mouse6rep1


title: Stk11f/f -2

description: Library name: Sample 4


title: Replicate 8, triple-KO control

description: Library name: Sample 14


title: patient83

city: San Francisco

first: Isabelle

last: Liu

state: California

department: Department of Biochemistry and Biophysics

institute: UCSF

description: Library name: Sample83

data_processing:
Bam files were input into Pacbio's Iso-Seq analysis pipeline. First, patient samples were demultiplexed by PCR and SMRTbell barcodes using the lima package.
The isoseq-refine tool was used for further read refinement, including polyA tail trimming and concatemer removal, resulting in Full-Length Non-Chimeric (FLNC) reads that capture complete transcript structures with minimal errors. Then the ‘cluster’ command was called to cluster reads that represent the same transcript.
Following the generation of FLNC reads, the data was aligned to the reference genome using minimap2.
Transcript isoform quantification was performed using the bambu package in the quantification mode.
Assembly: hg38, gencode v47
Supplementary files format and content: a csv file of transcript TPM values generated by bambu for all samples

source_name: meningioma

extract_protocol:
Meningiomas were removed, flash frozen in liquid nitrogen, mechanically lysed using a TissueLyser II, and RNA was extracted from the lysed tissue using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (CAT# 80224).
Long-read RNA-seq libraries were constructed using the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, PacBio Iso-Seq Express Oligo Kit and SMRTbell express template prep kit 3.0 according to the manufacturer’s protocol.

value: meningioma


title: EL.CS8.m.008.Epithelium

description: Library name: DSP-1001660009341-B-A10

value: Ovarian Cancer, Tumor

value: Epithelium


title: Replicate 7, triple-KO control

description: Library name: Sample 13

value: Kidney


title: EL.CS8.m.005.Stroma

description: Library name: DSP-1001660009341-B-A09


title: patient84

description: Library name: Sample84


title: LCMV-lymphnode-vehicle-7Day-mouse6rep3

source_name: lymph node

value: lymph node


title: patient81

description: Library name: Sample81


title: patient82

description: Library name: Sample82


title: EL.CS8.m.005.Epithelium

description: Library name: DSP-1001660009341-B-A08


title: patient80

description: Library name: Sample80


title: Replicate 2, triple-KO + CREB1 WT

description: Library name: Sample 11

value: mpkCCD

value: Immortalized mouse collecting duct

value: ATF1/CREB1/CREM-KO +CREB1 WT


title: EL.CS8.m.004.Stroma

description: Library name: DSP-1001660009341-B-A07

value: SBT


title: Replicate 1, triple-KO + CREB1 WT

description: Library name: Sample 10

value: dDAVP 0.1nM 72 hrs


title: patient79

description: Library name: Sample79


title: LCMV-lymphnode-vehicle-7Day-mouse6rep1


title: patient78

description: Library name: Sample78


title: EL.CS8.m.003.Stroma

description: Library name: DSP-1001660009341-B-A05

value: Stroma


title: Replicate 5, triple-KO control

description: Library name: Sample 8


title: LCMV-lymphnode-vehicle-7Day-mouse6rep4

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: LCMV-pancreas-vehicle-7Day-mouse6rep3

value: pancreas

value: RIP-LCMV-GP


title: LCMV-pancreas-vehicle-7Day-mouse6rep2

value: 8-week old

value: Male


title: Replicate 3, triple-KO + CREB1 WT

description: Library name: Sample 12


title: patient76

description: Library name: Sample76


title: EL.CS8.m.002.Stroma

description: Library name: DSP-1001660009341-B-A03


title: LCMV-pancreas-vehicle-7Day-mouse6rep1


title: Replicate 2, triple-KO + ATF1 WT

description: Library name: Sample 5

value: ATF1/CREB1/CREM-KO + ATF1 WT


title: patient74

description: Library name: Sample74

value: meningioma


title: EL.CS5.m.014.Stroma

description: Library name: DSP-1001660009340-A-H01

value: Ovarian Cancer, Tumor


title: LCMV-lymphnode-vehicle-7Day-mouse6rep2


title: EL.CS5.m.014.Epithelium

description: Library name: DSP-1001660009340-A-G12

value: Epithelium


title: Replicate 1, triple-KO + ATF1 WT

description: Library name: Sample 4

value: Kidney


title: LCMV-spleen-vehicle-7Day-mouse5rep4

value: spleen


title: LCMV-spleen-vehicle-7Day-mouse5rep3


title: EL.CS5.m.013.Stroma

description: Library name: DSP-1001660009340-A-G11


title: patient73

description: Library name: Sample73


title: Replicate 3, triple-KO control

description: Library name: Sample 3

value: mpkCCD


title: EL.CS8.m.004.Epithelium

description: Library name: DSP-1001660009341-B-A06


title: LCMV-pancreas-vehicle-7Day-mouse6rep4


title: Replicate 6, triple-KO control

description: Library name: Sample 9

value: Immortalized mouse collecting duct


title: EL.CS8.m.003.Epithelium

description: Library name: DSP-1001660009341-B-A04


title: LCMV-spleen-vehicle-7Day-mouse5rep2


title: patient77

description: Library name: Sample77


title: patient72

description: Library name: Sample72


title: Replicate 4, triple-KO control

description: Library name: Sample 7


title: EL.CS5.m.013.Epithelium

description: Library name: DSP-1001660009340-A-G10


title: Replicate 3, triple-KO + ATF1 WT

description: Library name: Sample 6


title: patient75

description: Library name: Sample75


title: Replicate 2, triple-KO control

description: Library name: Sample 2


title: patient71

description: Library name: Sample71


title: EL.CS5.m.012.Stroma

description: Library name: DSP-1001660009340-A-G09


title: LCMV-spleen-vehicle-7Day-mouse5rep1


title: LCMV-lymphnode-vehicle-7Day-mouse5rep7

value: lymph node


title: patient70

description: Library name: Sample70


title: Replicate 1, triple-KO control

description: Library name: Sample 1


title: EL.CS5.m.011.Stroma

description: Library name: DSP-1001660009340-A-G07

value: SBT


title: patient68

description: Library name: Sample68


title: EL.CS5.m.012.Epithelium

description: Library name: DSP-1001660009340-A-G08


title: patient69

description: Library name: Sample69


title: Multiome, MLN, Vehicle, GEX

city: Solna

first: Oscar

last: Diaz Perez

address: Nobels väg 13

country: Sweden

institute: Karolinska Institutet

description: Library name: MLN_Vehicle_RNA

data_processing:
Quantification using Cell Ranger ARC 2.0.1 and the 10x refdata-cellranger-arc-mm10-2020-A-2.0.0 reference
Analysis using Seurat 5.0.1 and Signac 1.14.0 in R 4.4.1
Assembly: mm10
Supplementary files format and content: Cell Ranger ARC filtered h5
Supplementary files format and content: Cell Ranger ARC ATAC fragments TSV
Supplementary files format and content: Cell Ranger ARC summary statistics CSV
Supplementary files format and content: 10x Loupe Browser file
Supplementary files format and content: TSV file of metadata from Seurat object after filtering

molecule: nuclear RNA

source_name: Colon-draining mensenteric lymph nodes

extract_protocol:
CD45+ immune cells and dendritic cells were isolated from the colon lamina propria and from the colon-draining mesenteric lymph nodes of C. rodentium infected mice. Single nuclei suspensions were prepared isolated according to the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (CG00053 – Rev C, 10x Genomics), using the Low Cell Input Nuclei isolation protocol.
Isolated single nuclei were transposed, then loaded on Chromium Chip and partitioned in nanolitre scale droplets using the Chromium Controller and Chromium Next GEM Single Cell Reagents (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide, User Guide, CG000338)

value: Colon-draining mensenteric lymph nodes

value: CD45+ cells and dendritic cells

value: WT

value: Infected with C. rodentium


title: LCMV-lymphnode-vehicle-7Day-mouse5rep5

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: RIP-LCMV-GP


title: EL.CS5.m.011.Epithelium

city: Chicago

description: Library name: DSP-1001660009340-A-G06


title: Multiome, MLN, Vehicle, ATAC, Illumina NovaSeq X

description: Library name: MLN_Vehicle_ATAC_NSX

library_source: genomic single cell


title: Multiome, MLN, TCDD, GEX

description: Library name: MLN_TCDD_RNA

value: AhrCAIR/CAIR


title: EL.CS5.m.010.Stroma

description: Library name: DSP-1001660009340-A-G05

value: Stroma


title: LCMV-lymphnode-vehicle-7Day-mouse5rep4

city: Indianapolis

value: 8-week old

value: Male


title: Multiome, MLN, TCDD, ATAC, Illumina NovaSeq X

description: Library name: MLN_TCDD_ATAC_NSX


title: patient66

description: Library name: Sample66

value: meningioma


title: patient67

description: Library name: Sample67


title: LCMV-lymphnode-vehicle-7Day-mouse5rep3


title: EL.CS5.m.010.Epithelium

description: Library name: DSP-1001660009340-A-G04

value: Ovarian Cancer, Tumor

value: Epithelium


title: Multiome, MLN, CAIR, GEX

description: Library name: MLN_CAIR_RNA


title: LCMV-lymphnode-vehicle-7Day-mouse5rep2


title: patient65

description: Library name: Sample65


title: Multiome, MLN, CAIR, ATAC, Illumina NovaSeq X

description: Library name: MLN_CAIR_ATAC_NSX


title: patient64

description: Library name: Sample64


title: EL.CS5.m.009.Epithelium

description: Library name: DSP-1001660009340-A-G02


title: LCMV-lymphnode-vehicle-7Day-mouse5rep6


title: patient63

description: Library name: Sample63


title: LCMV-pancreas-vehicle-7Day-mouse5rep5

value: pancreas


title: Multiome, MLN, AHR KO, GEX

description: Library name: MLN_AHR_KO_RNA

value: AHR KO/KO


title: EL.CS5.m.008.Stroma

description: Library name: DSP-1001660009340-A-G01


title: Multiome, MLN, AHR KO, ATAC, Illumina NovaSeq X

description: Library name: MLN_AHR_KO_ATAC_NSX


title: EL.CS5.m.008.Epithelium

description: Library name: DSP-1001660009340-A-F12


title: Multiome, Colon, Vehicle, GEX

description: Library name: Colon_Vehicle_RNA

source_name: Colon lamina propria

value: Colon lamina propria


title: patient62

description: Library name: Sample62


title: patient61

description: Library name: Sample61


title: EL.CS5.m.007.Stroma

description: Library name: DSP-1001660009340-A-F11

value: SBT


title: Multiome, Colon, Vehicle, ATAC, Illumina NovaSeq X

description: Library name: Colon_Vehicle_ATAC_NSX


title: EL.CS5.m.007.Epithelium

description: Library name: DSP-1001660009340-A-F10


title: LCMV-pancreas-vehicle-7Day-mouse5rep2


title: Multiome, Colon, TCDD, GEX

description: Library name: Colon_TCDD_RNA


title: patient59

description: Library name: Sample59


title: EL.CS5.m.009.Stroma

description: Library name: DSP-1001660009340-A-G03


title: EL.CS5.m.006.Stroma

description: Library name: DSP-1001660009340-A-F09


title: LCMV-pancreas-vehicle-7Day-mouse5rep1


title: Multiome, Colon, TCDD, ATAC, Illumina NovaSeq X

description: Library name: Colon_TCDD_ATAC_NSX


title: patient58

description: Library name: Sample58


title: LCMV-lymphnode-vehicle-7Day-mouse4rep4

value: lymph node


title: LCMV-lymphnode-vehicle-7Day-mouse5rep1


title: Multiome, Colon, CAIR, GEX

description: Library name: Colon_CAIR_RNA

value: CD45+ cells and dendritic cells


title: patient57

description: Library name: Sample57


title: LCMV-lymphnode-vehicle-7Day-mouse4rep3


title: EL.CS5.m.005.Stroma

description: Library name: DSP-1001660009340-A-F07


title: Multiome, Colon, CAIR, ATAC

description: Library name: Colon_CAIR_ATAC


title: patient56

description: Library name: Sample56


title: EL.CS5.m.005.Epithelium

description: Library name: DSP-1001660009340-A-F06


title: LCMV-pancreas-vehicle-7Day-mouse5rep4


title: LCMV-lymphnode-vehicle-7Day-mouse4rep2


title: Multiome, Colon, AHR KO, GEX

description: Library name: Colon_AHR_KO_RNA


title: LCMV-pancreas-vehicle-7Day-mouse5rep3


title: EL.CS5.m.004.Stroma

description: Library name: DSP-1001660009340-A-F05


title: patient60

description: Library name: Sample60


title: patient55

description: Library name: Sample55


title: LCMV-lymphnode-vehicle-7Day-mouse4rep1


title: LCMV-spleen-vehicle-7Day-mouse4rep4

value: spleen


title: Multiome, Colon, AHR KO, ATAC, Illumina NovaSeq X

description: Library name: Colon_AHR_KO_ATAC_NSX

value: Infected with C. rodentium


title: Langerhans cells extracted from mice ear skin treated with multiple microneedle punches

city: East Lansing

first: Artem

last: Kiselev

state: Michigan

address: 775 Woodlot Dr

department: The Institute for Quantitative Health Science & Engineering

institute: Michigan State University

description:
Library name: LC_Stamp
10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1

data_processing:
Raw scRNA-seq data were processed using Cell Ranger (v8.0, 10x Genomics) with default parameters and aligned to the GRCm39 reference genome, custom-modified to include additional coding sequences (CDS) for mCherry (AY678264.1) and eGFP (OQ870305.1).
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Epidermis

extract_protocol:
Mice were treated as described above, while control mice received only Nair treatment at the same time as experimental animals. The procedure was performed 48 hours after the initial treatment in both the croton oil and microneedle punch. Mice were then euthanized following standard protocols after anesthesia with isoflurane. Subsequently, ears were excised, and the skin layer was carefully separated from the underlying cartilage. The isolated skin was placed epidermis-side up in a trypsin solution (0.3% trypsin (Thermofisher; 15090046) in 150 mM NaCl, 0.5 mM KCl and 0.5 mM glucose) and incubated for 1 hour and 45 minutes at 37 °C. Following incubation, the epidermis was gently separated from the dermis using fine forceps. The epidermal sheet was transferred to a scratched-wall plastic Petri dish (Fisher; FB0875711YZ) containing HBSS buffer supplemented with 10% FBS, trypsin inhibitor (Sigma; T6522) and DNaseI (Sigma; D4513), pre-warmed to 37 °C. The epidermis was then mechanically dissociated by pressing it against the scratched surface using forceps, producing cloudy cell suspension. This suspension was incubated for 15 minutes at 37 °C, then filtered through a 70 µm cell strainer. Dead cells were removed via magnetic separation (Miltenyibiotec; 130-090-101), followed by magnetic enrichment of LCs (Miltenyibiotec; 130-095-408). Cell viability was assessed using either trypan blue staining or flow cytometry.
For single-cell RNA sequencing, libraries were prepared according to the manufacturer’s manual using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, USA). And sequenced using 2 lanes (2.5GB) NovaSeq X 10B 100 SR (Illumina, USA).

value: Epidermis

value: Langerhans cells

value: male

value: multiple microneedle punches


title: patient53

description: Library name: Sample53


title: EL.CS5.m.003.Stroma

first: CRI

last: Bioinformatics

institute: University of Chicago

description: Library name: DSP-1001660009340-A-F03

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

extract_protocol:
FFPE tissue sections (5 μm) sliced consecutively to Deep Viusal Proteomics samples were processed following the Nanostring GeoMx user manual (MAN-10132-04). In brief, tissue slides were deparaffinized and rehydrated, followed by protein target retrieval using antigen retrieval buffer (Tris-EDTA) for 20 min in a pressure cooker. RNA target retrieval was accomplished by a digest with proteinase K for 15 min at 37°C. Tissue was post-fixed in 10% NBF, followed by an overnight hybridization at 37°C with the RNA probes (Human Whole Transcriptome Atlas, 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Excess probes were removed the next day by washing the samples twice in stringent washes at 37°C, followed by an incubation period in blocking buffer W (Nanostring LOT#:2-23020032). Thereafter, tissue was stained using conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488, 1:100) and vimentin (mouse monoclonal IgG1κ, Santa Cruz sc-373717, 1:100) as well as the SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomics data acquisition, slides were placed on the GeoMx Digital Spatial Profiler (DSP) and scanned in 20x magnification. Based on immunofluorescence images, regions of interest (ROI) were collected under supervision of an experienced pathologist (AB) and matched to the regions selected in DVP. Upon ROI selection, oligonucleotide barcodes were collected into a 96-well plate by UV-ablation while precisely separating compartments in each region.
Sequencing libraries were prepared using the Illumina TruSeq technology for the ligation of sequencing adaptors and amplification. Amplified libraries were purified using two rounds of Ampure XP magnetic bead cleanup (ratio 1.2:1 (beads: library)) (HighPrep PCR from MAGBIO (Cat#: AC-60500). Purified libraries were sequenced in an Illumina NovaSeq flowcell PE50 at a depth of 100x /μm2.

value: Stroma


title: EL.CS5.m.006.Epithelium

description: Library name: DSP-1001660009340-A-F08


title: EL.CS5.m.004.Epithelium

description: Library name: DSP-1001660009340-A-F04


title: EL.CS5.m.003.Epithelium

description: Library name: DSP-1001660009340-A-F02


title: patient52

description: Library name: Sample52


title: LCMV-spleen-vehicle-7Day-mouse4rep3

first: Carmella

last: Evans-Molina

institute: Indiana University School of Medicine

data_processing:
Fastq files were processed to dcc files using GeoMx NGS pipeline software. Using the dcc files, spatial transcriptomics analysis was conducted in R studio v4.2.1 using the GeomxTools 3.4.0 package
The GeoMx whole mouse transcriptome atlas was used as the probe assay metadata
Sequencing quality was assessed using the default quality control (QC) parameter cut-offs, namely: minimum number of reads (1000); minimum percentage of reads trimmed (80%), stitched (80%), and aligned (80%); sequencing saturation (50%); negative control counts (10); maximum counts observed in no treatment control (NTC) well (1000); minimum number of nuclei estimated (100); and minimum segment area (5000). Any ROI that did not satisfy the above criteria was removed as part of QC filtering.
Following segment QC, probe QC was also performed to remove any outlier either globally or locally before generating gene-level count data.
The limit of quantification was determined per segment using the value recommended in the workflow, and segments with less than 1-5% of genes detected were removed. Furthermore, only genes that were detected in at least 1% of segments were retained.
The data was normalized using the quartile 3 method and log transformed.
For each organ, a linear mixed model without random slope was used to identify differentially expressed genes between vehicle and treatment groups for both the 3- and 7-day timepoints. Genes with linear scale fold change ³ 1.5 and p-value < 0.05 were considered as differentially expressed.
Assembly: GeoMx mouse whole transcriptome assay v1
Supplementary files format and content: .dcc files = Digital count conversion file (dcc file)
Supplementary files format and content: Rawcounts_LCMV.txt = raw counts for LCMV mouse dataset
Supplementary files format and content: q3 normalized counts_LCMV.txt = q3 normalized and log transformed values for LCMV mouse dataset
Supplementary files format and content: Rawcounts_NOD.txt = raw counts for NOD mouse dataset
Supplementary files format and content: q3 normalized counts_NOD.txt = q3 normalized and log transformed values for NOD mouse dataset
Library strategy: Spatial transcriptomics

extract_protocol:
Mouse pancreas sections (5 µm) were fixed, sectioned, and mounted on positively charged slides. The slideswere deparaffinized, heated in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 min, and treated with 1 µg/mL proteinase K at 37 °C for 15 min. Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (NanoString Technologies, GMX-RNA-NGS-MsWTA). An overnightin situhybridization was performed with a mouse WTA probe, and the next day, the slides were washed twice at 37 °C for 25 min with 50% formamide/2X SSC buffer to remove unbound probes. The slides were then washed twice with 2X SSC buffer for 2 minutes at RT and blocked with blocking buffer containing Buffer W (Nanostring) with 1% Fc-Receptor blocker (Milteny) and 5% Normal Donkey Serum (Jackson Laboratories) as described previously (98). The slides were incubated with guinea pig anti-insulin (Dako), 1:200 rabbit anti-CD3 (Abcam), mouse anti-CD68 (Santa Cruz).The slides were washed twice with 2xSSC and incubated with secondary antibodies (1:400 goat-anti-guinea pig Alexa-488; 1:200 goat-anti rabbit Alexa-594 and 1:200 goat-anti mouse Alexa-647) for 30 minutes. Then, the slides were washed four times with 2xSSC for 3 minutes and counter-stainedwith 1:20,000 Syto83 (Invitrogen) for 1 h at room temperature. Stained slides were loaded onto the GeoMx instrument and scanned. After visual inspection using the GeoMx Digital Spatial Profiler (DSP; NanoString Technologies), geometrical ROIs (100 μm diameter) with different histologies were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq500 sequencer (Illumina).
The GeoMx libraries were prepared according to the GeoMx DSP NGS Readout User Manual. Briefly, for each plate, 4 μl of a GeoMx DSP sample was used for amplification. Each GeoMx DSP sample in a well was uniquely indexed with dual indexes. 4 μL of each resulting PCR product, including the NTC negative control, were pooled and purified with AMPure XP beads (Beckman Coulter). The final libraries were qualified and quantified using TapeStation and Qubit, respectively. The libraries were sequenced on an Illumina NextSeq 500 to generate 27 bp paired-end sequence reads.

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)

value: RIP-LCMV-GP

value: 8-week old

value: Male


title: Langerhans cells extracted from untreated mice ear skin

description:
Library name: LC_Ctrl
10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1

value: untreated


title: Langerhans cells extracted from mice ear skin treated with actone/croton oil/ olive oil

description:
Library name: LC_Oil
10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1

value: actone/croton oil/ olive oil


title: patient51

description: Library name: Sample51

value: meningioma


title: LCMV-spleen-vehicle-7Day-mouse4rep2


title: EL.CS5.m.002.Stroma

description: Library name: DSP-1001660009340-A-F01

value: Ovarian Cancer, Tumor

value: SBT


title: patient50

description: Library name: Sample50


title: LCMV-spleen-vehicle-7Day-mouse4rep1


title: patient54

description: Library name: Sample54


title: Mut_Yolk sac replicate1

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: Mut_Ys1
scRNA_seq on Sp8 GOF_Yolksac_replicate1

data_processing:
The Cell Ranger Single Cell software suite (10x Genomics) was used to demultiplex samples, align reads, and generate feature-barcode matrices. The reference genome used was the Genome Reference Consortium Mouse Build 38 (GRCm38, Gencode annotation mm10). Raw reads were processed using the Cell Ranger count program using default parameters.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5 including barcodes, feature and matrix files for replicates.

source_name: yolk sac

growth_protocol: mouse embryos dissected at E8.5,

extract_protocol:
Yolk sac from E8.5 mouse embryos were dissected, disassocited into single cells, sorted for live cells before pool loading to 10x Chips. Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction.
10x library (3' scRNA-seq)

value: yolk sac

value: not appliable

value: Doxycycline, E5.5-8.7


title: patient49

description: Library name: Sample49


title: EL.CS5.m.001.Stroma

description: Library name: DSP-1001660009340-A-E11


title: Mut_Yolk sac replicate2

description:
Library name: Mut_Ys2
scRNA_seq on Sp8 GOF_Yolksac_replicate2

value: Doxycycline, E5.5-8.8


title: EL.CS5.m.002.Epithelium

description: Library name: DSP-1001660009340-A-E12

value: Epithelium


title: EL.CS5.m.001.Epithelium

description: Library name: DSP-1001660009340-A-E10


title: LCMV-pancreas-vehicle-7Day-mouse4rep7

value: pancreas


title: LCMV-pancreas-vehicle-7Day-mouse4rep6


title: LCMV-pancreas-vehicle-7Day-mouse4rep5


title: WT_Yolk sac replicate2

description:
Library name: WT_Ys2
scRNA_seq on WT_Yolksac_replicate2

value: Doxycycline, E5.5-8.6


title: WT_Yolk sac replicate1

description:
Library name: WT_Ys1
scRNA_seq on WT_Yolksac_replicate1

value: Doxycycline, E5.5-8.5


title: patient48

description: Library name: Sample48


title: patient47

description: Library name: Sample47


title: LCMV-pancreas-vehicle-7Day-mouse4rep4

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: EL.CS3.m.004.Stroma

description: Library name: DSP-1001660009340-A-E09

value: Stroma


title: EL.CS3.m.004.Epithelium

description: Library name: DSP-1001660009340-A-E08


title: LCMV-pancreas-vehicle-7Day-mouse4rep3

value: RIP-LCMV-GP

value: 8-week old


title: patient46

description: Library name: Sample46


title: patient45

description: Library name: Sample45


title: Succ3

city: Quanzhou

first: wei

last: zhang

address: NO. 1028 Anji South Road, Fengze District

institute: quanzhou first hospital affiliated to fujian medical university

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Hisat2 v2.0.5
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Spleen CD4+ T cells

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher). 1.5 μg RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Spleen CD4+ T cells

value: WT

value: Dimethyl succinate


title: Succ4


title: LCMV-pancreas-vehicle-7Day-mouse4rep2

value: Male


title: EL.CS3.m.003.Stroma

address: 5801 S. Ellis Ave.

description: Library name: DSP-1001660009340-A-E07

value: Ovarian Cancer, Tumor

value: SBT


title: Succ2


title: LCMV-pancreas-vehicle-7Day-mouse4rep1

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100


title: patient44

description: Library name: Sample44

value: meningioma


title: EL.CS3.m.003.Epithelium

description: Library name: DSP-1001660009340-A-E06


title: Succ1


title: patient43

description: Library name: Sample43


title: EL.CS3.m.002.Stroma

description: Library name: DSP-1001660009340-A-E05


title: left ventricular wall, sham, 12 weeks, sample 6

city: Cincinnati

first: Jose

last: Gomez-Arroyo

state: Ohio

address: 3333 Burnet Ave

department: Pulmonary and Critical Care Medicine

institute: University of Cincinnati

description: Library name: 6_S4

data_processing:
Reads were pseudo-aligned and quantified using an index transcriptome version of the CanFam3.1 dog genome assembly (GCA_000002285.2) using Kallisto with standard settings
Transcript-level abundance estimates were imported and summarized as a counts matrix using tximport
Assembly: GCA_000002285.2
Supplementary files format and content: tab delimited, tsv file

organism: Canis lupus familiaris

source_name: heart

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen, MD, USA) to generate fourteen ribo-depleted, paired-end, 75 base-pair stranded RNA libraries
Enzymatic rRNA depletion, ligation-based addition of adapters and indexes were generated using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

treatment_protocol: After a 2-week surgical recovery, animals were randomized into 2 groups: 1) PVC-CM group, receiving bigeminal PVCs (50% burden) with a 200-220 ms coupling interval for 12 weeks, and 2) sham group where PVCs were not enabled.

value: heart

value: wild-type

value: sham


title: EL.CS3.m.002.Epithelium

description: Library name: DSP-1001660009340-A-E04

value: Epithelium


title: Con4

value: Vehicle


title: Con3


title: left ventricular wall, sham, 12 weeks, sample 5

description: Library name: 5_S6


title: EL.CS3.m.001.Stroma

description: Library name: DSP-1001660009340-A-E03


title: patient42

description: Library name: Sample42


title: left ventricular wall, pvc, 12 weeks, sample 4

description: Library name: 4_S3

value: pvc


title: EL.CS3.m.001.Epithelium

description: Library name: DSP-1001660009340-A-E02


title: patient41

description: Library name: Sample41


title: patient39

description: Library name: Sample39


title: Con2


title: left ventricular wall, pvc, 12 weeks, sample 36

description: Library name: 36_S7


title: EL.CS2.m.012.Stroma

description: Library name: DSP-1001660009340-A-E01


title: EL.CS2.m.012.Epithelium

description: Library name: DSP-1001660009340-A-D12


title: left ventricular wall, sham, 12 weeks, sample 33

description: Library name: 33_S2


title: patient38

description: Library name: Sample38


title: Lung_Pos_2

city: Covington

first: Alexandra

last: Melton

address: 18703 Three Rivers Road

institute: Tulane National Primate Research Center

description: 10x Genomics

data_processing:
10x Genomics Cell Ranger 3.1.0 pipeline was used to process raw data and generate separate barcodes, features, and matrix files for each sample, referencing GTF annotations for the Rhesus macaque genome (Macaca mulatta, GCA_003339765.3). The Seurat package in R was used to perform data analysis. Briefly, individual Seurat objects were generated for each sample, and the raw count matrices were merged using the merge command. Cells with more than 5% mitochondrial genes or more than 2500 genes were excluded from further analysis. The standard Seurat workflow for downstream analyses comprised normalization, scaling, graph-based clustering using shared nearest-neighbor, differential gene expression (DEG), pathway enrichment analysis (PEA), and data visualization. The Harmony algorithm was applied to account for batch effects and biological variability.
Assembly: Rhesus macaque genome (Macaca mulatta, GCA_003339765.3)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Lung vasculature

extract_protocol:
Thawed PBMC, lung, and bronchial lymph node (BLN) cells were stained in 15 mL conical tubes with live/dead and surface cocktails with 2x the typical antibody concentration. Cells were washed in FACS buffer and resuspended in RPMI-1640 without phenol red supplemented with 10% FBS. Cells were sorted using fluorescence-activated sorting (FACS) to isolate CD3+ T cells from blood and BLN as well as CD3+ ivs- and CD3+ ivs+ cells from lung using the BD FACSAria (BD Bioscience) or MACSQuant Tyto (Miltenyi Biotec). Sorted CD3+ ivs- and CD3+ ivs+ cells from lung, as well as CD3+ T cells from blood and BLN, were processed for single-cell RNA sequencing (scRNAseq) following the 10x Genomics® Single Cell Protocols – Cell Preparation Guide for the “preparation of limited samples.”
10x libraries were generated using the Chromium Next GEM Single Cell 3' LT Reagent Kits v3.1 (Dual Index) kits following the manufacturer protocol.

value: Lung vasculature

value: CD3+ Lymphocytes


title: patient37

description: Library name: Sample37


title: EL.CS2.m.011.Stroma

description: Library name: DSP-1001660009340-A-D11

value: Stroma


title: left ventricular wall, sham, 12 weeks, sample 31

description: Library name: 31_S8


title: Lung_Neg_2

description: 10x Genomics

source_name: Lung tissue

value: Lung tissue


title: Bronch_LN

description: 10x Genomics

source_name: Bronchial Lymph Node

value: Bronchial Lymph Node


title: patient36

description: Library name: Sample36


title: left ventricular wall, pvc, 12 weeks , sample 30

description: Library name: 30_S1


title: EL.CS2.m.011.Epithelium

description: Library name: DSP-1001660009340-A-D10

source_name: Epithelium


title: patient35

description: Library name: Sample35


title: EL.CS2.m.010.Epithelium

description: Library name: DSP-1001660009340-A-D08


title: patient40

description: Library name: Sample40


title: patient34

description: Library name: Sample34


title: PBMC_2

description: 10x Genomics

source_name: Peripheral blood mononuclear cells

value: Peripheral blood mononuclear cells


title: EL.CS2.m.010.Stroma

description: Library name: DSP-1001660009340-A-D09


title: left ventricular wall, pvc, 12 weeks, sample 27

description: Library name: 27_S5


title: Lung_Neg_1

description: 10x Genomics


title: patient33

description: Library name: Sample33


title: Con1

value: Spleen CD4+ T cells

value: WT


title: Lung_Pos

description: 10x Genomics


title: left ventricular wall, sham, 12 weeks , sample 34

description: Library name: 34_S6


title: Lung_Neg

description: 10x Genomics


title: patient32

description: Library name: Sample32


title: left ventricular wall, pvc, 12 weeks , sample 26

description: Library name: 26_S3


title: EL.CS2.m.009.Stroma

description: Library name: DSP-1001660009340-A-D07

value: Ovarian Cancer, Tumor


title: EL.CS2.m.009.Epithelium

description: Library name: DSP-1001660009340-A-D06

value: SBT


title: patient31

description: Library name: Sample31

value: meningioma


title: PBMC

description: 10x Genomics


title: left ventricular wall, pvc, 12 weeks, sample 25

description: Library name: 25_S1

value: heart


title: left ventricular wall, pvc, 12 weeks, sample 24

description: Library name: 24_S4

value: wild-type


title: patient30

description: Library name: Sample30


title: EL.CS2.m.008.Stroma

description: Library name: DSP-1001660009340-A-D05


title: left ventricular wall, pvc, 12 weeks, sample 23

description: Library name: 23_S5


title: EL.CS2.m.008.Epithelium

description: Library name: DSP-1001660009340-A-D04


title: DBLab_ChIP_seq_WT_anti_SegB_5

city: York

first: Daniela

last: Barilla`

address: Wentworth Way

department: Biology

institute: University of York

data_processing:
Sequence reads were mapped to the S. solfataricus P2 genome (NCBI Reference Sequence: NC_002754) with Bowtie 1.0.0-5 (Langmead et al 2009 PMID: 19261174) using the following command:   bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NC_002754_bowtie --sam *.fastq > output.sam  Samtools 0.1.19-1 and Bedtools 2.17.0-1 (Li et al 2009 PMID:  19505943, Quinland et al 2010 PMID: 20110278) were used to compute and extract the sequencing coverage using the following command:  samtools faidx NC_002754.fna  samtools import NC_002754.fna.fai *.sam output.bam  samtools sort output.bam output.sorted  samtools index output.sorted.bam  bedtools genomecov -d -ibam output.sorted.bam -g NC_002754.fna > coverage_output.txt
Peak calling - Homer v4.9.1
Genome_build: NC_002754
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Saccharolobus solfataricus P2

source_name: Sulfolobus solfataricus P2

growth_protocol: S. solfataricus P2, PBL2025 and ∆Sso_segB strains were grown at 75 °C in 200 ml Brock media, pH 3.0 and supplemented with 0.1% of tryptone. When the cells reached mid-exponential growth phase (OD600nm 0.4 – 0.6), the cultures were taken from 75 °C and cooled down at room temperature before cross-linking with 1% formaldehyde, shaking at 37 °C for 30 minutes. The cross-linked reactions were stopped by adding 125 mM glycine and incubated at 37 °C, shaking for further 15 minutes.

extract_protocol:
DNA was purified from samples using PCR purification kit (Qiagen) and eluted in 40 µl 0.1 x EB buffer (Qiagen).
To construct ChIP-Seq libraries, NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs). Standard library construction for Illumina Miseq (paired end 75bp reads) or Hiseq3000 (paired end 150 bp reads) sequencing platform

treatment_protocol:
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated  with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified.
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified (Detailed protocols are listed in the Supplementary Materials)

tag: developmental stage

value: No synchronization, mixed population of cells, exponential phase

tag: antibody

value: SegB


title: patient29

description: Library name: Sample29


title: left ventricular wall, pvc, 12 weeks, sample 28

description: Library name: 28_S7


title: left ventricular wall, pvc, 12 weeks, sample 22

description: Library name: 22_S2


title: EL.CS2.m.007.Stroma

description: Library name: DSP-1001660009340-A-D03


title: patient28

description: Library name: Sample28


title: BnaC3.lfy△I2, rep3

description: Library name: Sample6

data_processing:
All clean reads were mapped to B. napus Westar v0 genome by HISAT2 v2.2.1 to obtain FeatureCounts
Assembly: Brassica napus Westar
Supplementary files format and content: The csv file includes counts for each sample.

source_name: shoot apices

growth_protocol: in the chamber

extract_protocol:
Total RNAs were extracted using steadyPure RNA Extraction Kit without Lysis Buffer (Accurate Biology, AG21024, China).
Th polyA-selected RNA-sequencing libraryies of Westar wild-type and BnaC3.lfy△I2 were constructed and sequenced by Novogene Co., Ltd. (Beijing, China) using the Illunima platform.

value: shoot apices


title: EL.CS2.m.007.Epithelium

description: Library name: DSP-1001660009340-A-D02

value: Epithelium


title: left ventricular wall, sham, 12 weeks, sample 2

description: Library name: 2_S8

value: sham


title: patient27

description: Library name: Sample27


title: BnaC3.lfy△I2, rep2

description: Library name: Sample5


title: EL.CS2.m.006.Epithelium

description: Library name: DSP-1001660009340-A-C12


title: Westar, rep3

description: Library name: Sample3


title: patient26

description: Library name: Sample26


title: patient25

description: Library name: Sample25


title: EL.CS2.m.005.Stroma

description: Library name: DSP-1001660009340-A-C11

source_name: Stroma


title: BnaC3.lfy△I2, rep1

description: Library name: Sample4


title: DBLab_ChIP_seq_WT_anti_SegB_6


title: EL.CS2.m.005.Epithelium

description: Library name: DSP-1001660009340-A-C10


title: patient24

description: Library name: Sample24


title: patient23

description: Library name: Sample23


title: EL.CS2.m.004.Stroma

description: Library name: DSP-1001660009340-A-C09