title: Vexas patients, monocytes, rep3

description:
S06
count_matrix_monocytes.txt

data_processing:
After quality checking with FastQC, a preprocessing step including trimming and adapter removal was performed using TrimGalore (v0.5.0). The trimmed reads were mapped to the GRCh38 reference genome assembly using STAR (v2.7.0d) with the parameter outFilterMultimapNmax set to 1 to consider only uniquely mapped reads. Reads were assigned to genes using featureCounts (v1.6.3), with the parameter minOverlap set to 10 and discarding chimeric reads.
Assembly: GRCh38
Supplementary files format and content: count_matrix_HSPCs.txt
Supplementary files format and content: count_matrix_monocytes.txt

source_name: human monocytes

extract_protocol:
Total RNA was purified using RNeasy Micro Kit (QIAGEN). DNase treatment was performed using RNase-free DNAse Set (QIAGEN), according to the manufacturer’s instructions. RNA was quantified with Qubit 2.0 Fluorometer (Thermo Fisher) and its quality assessed by a 2100 Agilent Bioanalyser (Agilent Technologies).
Minimum quality was defined as RNA integrity number (RIN) > 8. 300 ng of total RNA were used for library preparation with TruSeq Stranded mRNA (Illumina)

value: Vexas patients

value: human monocytes


title: Vexas patients, monocytes, rep4

status: Public on Feb 06 2025

type: SRA

city: Segrate

first: Roberta

last: Alfieri

state: MI

address: Via Fratelli Cervi 93

department: ITB

country: Italy

institute: CNR

description:
S07
count_matrix_monocytes.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: individual

tag: cell type


title: RNA_seq_Bulk_Progenitor cells_Young_Female_5

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
The sequenced reads were trimmed to remove low-quality bases and adaptor sequences using cutadapt v3.0. The sequenced reads were mapped to the mm10 mouse reference genome using STAR version 2.7.9a with the GENCODE vM23 annotation gtf file. The read counts per gene were calculated using HTSeq-count v0.13.5. Uniquely mapped reads (MAPQ ≥ 20) were used. Uniquely mapped reads to mitochondrial genes were excluded for further analysis.
Each gene expression level was calculated as reads per million mapped reads (RPM) using DESeq2 version 1.30.1.
Assembly: mm10
Supplementary files format and content: *.tsv: Tab-separated text files include raw counts or CPM (= RPM) values.

molecule: total RNA

organism: Mus musculus

source_name: Progenitor cells

extract_protocol:
The proximal half of the small intestines were dissected, washed with cold PBS (Mg-/Ca-) and opened. Villi were removed by scraping with glass slides. The tissues were cut into 3-5mm fragments and washed 5-6 times in cold PBS (Mg-/Ca-) with gentle shaking by hand. The pieces were then incubated for 30 min at 4°C in PBS (Mg-/Ca-) containing 5mM EDTA. Crypts were then mechanically isolated by vigorous shaking, and filtered through a 70-um mesh to remove remaining villus and tissue fragments. The isolated crypts were dissociated into single cells by treating the cells with TrypLE Express (Gibco) containing DNase I (10U uL-1, Roche1) for 30 min at 37°C and gentle pipetting. The dissociated cells were resuspended in cold SMEM (Gibco) and incubated with the following antibodies for 30 min at 4°C: EPCAM-APC (G8.8) (Biolegend) and CD24-Pacific Blue (M1/69) (Biolegend), both at 1:500. Finally, cells were resuspended in SMEM supplemented with 7-AAD (BD Bioscience, dilution 1:100), 100 U mL-1　RNase inhibitor (Invitrogen) and 10 uM Y27632 (Tocris Bioscience). Cells were sorted using FACSAriaII or FACSAriaIIu (BD Biosciences). ISCs were isolated as Lgr5GFPhighEpcamhighCD24low7-AAD−, progenitors were isolated as Lgr5GFPmedium/lowEpcamhighCD24low7-AAD−, and Paneth cells were isolated as CD24highSidescatterhighLgr5GFP−Epcamhigh7-AAD−.
The cells were lysed and the total RNAs were purified using an RNeasy micro kit (Qiagen). 1 ng of total RNAs from each sample was used for synthesis and amplification of cDNA according to the single cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., Nucleic Acids Res., 2015). RNA-seq libraries were sequenced on a Nextseq 500 (Illumina) with a NextSeq 500 High Output v2 Kit (Illumina).

tag: strain

tag: genotype

tag: age

value: 2 months

tag: Sex

value: female

value: Progenitor cells


title: ACC-MESO-4_DN_3days_rep1

type: RNA

city: Sapporo-shi

first: Marie

last: Kato-Shinomiya

state: Hokkaido

address: Kita-ku, N15W7

department: Department of Cancer Pathology, Faculty of Medicine

institute: Hokkaido University

description: Gene expression of ACC-MESO-4 cells cultured on DN gel for 3 days

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: human mesothelioma cell line, DN gel, 3days, replicate1

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: ACC-MESO-4 cells were cultured on DN gel, PS dish and ULA dish in RPMI1640 medium with 10% fetal bovine serum, penicillin-streptomycin (100 U/mL penicillin and 0.1 mg/mL streptomycin), and L-glutamine (2 mM). The cultures were incubated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA of ACC-MESO-4 cells was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations.

tag: tissue

value: Pleural mesothelioma cell line established from pleural effusion

tag: cell name


title: Vexas patients, monocytes, rep2

description:
S05
count_matrix_monocytes.txt


title: RNA_seq_Bulk_Progenitor cells_Young_Female_4

value: 3 months


title: Vexas patients, monocytes, rep1

description:
S04
count_matrix_monocytes.txt


title: Splenocytes, mRNA-LNP, intradermal

city: Changchun city

first: Cenrong

last: Wang

state: Jilin Province

address: 吉林省长春市朝阳区前进大街吉林大学前卫南区

country: China

institute: Jilin University

description: Library name: SAMPLE 3

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: Rats / SARS-Cov-2
Supplementary files format and content: Raw data and matrix files

organism: Rattus norvegicus

extract_protocol:
The splenocytes were obtained at 4 weeks of boost. CD45+ splenocytes were sorted by flow cytometry. The cells were then loaded into a 10× chromium microfluidic system based on the manufacturer’s guidelines.
Library was perfomred according to the manufacter's instruction. A set of libraries was obtained from 10× loaded samples: a 3 × gene expression messenger RNA library. The Illumina NovaSeq 6000 sequencing platform and PE150 sequencing mode were used to sequence the completed library; the sequencing amounts should be more than 20 k reads/cell.

treatment_protocol: Rats inoculated with RBD3-Fc vaccines

value: Splenocytes

tag: treatment

value: SARS-Cov-2 Vaccines


title: Male healthy donors, monocytes, rep3

description:
S03
count_matrix_monocytes.txt

value: Male healthy donors


title: ACC-MESO-4_ULA_3days_rep1

description: Gene expression of ACC-MESO-4 cells cultured on ULA dish for 3 days

source_name: human mesothelioma cell line, ULA dish, 3days, replicate1


title: Splenocytes, mRNA, intradermal

address: 吉林省长春市朝阳区前进大街吉林大学前卫南区

description: Library name: SAMPLE 4


title: Neuroblastoma 17

type: genomic

city: Shanghai

first: Ying

last: Li

address: Lane 2555, Xiu-Pu Road, Pudong New District, Shanghai 200120, China

institute: Shanghai Cinopath Medical Laboratory Co., Ltd.

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
206863220111_R08C01

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48℃, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a NextSeq 550 (Illumina).

data_processing:
Genomic DNA extracted fromneuroblastoma or ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Biotin and 2,4-Dinitrophenol

molecule: genomic DNA

source_name: Neuroblastoma

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (AM1) and primer/neutralization mix (MA2-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (FAM), precipitated with isopropanol and precipitation mix (PA1) and resuspended in resuspension solution (RA1).

extract_protocol: Add Deparaffinization solution at 56℃ to get rid of paraffin on the surface of the sample, add buffer FTB, a combination of RNA-free enzyme water and proteinase K cleavage, incubate at 90℃ for 1h to decrosslink, and add proteinase K again to cleave the tissue by incubation at 65℃, and then transfer it to the adsorption column to filter out impurities.

tag: gender

value: Male

value: Neuroblastoma

tag: disease state

value: carcinoma


title: RNA_seq_Bulk_Progenitor cells_Young_Female_2


title: Ganglioneuroblastoma 11

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205841280011_R07C01

source_name: Ganglioneuroblastoma

value: Female

value: Ganglioneuroblastoma


title: Ganglioneuroblastoma 10

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205841280011_R03C01


title: RNA_seq_Bulk_Progenitor cells_Young_Female_1


title: Neuroblastoma 16

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
206350350009_R05C01


title: Male healthy donors, monocytes, rep2

description:
S02
count_matrix_monocytes.txt


title: ACC-MESO-4_PS_3days_rep1

description: Gene expression of ACC-MESO-4 cells cultured on PS dish for 3 days

source_name: human mesothelioma cell line, PS dish, 3days, replicate1


title: Vexas patients, monocytes, rep5

description:
S08
count_matrix_monocytes.txt


title: BECs-P100-4

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Illumina adapter sequences were removed using the Flexbar software (version 3.5.0), and the remaining reads sequences were aligned to the mouse genome (GRCm38) using Tophat2 software (version 2.1.1) with the default parameters.
After the alignment, the numbers of reads mapped to the gene features (GTF file of GRCm38.91) were counted using HTseq sofrware. The read counts for the samples in each condition were then normalized using the TMM (trimmed mean of M-values) normalization of the edgeR package.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TMM-normalized read counts for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: brain endothelial cells

extract_protocol:
Total RNAs were obtained from BECs of the whole cortex tissues using Trizol reagent (Invitrogen Life Technologies, Grand Island, NY). NEBNext Single Cell/Low Input RNA Library Prep Kit for  Illumina kit was used for the construction of sequencing libraries, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain endothelial cells (BECs)

value: visual cortex

value: Postnatal 100 day male tie2-Cre; ai9; rpl22HA/HA mice


title: Male healthy donors, monocytes, rep1

description:
S01
count_matrix_monocytes.txt

value: human monocytes


title: Neuroblastoma 15

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
206535470088_R04C01


title: RNA_seq_Bulk_Progenitor cells_Young_Male_5

value: male


title: BECs-P100-3


title: Vexas patients, 7 days after editing, rep3

description:
S12
count_matrix_HSPCs.txt

source_name: human HSPCs

value: Vexas patients

value: human HSPCs

tag: time

value: 7 days after editing


title: Ganglioneuroblastoma 9

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205495650080_R06C01


title: RNA_seq_Bulk_Progenitor cells_Young_Male_4

value: 2 months

value: Progenitor cells


title: RNA_seq_Bulk_Progenitor cells_Young_Male_3


title: Splenocytes, mRNA, intramuscular

address: 吉林省长春市朝阳区前进大街吉林大学前卫南区

description: Library name: SAMPLE 2

value: Splenocytes

value: SARS-Cov-2 Vaccines


title: RNA_seq_Bulk_Progenitor cells_Young_Female_3

value: female


title: Neuroblastoma 14

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205841290149_R03C01

value: Male

value: Neuroblastoma


title: BECs-P100-2


title: Vexas patients, 7 days after editing, rep2

description:
S11
count_matrix_HSPCs.txt


title: Ganglioneuroblastoma 8

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
206443730171_R08C01

value: Female

value: carcinoma


title: BECs-P30-4

value: brain endothelial cells (BECs)

value: Postnatal 30 day male tie2-Cre; ai9; rpl22HA/HA mice


title: Male healthy donors, 7 days after editing, rep3

description:
S09
count_matrix_HSPCs.txt

value: Male healthy donors


title: RNA_seq_Bulk_Progenitor cells_Young_Male_2


title: Neuroblastoma 13

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205495650027_R08C01


title: Vexas patients, 7 days after editing, rep1

description:
S10
count_matrix_HSPCs.txt


title: RNA_seq_Bulk_Progenitor cells_Young_Male_1


title: Male healthy donors, 7 days after editing, rep2

description:
S08
count_matrix_HSPCs.txt


title: BECs-P100-1

value: visual cortex

value: Postnatal 100 day male tie2-Cre; ai9; rpl22HA/HA mice


title: BECs-P30-3


title: Neuroblastoma 12

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205065750049_R08C01


title: RNA_seq_Bulk_ISCs_Aged_Female_5

source_name: ISCs

value: 23 months

value: ISCs


title: BECs-P30-2


title: Ganglioneuroblastoma 7

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
205065750074_R02C01

value: Ganglioneuroblastoma


title: RNA_seq_Bulk_ISCs_Aged_Female_3

value: 24 months


title: RNA_seq_Bulk_ISCs_Aged_Female_4


title: Ganglioneuroblastoma 6

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
202564360006_R04C01


title: BECs-P30-1


title: BECs-P10-4

value: Postnatal 10 day tie2-Cre; ai9; rpl22HA/HA mice


title: Ganglioneuroblastoma 4

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
202560410008_R05C01


title: Vexas patients, 24h after editing, rep2

description:
S05
count_matrix_HSPCs.txt

value: Vexas patients

value: human HSPCs

value: 24h after editing


title: Vexas patients, 24h after editing, rep1

description:
S04
count_matrix_HSPCs.txt


title: Vexas patients, 24h after editing, rep3

description:
S06
count_matrix_HSPCs.txt


title: BECs-P10-3


title: RNA_seq_Bulk_ISCs_Aged_Female_1

value: female


title: Male healthy donors, 24h after editing, rep3

description:
S03
count_matrix_HSPCs.txt


title: BECs-P10-2


title: Splenocytes, mRNA-LNP, intramuscular

address: 吉林省长春市朝阳区前进大街吉林大学前卫南区

description: Library name: SAMPLE 1

value: Splenocytes

value: SARS-Cov-2 Vaccines


title: Neuroblastoma 11

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
202560410006_R05C01

value: Male

value: Neuroblastoma

value: carcinoma


title: RNA_seq_Bulk_ISCs_Aged_Male_6

value: male


title: BECs-P10-1

value: brain endothelial cells (BECs)

value: visual cortex


title: Male healthy donors, 24h after editing, rep2

description:
S02
count_matrix_HSPCs.txt

value: Male healthy donors


title: Neuroblastoma 10

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
202560410019_R03C01

value: Female


title: nfya1_rhizo_72h_rep4

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
The quality of the fastq files were validated with fastqc
Sequence reads were trimmed for adapter and repetitive sequences with Cutadept
The resulting reads from the raw fastq data were quality controlled and and mapped to the M. truncatula reference genome version 4.0 with STAR 2.7.3a
The raw count values were calculated with featureCounts in R package Rsubread
Assembly: Mt4.0v1
Supplementary files format and content: tab separated files with raw count values

organism: Medicago truncatula

source_name: 2-3mm segment of root

growth_protocol: Seeds were scarified, surface sterilized with 10 % (v/v) bleach solution, stratified for 3 days  at 4 °C and germinated on water agar plates. Plants were grown in sterile conditions in controlled  environment rooms at 22 °C (80 % humidity, 16 h light/8 h dark, 300 μmol m2 s-1 light intensity)  on filter paper-lined agar media in sealed plates unless otherwise specified. For rhizobial spot  inoculation seedlings were grown for 2 days on buffered nodulation medium (BNM) (Ehrhardt et  al., 1992) supplemented with 1 μM aminoethoxyvinylglycine (AVG; Sigma-Aldrich Company  Ltd, Darmstadt, Germany) at 22 °C (16 hours light/8 hours dark, 300 μmol m-2 s-1 light intensity).

extract_protocol:
Total RNA was isolated with the RNeasy PlantMini Kit (Qiagen) following the manufacturer’s instructions.
The library was constructed with Illumina TruSeq® Stranded mRNA HT kit

treatment_protocol: Sinorhizobium meliloti strain 2011 (Lerouge et al., 1990) was grown in minimal medium  supplemented with 3 μM luteolin (Sigma-Aldrich Company Ltd, Darmstadt, Germany) and diluted  to a final concentration of 0.02 OD 600 nm using Fahraeus medium (Boisson-Dernier et al., 2001).  The mock treatment consisted of Fahraeus medium with luteolin diluted to an equivalent  concentration as the inoculum. Approximately 1 μL of S. meliloti suspension or mock treatment  was inoculated onto the susceptibility zone (where the root hairs first appear) and marked by  puncturing the filter paper alongside the site of inoculation. After 24 and 72 hours

value: 2-3mm segment of root

value: nf-ya1 mutant in A17 background

value: rhizobia S. meliloti 2011


title: RNA_seq_Bulk_ISCs_Aged_Male_5

value: 24 months

value: ISCs


title: Male healthy donors, 7 days after editing, rep1

description:
S07
count_matrix_HSPCs.txt

value: human HSPCs

value: 7 days after editing


title: Neuroblastoma 9

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204667530071_R03C01


title: human, pbs_r1

city: Zhengzhou City

first: Yuan

state: Henan

address: No.1 Jianshe East Road, Jinshui District

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes row counts for each sample
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

extract_protocol:
Total RNA was extracted using Trizol
RNA transcriptome profiles were generated by the Beijing Genomics Institute (BGI) using the DNA Nanoball sequence (DNBSEQ) platform.

tag: cell line

value: Human breast cancer cells

value: WT

value: pbs


title: nfya1_rhizo_72h_rep3


title: Neuroblastoma 8

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480091_R05C01

value: Neuroblastoma


title: RNA_seq_Bulk_ISCs_Aged_Male_4


title: RNA_seq_Bulk_ISCs_Aged_Female_2

value: female


title: Ganglioneuroblastoma 5

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
202564360006_R01C01

value: Ganglioneuroblastoma

value: carcinoma


title: Neuroblastoma 7

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480035_R07C01


title: RNA_seq_Bulk_ISCs_Aged_Male_3

value: 26 months

value: male


title: nfya1_rhizo_72h_rep2


title: human, APA_r2

value: APA


title: RNA_seq_Bulk_ISCs_Aged_Male_2


title: Neuroblastoma 6

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480035_R01C01

value: Male


title: Neuroblastoma 5

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480015_R06C01

value: Female


title: RNA_seq_Bulk_ISCs_Aged_Male_1

value: 27 months


title: nfya1_rhizo_24h_rep4

value: 2-3mm segment of root

value: nf-ya1 mutant in A17 background

value: rhizobia S. meliloti 2011


title: human, pbs_r2


title: nfya1_rhizo_72h_rep1


title: resT_15min_ara_1

city: Seoul

first: Seok-Won

last: Jang

address: 1, Gwanak-ro, Gwanak-gu,

institute: Seoul National University

data_processing:
The sequencing adapter removal and quality-based trimming for the raw data were performed using Trimmomatic v. 0.36. Cleaned reads were mapped to the reference genome using HISAT2 v. 2.1.0 For counting the reads mapped to each CDS (coding sequence), featureCounts (v. 2.0.0) was used. Finally, the count from each CDS was normalized using edgeR package.
Assembly: GCF_000022165.1
Supplementary files format and content: tab-limited file includes DeSeq2 normalized result between wild type and resT induction strain

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: bacteria

growth_protocol: Bacteria were grown at 37°C in N-minimal media supplemented with 0.1% casamino acids, 38 mM glycerol, and the 500 uM MgCl2.

extract_protocol:
RNA was harvested using Rneasy Mini kit (Qiagen). For ribosomal RNA depletion, total RNA were processed by using NEBNext rRNA Depletion Kit (Bacteria)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit following manufacturer's protocols

treatment_protocol: L-arabinose at 2 mM was used for overexpression of resT.

value: bacteria

value: arabinose

value: harbouring a pBAD33::resT


title: nfya1_rhizo_24h_rep3


title: Ganglioneuroblastoma 3

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480071_R08C01


title: nfya1_rhizo_24h_rep2


title: RNA_seq_Bulk_ISCs_Young_Female_6

value: 2 months

value: ISCs


title: resT_15min_ara_2

value: WT


title: RNA_seq_Bulk_ISCs_Young_Female_5

value: female


title: Neuroblastoma 4

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480071_R01C01

value: Neuroblastoma

value: carcinoma


title: wild-type_1

value: wild-type


title: nfya1_rhizo_24h_rep1


title: RNA_seq_Bulk_ISCs_Young_Female_4


title: RNA_seq_Bulk_ISCs_Aged_Male_7

value: 24 months

value: male


title: wild-type_2


title: Neuroblastoma 3

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204111480184_R08C01

value: Male


title: nfya1_mock_72h_rep4

value: mock


title: 30 DAP-A

city: Mohali

first: Rita

last: Sharma

state: Punjab

address: Sector 81

department: Food Biotechnology

country: India

institute: National Agri-Food Biotechnology Institute

description: Transcriptome

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using NGS QC Toolkit (v.2.3)
Read alignment to the reference genome using  HISAT2
Estimation of gene raw counts using FeatureCounts (v.2.2.0)
Pairwise differential expression analysis using DESeq2
Assembly: Phytozome v5.1
Supplementary files format and content: TPM values for each stage in excel format

organism: Sorghum bicolor

source_name: Seed

growth_protocol: Soghum bicolor M35-1 plants were raised in an open field

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit and NEBNext® UltraTM II Directional RNA library prep kit using manufacturer’s instructions

value: Seed

value: After pollination


title: RNA_seq_Bulk_ISCs_Young_Female_3


title: Ganglioneuroblastoma 1

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480025_R01C01

value: Ganglioneuroblastoma


title: Ganglioneuroblastoma 2

description:
Genomic DNA extracted from ganglioneuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
204127480005_R04C01

value: Female


title: RNA_seq_Bulk_ISCs_Young_Female_2


title: human, APA_r1

value: Human breast cancer cells

value: APA


title: nfya1_mock_72h_rep2

value: 2-3mm segment of root

value: nf-ya1 mutant in A17 background


title: 20 DAP-C

description: Transcriptome


title: RNA_seq_Bulk_ISCs_Young_Female_1

value: 2 months

value: ISCs


title: Neuroblastoma 2

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
203714400093_R01C01

value: Neuroblastoma


title: Neuroblastoma 1

description:
Genomic DNA extracted from neuroblastoma was genotyped using CytoSNP-850K v1.2 Genotyping BeadChips (Illumina).
203714400122_R03C01

value: carcinoma


title: 20 DAP-B

description: Transcriptome


title: RNA_seq_Bulk_ISCs_Young_Male_5


title: 20 DAP-A

description: Transcriptome


title: nfya1_mock_72h_rep1


title: nfya1_mock_24h_rep4


title: RNA_seq_Bulk_ISCs_Young_Male_4


title: 10 DAP-C

description: Transcriptome


title: Flox+RI

city: Guangzhou

first: Yanpei

last: Zhang

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China

institute: Southern Medical University

data_processing:
The raw fastq data was first filtered for low quality using trimomatic software (Version 0.39), and then computationally aligned using CellRanger (version 6.0) to map to the mm10 reference genome (GRCm38.91). Quality control steps were performed using Seurat package (version 5.0.3) to select cells with a library complexity of 500-6000 features, genes expressed by at least three cells, and filter out cells with high percentages of mitochondrial genes (>20%). This resulted in 29,291 cells for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
The tumor tissues were removed from the mice and preserved in the tissue storage solution (Miltenyi, 130-100-008) while being kepton ice. Tissues were digested into single cell suspension, library was constructed, quality control was performed and library was sequenced on an Illumina HiSeq platform by Haplox.
RNA libraries were prepared for sequencing using standard protocols.

value: tumor

value: Lewis lung carcinoma cells

value: LKB1 knockdown

value: radiation+immune checkpoint inhibitor


title: nfya1_mock_24h_rep3

value: mock


title: RNA_seq_Bulk_ISCs_Young_Male_3

value: male


title: 10 DAP-B

description: Transcriptome

value: Seed

value: After pollination


title: Flox+ICI

value: immune checkpoint inhibitor


title: nfya1_mock_24h_rep2


title: CKO+RI


title: 30 DAP-B

description: Transcriptome


title: RNA_seq_Bulk_ISCs_Young_Male_2


title: 10 DAP-A

description: Transcriptome


title: nfya1_mock_72h_rep3


title: nfya1_mock_24h_rep1


title: RNA_seq_Bulk_ISCs_Young_Male_1


title: MtWT_4h_1

status: Public on Feb 05 2025

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using HISAT with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by Bowtie2.
Genome_build: Myceliophthora thermophila ATCC 42464(https://www.ncbi.nlm.nih.gov/genome/?term=Myceliophthora%20thermophila)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for each sample.

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT


title: MtWT_4h_2


title: MtTrh-1_4h_2

value: MtTrh-1 deletion


title: YO-P2

city: Lanzhou

first: Liyan

last: hu

address: No. 335, Mogou Lane, Qilihe District

department: Key Laboratory of Yak Breeding in Gansu Province

institute: Lanzhou Institute of Animal Husbandry and Veterinary Pharmaceutics, Chinese Academy of Agricultural Sciences

description: Library name: Sample 8

library_source: other

data_processing:
Fastp filters low-quality readings.
The short reading comparison tool Bowtie2 is used to map readings to ribosomal RNA (rRNA) databases, GenBank, and Rfam databases. Remove readings of rRNA, transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and miRNA.
Compare the processed RNA seq readings with the genome.
A trinucleotide cycle diagram was drawn using the riboWaltz R software package.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Calculate the number of reads in the open reading frame of coding genes using software RSEM, and normalize gene expression levels using FPKM method
Library strategy: Ribo-Seq

molecule: other

organism: Bos grunniens

source_name: ovary

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
Grind the frozen tissue into powder using a mortar and pestle in liquid nitrogen, and then dissolve it in 400 μ L lysis buffer. The ribosomal profiling technique was carried out according to the report. Add short (50-80 base) antisense DNA probes complementary to rRNA sequences to a solution containing RFs, and then add RNase H and DNase I to digest rRNA and residual DNA probes. Finally, further purification of RFs was carried out using magnetic beads.
Add adapters to both ends of RFs and perform reverse transcription and PCR amplification. Enrich PCR products with sizes of 140-160bp to generate cDNA libraries, and sequence using Illumina HiSeqTM X10.

treatment_protocol: Yaks were supplied by Menyuan Hui Autonomous County, Haibei Tibetan Autonomous Prefecture, Qinghai Province, China (37◦3900 N, 101◦6200 E). The ovarian tissues of three 6-year-old adult yaks in different reproductive stages (April [anestrus, YO-A], August [estrus, YO-F], and December [pregnancy, YO-P]) were used as the research material. Within 60 min of euthanasia induction, the ipsilateral ovarian tissue of the yak was collected (three biological replicates), rinsed with physiological saline, and rapidly frozen in liquid ammonia.

value: ovary


title: YO-P3

description: Library name: Sample 9


title: YO-P1

description: Library name: Sample 7


title: YO-F3

description: Library name: Sample 6


title: YO-F1

description: Library name: Sample 4


title: YO-A2

description: Library name: Sample 2


title: YO-A3

description: Library name: Sample 3


title: YO-A1

description: Library name: Sample 1


title: MtTrh-1_4h_1


title: H07M1.1 HYP

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: Michigan

address: 109 Zina Pitcher Pl.

department: Michigan Neuroscience Institute (MNI)

country: USA

institute: University of Michigan

hyb_protocol: The samples were transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures. The samples were run in two batches: the first included the hippocampus and cortex samples and the second included the hypothalamus samples. Each brain region was run on a separate chip. Only data from the cortex and hypothalamus samples are included in this data release.

scan_protocol: Affymetrix standard protocol

data_processing: For our current analyses, the ReadAffy() function (from R package affy, v.1.84.0; (Gautier et al., 2004)) was used to read the data from the .CEL files into R studio (v.1.0.153). An expression set was generated using the Robust Multi-Array Average method (RMA: (Irizarry et al., 2003)). An updated custom chip definition file for the RAE230A chip (.cdf (Dai et al., 2005): “rae230arnentrezgcdf_25.0.0”) was used to summarize the probe signals into probesets targeting genes annotated by Entrez Gene ID (downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/25.0.0/entrezg.asp on Dec 9 2024, released on Jan 5, 2021). Additional gene annotation was later added using the org.Rn.eg.db package (v.3.20.0, (Carlson, 2019)). Quality control identified two hippocampal samples with low sample-sample correlation values (median R= 0.68 & 0.89, respectively), leaving a final sample size of n=5/group for the hippocampus, and n=6/group for both the cortex and hypothalamus. Separate bHR/bLR differential expression analyses were conducted for each brain region using the limma pipeline (no covariates, v.3.62.1, (Ritchie et al., 2015)), followed by an empirical Bayes correction. Nominal p-values were corrected for multiple comparisons using the Benjamini-Hochberg method (False Discovery Rate or FDR) within the multtest package (v. 2.62.0, (Pollard et al., 2005)).The full analysis code is available at: https://github.com/hagenaue/NIDA_bLRvsbHR_F2Cross_HC_RNASeq.

label: biotin

source_name: Hypothalamus

extract_protocol: The rats were sacrificed in adulthood (between P102-P108) via rapid decapitation followed by immediate brain extraction. The whole hippocampus, frontal cortex, and hypothalamus samples were rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.

tag: bred line

value: bred High Responder (bHR)

tag: locomotor activity in a novel field (beam breaks)

value: Male


title: L08M2.0 HYP

label_protocol: The samples were transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures. The samples were run in two batches: the first included the hippocampus and cortex samples and the second included the hypothalamus samples.

value: bred Low Responder (bLR)


title: H10M2.2 HYP


title: H03M1.1 HYP


title: H01M2.0 HYP


title: L09M1.0 HYP


title: L05M2.1 CTX

source_name: Frontal Cortex


title: L05M2.1 HYP


title: YO-F2

description: Library name: Sample 5


title: L10M2.2 HYP


title: L11M2.0 HYP


title: L08M2.0 CTX


title: H03M1.1 CTX


title: H09M1.0 HYP


title: KPC8069_input3

city: Portland

first: Yifei

last: Guo

address: 2730 S Moody Ave

institute: Oregon Health & Science University

description: Library name: Sample3

data_processing:
FastQC (Andrews S., 2010) was used to clean the raw data.  The Skewer (Jiang et al., 2014) is used to filter raw data and trimming off the adapter sequences and low quality bases.
Duplicates were labeled using SAMBLAST (Faust et al., 2014) and mapping quality value was calculated (MAPQ). Proper quality value was chosen as the only threshold for mapping. Here we choose 13 as the threshold, which means that the mapping chance of the accordingly non-unique region is only 0.05.
By making use of MACS2 software (Zhang et al., 2008) (threshold q value = 0.05) to finish the peak calling, we can calculate the number of peaks, the peak width and its distribution, and find the peak related genes.
Assembly: ensembl_102_mus_musculus_grcm38_toplevel
Supplementary files format and content: bigWig

source_name: pancreas

extract_protocol:
RNA-binding protein immunoprecipitation (RIP) was performed with EZ-Magna RIP kit (Merck). RNA was further cleaned with micro Rneasy kit (Qiagen).
NEBNext Ultra™ II RNA Library Prep Kit for Illumina was used.

value: pancreas

value: PDAC


title: KPC8069_HuR3

description: Library name: Sample6


title: H11M1.1 CTX


title: KPC8069_HuR1

description: Library name: Sample4


title: L11M2.0 CTX


title: KPC8069_HuR2

description: Library name: Sample5


title: H10M2.2 CTX


title: L07M3.1 HYP


title: H09M1.0 CTX


title: L10M2.2 CTX


title: L09M1.0 CTX


title: H07M1.1 CTX


title: H11M1.1 HYP


title: KPC8069_input2

description: Library name: Sample2


title: H01M2.0 CTX


title: Ctrl-2

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr. Molewaterplein 40

department: Department of Urology, Department of Biochemistry, Department of Pathology

country: Netherlands

institute: Erasmus MC Cancer Institute

description: Library name: Sample 2

library_source: genomic

data_processing:
Fastq files were aligned to the human genome (hg38) with Bowtie2. Duplicate reads and reads mapped to extra chromosomes were removed from the resulting BAM files prior to peak calling.
Peaks were identified using MACS2 (83) using the parameters --broad --nomodel --shift 100 --extsize 200.
Counting and differential accessibility analysis were performed using the bioconductor package DiffBind (84) with the DESEQ2 algorithm
Assembly: hg38
Supplementary files format and content: broadPeak, contains the peaks identified by MACS2

source_name: Bladder

extract_protocol: ATAC-seq libraries were prepared using the Active motif ATAC-Seq Kit (#53150) according to the accompanying protocol. Library DNA quality was assessed using the Agilent Tapestation 4150 and the High Sensitivity D1000 assay kit while library DNA quantity was assessed using the Invitrogen Qubit 4 Fluorometer and the Invitrogen Qubit dsDNA HS Assay. The quantified libraries were pooled equimolarly, and a total of 25ng were used for Adapter Conversion PCR Amplification using the Universal Library Conversion Kit (App-A), Version: V1.0 (MGI Tech Co., Ltd.), following the Universal Library Conversion Kit (App-A) User Manual (Version: A3). The quality of the purified adapter conversion PCR (AC-PCR) product was evaluated using the Agilent Tapestation 4150 and the High Sensitivity D1000 assay kit, and the quantity was assessed using the Invitrogen Qubit 4 Fluorometer and the Invitrogen Qubit dsDNA HS Assay. DNA denaturation, Single-Strand Circularization, Enzymatic Digestion, Enzymatic Digestion Product Cleanup and Quality Control steps were performed on 1 pmol of AC-PCR product according to the Universal Library Conversion Kit (App-A) User Manual (Version: A3).

value: Bladder

value: Patient-derived tumoroids

value: Bladder Cancer

value: shCTRL


title: 1 week_Chow_ LSEC_Iso_S5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCm38.p6
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

source_name: liver

extract_protocol:
Mouse livers were perfused and LSEC were separated by gradient centrifugation and then selected with CD146+ coupled magnetic beads. Quality analysis was performed by FACS. RNA was then isolated using the innuPREP RNA Mini Kit 2.0 (845-KS-2040250, Analytik Jena). RNA libraries were prepared for sequencing using standard BGISeq 500 protocols. RNA was then extracted using the innuPREP RNA Mini Kit 2.0 (catalogue number 845-KS-2040250, Analytik Jena). Finally, the RNA libraries were prepared for sequencing according to the standard protocols for the BGISeq 500 platform.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: The mice were fed the CDAA diet for one week, while the control group was fed chow.

value: liver

value: Liver sinusoidal endothelial cells

value: Std


title: ShARID1A-1

description: Library name: Sample 3


title: ShARID1A-2

description: Library name: Sample 4


title: 1 week_Chow_ LSEC_Iso_S4


title: KPC8069_input1

description: Library name: Sample1


title: ShE2F8-1

description: Library name: Sample 5


title: ShE2F8-2

description: Library name: Sample 6


title: 1 week_Chow_ LSEC_Iso_S3


title: 1 week_Chow_ LSEC_Iso_S1


title: 1 week_CDAA_ LSEC_Iso_C2

value: CDAA


title: L07M3.1 CTX


title: 1 week_CDAA_ LSEC_Iso_C3


title: 1 week_CDAA_ LSEC_Iso_C5


title: 1 week_CDAA_ LSEC_Iso_C1


title: CcS-11, control, biological rep3

city: Brno

first: Daniel

last: Růžek

address: Žerotínovo nám. 617/9

country: Czech Republic

institute: Masaryk University

description: mock infected

hyb_protocol: Fragmented cRNA (5.5 ug) was hybridized in GeneChip 640 Hybridization Oven (Affymetrix) to a GeneChip Mouse Gene ST 1.0 Array (Affymetrix) according to standard protocol. The washing and staining of the arrays with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) was completed in Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip 3000 7G Scanner (Affymetrix).

data_processing: Data were background corrected using the RMA method, quantile normalized and variance stabilized using base-2 logarithmic transformation. The LIMMA package was then used for analysis and annotation package mogene10sttranscriptcluster.db was used for mapping of probes to gene symbols.

source_name: mouse brain tissue, control

label_protocol: Total RNA (100 ng) was amplified and labelled using standard protocols for Ambion WT Expression Kit (Applied Biosystems).

growth_protocol: Specific pathogen-free adult female mice of the strains BALB/c, CcS-11, and STS, originally provided by Professor Peter Démant (Roswell Park Comprehensive Cancer Center, Buffalo, NY), were obtained from the breeding colony of Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic, for use in the experiments. The mice, aged approximately 9 weeks at the time of infection, were housed in plastic cages with wood-chip bedding in a specific pathogen-free room maintained at a constant temperature of 22°C and a relative humidity of 65%. They were provided with sterilized pellet diet and water ad libitum.

extract_protocol: Brains from both mock- and virus-infected mice were removed, individually weighed, and prepared as 20% suspensions in phosphate-buffered saline (PBS) using a TissueLyser II (Qiagen). For microarray analysis, brain homogenates were clarified by centrifugation at 14,000× g for 10 minutes at 4°C. RNA was then isolated from the brain tissue pellets using the RNeasy Mini Kit (Qiagen), following the manufacturer's recommendations.

treatment_protocol: Adult mice of all three strains were infected with 10 pfu of TBEV (strain Neudoerfl) via intracerebral (i.c.) inoculation. At 6 days post-infection (dpi), when the infected mice exhibited neurological symptoms, infected and mock-infected mice were sacrificed.

tag: infection

value: control


title: 1 week_Chow_ total_Liver_K8

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCm39
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

extract_protocol:
For the isolation of RNA from whole liver tissue, frozen samples were homogenized in lysis buffer (catalog number 845-KS-2040250, Analytik Jena) using a Precellys 24 tissue homogenizer (model P000669-PR240-A, Bertin-Instruments). Subsequent RNA extraction was performed using the innuPREP RNA Mini Kit 2.0 (catalog number 845-KS-2040250, Analytik Jena). Finally, the RNA libraries were prepared for sequencing according to the standard protocols for the BGISeq 500 platform.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: Control


title: CcS-11, control, biological rep4

description: mock infected


title: 1 week_Chow_ total_Liver_K7


title: 1 week_Chow_ total_Liver_K6


title: CcS-11, control, biological rep2

description: mock infected


title: STS, infected, biological rep5

description: infected with 10 pfu of TBEV - Neudoerfl via intracerebral inoculation, sacrificed 6 days post-infection

source_name: mouse brain tissue, TBEV infected

value: infection

value: STS


title: Ctrl-1

description: Library name: Sample 1


title: 1 week_Chow_ LSEC_Iso_S2


title: STS, control, biological rep3

description: mock infected


title: CcS-11, infected, biological rep1


title: 1 week_CDAA_ total_Liver_C6


title: 1 week_CDAA_ total_Liver_C8


title: 1 week_CDAA_ LSEC_Iso_C4


title: 1 week_Chow_ total_Liver_K5


title: 1 week_CDAA_ total_Liver_C7


title: 1 week_CDAA_ total_Liver_C5


title: CcS-11, infected, biological rep4


title: 1 day_Chow_ LSEC_Iso_S3

treatment_protocol: The mice were fed the CDAA diet for one day, while the control group was fed chow.


title: 1 day_Chow_ LSEC_Iso_S2


title: 1 day_Chow_ LSEC_Iso_S4


title: Pooled plasma exosome RNA, exercise mice

city: Brisbane

first: Michael

last: Pearen

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
QC, contamination filtering, mapping of trimmed reads onto mature and precusor miRNAs, novel and known miRNA discory and expression profiling was conducted using the nextflow nf-core/smRNAseq pipeline (version 2.1.0) https://nf-co.re/smrnaseq
Assembly: miRBase (version 22)
Supplementary files format and content: Tab-delimited text file includes raw mature microRNA counts for each Sample
Supplementary files format and content: Tab-delimited text file of mature microRNA counts for each sample normalized to total microRNA count for each sample.

source_name: Plasma

growth_protocol: Eight-week-old wild type C57BL/6 mice on normal chow diet

extract_protocol:
The blood was centrifuged at 2500 × g for 10 min at room temperature (RT). EVs were isolated using qEV10 columns from ~10 ml of pooled exercised and sedentary mouse plasma (from 20 mice in each group). EV-rich fractions (1-3) were concentrated using Amicon Ultra-15 Centrifugal Filters to a volume of 600 µL before RNA was extracted using the qEV RNA Extraction Kit according to the manufacturer’s instructions (IZON Science, NZ).
Small RNA NGS libraries were prepared using Illumina’s TruSeq Small RNA Library Prep kit and were single-end sequenced at a read length of 50 nucleotides (nt).

treatment_protocol: Mice were placed into two groups: exercise and sedentary. In the exercise group, the mice were acclimatized for three days on a treadmill (day 1:10 m/min. day 2: 12 m/min. day 3: 14 m/min). Three days later, they underwent a 60-minute bout to exhaustion, increasing in speed from 10 m/min to 24m/min by 2m/min every 10 min. Exhaustion was defined as the inability to continue at the selected running speed despite gentle encouragement with a brush for 5-10s).

value: Plasma

value: Wild Type

value: Exercise


title: A904 rep3

city: 天津市

last: yang

state: 天津市

address: qixiangtai Road

institute: Tianjin medical university

description: Library name: A904_3

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances.R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RAW counts for each sample.
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: colon

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

value: HT-29 cells

value: enterocyte

value: wild type

value: Total RNA


title: 1 day_CDAA_ LSEC_Iso_C5


title: A904 rep2

description: Library name: A904_2


title: 1 day_Chow_ LSEC_Iso_S5


title: 1 day_CDAA_ LSEC_Iso_C4


title: A904 rep1

description: Library name: A904_1


title: BALB/c, infected, biological rep1

value: BALB/c


title: BALB/c, control, biological rep2

description: mock infected


title: CcS-11, infected, biological rep2


title: STS, infected, biological rep2


title: STS, control, biological rep1

description: mock infected


title: STS, infected, biological rep1


title: BALB/c, control, biological rep1

description: mock infected


title: BALB/c, infected, biological rep2


title: 1 day_CDAA_ LSEC_Iso_C3

value: liver


title: BALB/c, infected, biological rep3


title: 1 day_CDAA_ LSEC_Iso_C2

value: Liver sinusoidal endothelial cells


title: Control_rep2

description: Library name: Control_2


title: Control_rep1

description: Library name: Control_1


title: Osteoclasts, VERAPAMIL3, Day5

first: Xiankun

last: Cao

address: Zhizaoju load No.639

department: orthopedic

institute: Shanghai Ninth People's Hospital affiliated to Shanghai Jiao tong University School of Medicine

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cv3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: osteoclasts, derived from bone marrow-derived macrophages

growth_protocol: BMMs were extracted from the tibial and femoral bone marrow and suspended in α-MEM containing 10% FBS, and 1% penicillin/streptomycin, and 30ng/ml M-csf. The cell cultures were then placed in a humid environment at 37 °C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: osteoclastic differentiation was induced by  α-MEM with 10% FBS, 30ng/ml M-csf, and 50ng/ml Rankl.The medium was changed every 2 days until the 7th day.

value: VERAPAMIL-TREATED

tag: differentiation status

value: Osteoclastic differentiation


title: Osteoclasts, VERAPAMIL2, Day5

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cv2

value: osteoclasts, derived from bone marrow-derived macrophages


title: Pooled plasma exosome RNA, sedentary mice

value: Sedentary


title: 1 day_Chow_ LSEC_Iso_S1

value: Std


title: Osteoclasts, VERAPAMIL1, Day5

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cv1


title: Osteoclasts, CONTROL3, Day5

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cw3

value: CONTROL


title: Control_rep3

description: Library name: Control_3


title: K374_Tumor2_TCR

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

state: CA

address: 513 Parnassus Avenue, HSW 1201B

institute: UCSF

description: Library name: Sample 4

data_processing:
Cell Ranger analysis pipelines (version 3.0.2, 10X Genomics) were used to process the generated sequencing data
Data was demultiplexed into FASTQ and aligned to the GRCh38 human reference genome and counted
TCR library reads were assembled into single cell V(D)J sequences and annotations
Data normalization, dimension reduction, and differential expression analysis were performed using R version 4.0.5 and the Seurat R package (version 3.2.2)
Samples were integrated using the SCTransform Method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Assembly: GRCh38
Supplementary files format and content: .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR other metadata in the @meta.data field. The .h5ad file contains a Scanpy/Adata object with the count matrix, and the associated metadata in the .obs data field.
Library strategy: TCR-seq

source_name: melanoma, nodal metastasis

growth_protocol: Live cells were sort-purified using an BD FACSAria Fusion (BD Biosciences) from collagenase-digested human melanoma samples or from PBMCs isolated by Ficoll gradient

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument
Reverse transcription was performed and libraries were constructed according to the 10X Chromium Single Cell 5' Gene Expression and V(D)J Profiling Solution kit

value: melanoma, nodal metastasis

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+, CD45+CD3+CD4+CD8-, and CD45+CD3- and loaded into two channels in a 40:40:20 ratio

value: nivolumab


title: 1 day_CDAA_ LSEC_Iso_C1

value: CDAA


title: Osteoblasts, VERAPAMIL3, Day7

city: Shanghai

source_name: osteoblasts, derived from wildtype mesenchymal stem cells

growth_protocol: BMSCs were extracted from the tibial and femoral bone marrow and suspended in α-MEM containing 15% FBS, and 1% penicillin/streptomycin. The cell cultures were then placed in a humid environment at 37 °C and 5% CO2.

treatment_protocol: osteogenic differentiation was induced by Low-glucose DMEM with 15% FBS, 10-7mM dexamethasone, 5 mM β-glycerophosphate, 50 µg/mL ascorbic acid.The medium was changed twice a week until the 7th day.

value: Osteogenic differentiation


title: K374_Tumor2_GEX

description: Library name: Sample 3

data_processing:
Cell Ranger analysis pipelines (version 3.0.2, 10X Genomics) were used to process the generated sequencing data
Data was demultiplexed into FASTQ and aligned to the GRCh38 human reference genome and counted
TCR library reads were assembled into single cell V(D)J sequences and annotations
Data normalization, dimension reduction, and differential expression analysis were performed using R version 4.0.5 and the Seurat R package (version 3.2.2)
Samples were integrated using the SCTransform Method (Hafemeister and Satija, 2019, Genome Biol 20:196)
Assembly: GRCh38
Supplementary files format and content: .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR other metadata in the @meta.data field. The .h5ad file contains a Scanpy/Adata object with the count matrix, and the associated metadata in the .obs data field.


title: Osteoclasts, CONTROL1, Day5

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cw1


title: K374_Tumor1_TCR

description: Library name: Sample 2


title: K374_Tumor1_GEX

description: Library name: Sample 1


title: Osteoblasts, VERAPAMIL2, Day7

value: osteoblasts, derived from wildtype mesenchymal stem cells


title: LUAD-14C

city: Houston

first: Linghua

last: Wang

address: 1881 East Road,

institute: MD Anderson Cancer Center

description: Library name: LUAD-14C

data_processing:
METI takes spatial gene expression and histology image data as input. The ST gene expression data contains an N × M matrix of unique molecular identifier (UMI) counts, where N denotes the number of spots and M represents the number of genes. Each spot is associated with 2-dimensional spatial coordinates denoted as (x, y). The gene expression values for each spot are normalized by dividing the UMI count of each gene within that spot by the overall UMI count of all genes in the same spot. The result is then scaled up by a factor of 10,000 and converted to a natural logarithm scale.
Supplementary files format and content: Matrix
Supplementary files format and content: Matrix
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Two to three consecutive tissue sections of 5-μm thickness were collected for RNA extraction with the Qiagen RNeasy FFPE Kit.
The Visium spatial gene expression FFPE libraries were constructed using the Visium CytAssist Spatial Gene Expression for FFPE Human Transcriptome Probe Kit (PN-1000444) following the manufacturer's guidance

value: Lung


title: Osteoclasts, CONTROL2, Day5

description:
RNA seq of osteoclast differentiated from WT mouse bone marrow-derived macrophages
cw2


title: Osteoblasts, VERAPAMIL1, Day7


title: Osteoblasts, CONTROL1, Day7


title: 20230217_hpap_8_Pool_Well5_HTO, HTO derived library.

city: Philadelphia

first: Vincent

last: Wu

state: PA

address: 402 Johnson Pavilion

department: Microbiology

institute: University of Pennsylvania

description: Library name: 20230217_hpap_8_Pool_Well5_HTO

data_processing:
Raw BCL files were converted to fastq files using either cellranger mkfastq (for RNA) or bcl2fastq (for ADT/HTO)
For RNA, fastq files were aligned to hg38, counted, and filtered for QC using cellranger count.
For ADT/HTO, fastq files were aligned to ADT or HTO catalog references. Alignments were barcode corrected and counted as part of the kallisto bustools pipeline (KITE; see https://github.com/betts-lab/scc-proc for snakemake pipeline).
Assembly: hg38
Supplementary files format and content: RNA: tar.gz archive of cellranger output (matrix.tsv.gz, features.tsv.gz, barcodes.tsv.gz). ADT/HTO: tar.gz archive of kallisto bustools output (output.genes.txt, output.mtx, output.barcodes.txt)
Library strategy: CITE-seq

molecule: protein

source_name: mononuclear cells

extract_protocol:
Pooled samples were placed through the 3' scRNAseq v3.1 pipeline (10X Genomics) to generate single cell partitions sharing cDNA, antibody derived tag, and hashing antibody barcodes. Each well of a 10X chip was superloaded with ~1.75X manufacturer's recommended maximum cell count. cDNA extract protocol followed manufacturer's instructions. To extract antibody derived tag and hashing tag sequences, the supernatant from cDNA Cleanup - SPRIselect (Step 2.3d in Protocol CG000315 Rev C, or equivalent step) was saved for further processing following the standard CITEseq protocol (https://cite-seq.com/protocols/).
Dual indexed cDNA libraries were generated following manufacturer's instructions (10X Genomics Protocol CG000315 Rev C, or equivalent for high-throughput protocols). Dual indexed antibody derived tag and hashing tag libraries were generated following standard CITEseq protocol (https://cite-seq.com/protocols/) using primers recommended from Biolegend. Antibody derived tag and hashing tag sequences were enriched in the initial cDNA amplification step of the 3' scRNAseq v3.1 protocol via addition of additive primers (https://cite-seq.com/protocols/).

treatment_protocol: All samples were thawed from -150℃ cryopreservation. Individual tubes were gently shaken in a 37℃ water bath until the frozen cells were partially thawed. Cells were then quickly resuspended in at least 14 mL cold R10 + DNAse (RPMI-1640 supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin in the presence of 10 U/mL DNAse I) and spun down at 500 xg to pellet. The cell pellet was resuspended in R10 + DNase I and counted. Cells were then rested at 2E6 cells/mL in R10 + DNAse I for 2 hours. After resting, cells were washed in cold Cell Staining Buffer (Biolegend) 2 times, filtered through a 70 um filter, and counted. 5E5 cells from each sample were incubated with Human TruStain FcX (Biolegend) at 4℃ for 10 min at the manufacturer's recommended concentration of 10E6 cells/mL. Then, each individual sample was incubated with a unique TotalSeq-A compatible Hashing Antibody (Biolegend) at 0.5 ug antibody at 11.8E6 cells/mL. Then, samples were incubated with the TotalSeq-A Universal cocktail (Biolegend #399907) according to manufacturer's instructions. Samples were washed 3X with Cell Staining Buffer and counted. Cells from each sample were then pooled, concentrated to 2000 cells/uL, and filtered through a 40 um FlowMi filter (Bel-Art).

value: mononuclear cells

tag: individuals and_tissues

tag: run number


title: K415_Tumor_GEX

description: Library name: Sample 5

source_name: melanoma, skin metastasis

value: melanoma, skin metastasis

tag: cell type

value: Cells were sort-purified as live, singlet, CD45+CD3+CD4-CD8+ and loaded into a single channel


title: Osteoblasts, CONTROL3, Day7


title: 20230217_hpap_8_Pool_Well3_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well3_HTO


title: Total RNA, Siwi Kd, rep2

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

institute: The University of Tokyo

description: Library name: Total-RNA_Siwi-Kd_rep2

data_processing:
Raw reads were cleaned; adaptor sequences were removed using Rcorrector (version 1.0.6) (Song and Florea 2015), TranscriptomeAssemblyTools (https://github.com/harvardinformatics/TranscriptomeAssemblyTools), and TrimGalore (https://github.com/FelixKrueger/TrimGalore); and reads shorter than 36 nt were discarded. The reads were mapped against the p50T.SilkBase and remapped against the silkworm gene library using STAR (version 2.7.11a) (Dobin et al. 2012) in unique counting modes, allowing up to 4% mismatch relative to the read length. Gene-mapped reads were processed using SAMtools (version 1.19) (Li et al. 2009). The reads mapped to the sense direction were normalized against the number of genome-mapped reads to RPKM, with the addition of a pseudo-count for log transformation and FC calculation.
Assembly: the Bombyx mori genome assembly (Nov 2016) (Kawamoto et al. 2019) from the SilkBase database
Supplementary files format and content: Tab-separated text files contain the normalized read counts (RPKM) mapped against  the silkworm gene library in the sense direction.

organism: Bombyx mori

growth_protocol: B.mori ovary-derived cultured germ cells (BmN4 cells) were cultured in EX-CELL 420 serum-free medium for insect cells (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1× penicillin-streptomycin-glutamine (Gibco) at 37°C and with 5% CO2.

extract_protocol:
Total RNAs were isolated using ISOGEN II (FUJIFILM Wako Pure Chemical) and treated with DNase (Life Technologies) followed by phenol/chloroform treatment, and precipitated with ethanol.
RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with the Ribo-Zero Plus rRNA Depletion Kit (Human/Mouse/Rat) (Illumina) and sequenced on the NovaSeq platform (Illumina) to obtain paired-end reads.

treatment_protocol: To deplete endogenous proteins, the cells (1×10^6 cells) suspended in 100 μL of EP buffer [2.1 mM HEPES-KOH (pH 7.1), 137 mM NaCl, 5 mM KCl, and 0.5 mM Na2HPO4] were transfected with 500 pmol siRNA duplex by electroporation with Nucleofector 2b (Lonza). Luciferase (Luc) siRNA was used as a control.

value: Cultured germ cell derived from ovary

value: RNAi


title: Osteoblasts, CONTROL2, Day7


title: 20230217_hpap_8_Pool_Well2_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well2_HTO


title: 20230217_hpap_8_Pool_Well8_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well8_HTO


title: Total RNA, Siwi Kd, rep3

description: Library name: Total-RNA_Siwi-Kd_rep3


title: K415_Tumor_TCR

description: Library name: Sample 6


title: Total RNA, Siwi Kd, rep1

description: Library name: Total-RNA_Siwi-Kd_rep1


title: 20230217_hpap_8_Pool_Well1_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well1_HTO


title: 20230217_hpap_8_Pool_Well7_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well7_HTO


title: Total RNA, Luc Kd, rep3

description: Library name: Total-RNA_Luc-Kd_rep3


title: 20221004_hpap_7_Pool_Well8_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well8_HTO


title: Total RNA, Luc Kd, rep2

description: Library name: Total-RNA_Luc-Kd_rep2


title: Total RNA, Luc Kd, rep1

description: Library name: Total-RNA_Luc-Kd_rep1


title: 20221004_hpap_7_Pool_Well7_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well7_HTO


title: osnat10.RNAseq.b3

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: osnat10 RNA-seq replicate 3

data_processing:
Reads were mapped against the rice (IRGSP-1.0) genome with STAR (v 2.5.3a).
Assembly: IRGSP-1.0
Supplementary files format and content: Bigwig files were generated using bamCompare from deeptools; Scores represent Counts Per Million mapped reads (CPM); Scores of Input were subtracted from that of IP. Differentially expressed genes were analyzed using DESeq2.

organism: Oryza sativa

source_name: Seedlings

growth_protocol: Wild type rice and osnat10 plants were grown on Yoshida solution in a growth chamber under short-day (SD) conditions (10 h light/14 h dark) with a light intensity of 800 mmol m-2 s -1.

extract_protocol:
For acRIP-seq, seedlings were homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA was fragmented and isolated with ac4C antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. acRIP-seq libraries were prepared according to Arango, D. et al., Cell, 2018. Briefly, RNA was converted to final cDNA libraries in accordance with a dUTP dependent strand-specific library preparation. Libraries were sequenced on the Illumina Hiseq 4000 platform as single-end 150 bp reads.

value: Seedlings

tag: genotype


title: 20221004_hpap_7_Pool_Well6_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well6_HTO


title: 20221004_hpap_7_Pool_Well5_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well5_HTO


title: osnat10.RNAseq.b2

description: osnat10 RNA-seq replicate 2


title: 20230217_hpap_8_Pool_Well6_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well6_HTO


title: WT.RNAseq.b3

description: Wild type rice RNA-seq replicate 3

value: Kitaake


title: 20230217_hpap_8_Pool_Well4_HTO, HTO derived library.

description: Library name: 20230217_hpap_8_Pool_Well4_HTO


title: osnat10.RNAseq.b1

description: osnat10 RNA-seq replicate 1


title: 20221004_hpap_7_Pool_Well1_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well1_HTO


title: 20221004_hpap_7_Pool_Well4_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well4_HTO


title: 20221012_hpap_6_Pool_Well8_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well8_HTO


title: 20221004_hpap_7_Pool_Well3_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well3_HTO


title: 20221004_hpap_7_Pool_Well2_HTO, HTO derived library.

description: Library name: 20221004_hpap_7_Pool_Well2_HTO


title: WT.RNAseq.b1

description: Wild type rice RNA-seq replicate 1


title: osnat10.ac4C.IP.b2

description: osnat10 ac4C IP replicate 2

tag: rip antibody

value: ac4C (abcam, ab252215)


title: osnat10.ac4C.IP.b1

description: osnat10 ac4C IP replicate 1


title: 20221012_hpap_6_Pool_Well4_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well4_HTO


title: WT.ac4C.IP.b2

description: Wild type rice ac4C IP replicate 2


title: osnat10.ac4C.Input.b2

description: osnat10 input replicate 2


title: 20221012_hpap_6_Pool_Well6_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well6_HTO


title: WT.ac4C.IP.b1

description: Wild type rice ac4C IP replicate 1


title: 20221012_hpap_6_Pool_Well5_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well5_HTO


title: osnat10.ac4C.Input.b1

description: osnat10 input replicate 1


title: 20221012_hpap_6_Pool_Well7_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well7_HTO


title: 20221012_hpap_6_Pool_Well2_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well2_HTO


title: 20221012_hpap_6_Pool_Well3_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well3_HTO


title: WT.ac4C.Input.b2

description: Wild type rice input replicate 2


title: 20221012_hpap_6_Pool_Well1_HTO, HTO derived library.

description: Library name: 20221012_hpap_6_Pool_Well1_HTO


title: WT.ac4C.Input.b1

description: Wild type rice input replicate 1


title: W625_66B

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 East 60th St N

institute: Sanford Research

description:
Library name: Sample 8
Cortical sample from wildtype animal 625_66

data_processing:
trimming with Cutadapt
mappping with RNA star
read counts measured with featureCounts
Differential gene expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: Excel files containing the results of the DESeq2 DEG analysis and DESeq2 normalized read counts

source_name: 3-month cortex

extract_protocol:
TRIzol – Chloroform-Isopropanol protocol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: 3-month cortex

value: Wildtype


title: WT.RNAseq.b2

description: Wild type rice RNA-seq replicate 2


title: 20220923_hpap_5_Pool_Well7_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well7_HTO


title: W619_38B

description:
Library name: Sample 7
Cortical sample from wildtype animal 619_93


title: W607_96B

description:
Library name: Sample 6
Cortical sample from wildtype animal 607_96


title: 20220923_hpap_5_Pool_Well6_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well6_HTO


title: W607_95B

description:
Library name: Sample 5
Cortical sample from wildtype animal 607_95


title: 20220923_hpap_5_Pool_Well5_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well5_HTO


title: H625_65B

description:
Library name: Sample 4
Cortical sample from Wdr45 c52 C>T hemizygous animal 625_65

value: Wdr45 c52C>T


title: 20220923_hpap_5_Pool_Well4_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well4_HTO


title: H607_94B

description:
Library name: Sample 3
Cortical sample from Wdr45 c52 C>T hemizygous animal 607_94


title: 20220923_hpap_5_Pool_Well2_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well2_HTO


title: 20220923_hpap_5_Pool_Well1_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well1_HTO


title: 20220801_hpap_4_Pool_Well8_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well8_HTO


title: H607_92B

description:
Library name: Sample 2
Cortical sample from Wdr45 c52 C>T hemizygous animal 607_92


title: 20220801_hpap_4_Pool_Well7_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well7_HTO


title: 20220801_hpap_4_Pool_Well5_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well5_HTO


title: 20220801_hpap_4_Pool_Well6_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well6_HTO


title: H607_83B

description:
Library name: Sample 1
Cortical sample from Wdr45 c52 C>T hemizygous animal 607_83


title: E11.5_WT_XX_Nr5a1(+)cells_2

city: Suita

first: Naoki

last: Okashita

address: 1-3 Yamadaoka

institute: Osaka university

description: Library name: Sample12

data_processing:
Sequence reads were aligned using STAR (version 2.7.10b) with following parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --runRNGseed 7 --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMattributes All --quantMode TranscriptomeSAM.
Gene expression was quantified as TPM using rsem-calculateexpression command in RSEM software (version v1.3.1) with following parameters: --estimate-rspd --strandedness reverse --alignments --paired-end.
Statistical analysis and visualization of these data were performed with R software (version 4.1.2).
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each sample

source_name: E11.5 fetal gonads

growth_protocol: Left-right gonads with aorta, mesonephros and mesenchyme of E10.8 embryos were cultured on ISOPORE membrane filters (Millipore) in the medium consisted of 10% horse serum (GIBCO BRL) and DMEM (High Glucose) (Nacalai Tesque Inc.) for 19.2 hours.

extract_protocol:
Total RNA from NR5A1(+) cells was extracted using Direct-zol RNA MicroPrep kit (ZYMO RESEARCH).
The libraries of the samples were prepared using SMART-Seq Stranded Kit (Takara bio.) following manufacturer's  protocol.

treatment_protocol: The tissue was cultured with 150 µM Dfo (Sigma-Aldrich/D9533) added medium for 19.2hour.

value: E11.5 fetal gonads


title: E11.5_WT_XX_Nr5a1(+)cells_1

description: Library name: Sample11


title: E11.5_WT_XY_Nr5a1(+)cells_1

description: Library name: Sample9


title: IVC-Control_XX_Nr5a1(+)cells_2

description: Library name: Sample8

source_name: Cultured fetal gonads

value: Cultured fetal gonads


title: 20220923_hpap_5_Pool_Well8_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well8_HTO


title: 20220801_hpap_4_Pool_Well2_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well2_HTO


title: IVC-Control_XX_Nr5a1(+)cells_1

description: Library name: Sample7


title: IVC-Dfo_XY_Nr5a1(+)cells_3

description: Library name: Sample6

value: Deferoxamine


title: 20220801_hpap_4_Pool_Well3_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well3_HTO


title: 20220801_hpap_4_Pool_Well1_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well1_HTO


title: 20220923_hpap_5_Pool_Well3_HTO, HTO derived library.

description: Library name: 20220923_hpap_5_Pool_Well3_HTO


title: IVC-Dfo_XY_Nr5a1(+)cells_1

description: Library name: Sample4


title: IVC-Control_XY_Nr5a1(+)cells_3

description: Library name: Sample3


title: 20220531_hpap_2_Pool_Run2_Well16_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well16_HTO


title: 20220531_hpap_2_Pool_Run2_Well14_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well14_HTO


title: 20220531_hpap_2_Pool_Run2_Well12_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well12_HTO


title: IVC-Control_XY_Nr5a1(+)cells_1

description: Library name: Sample1


title: E11.5_WT_XY_Nr5a1(+)cells_2

description: Library name: Sample10


title: 20220531_hpap_2_Pool_Run2_Well13_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well13_HTO


title: KPC8069_KO_1

description:
Library name: Sample4
Column name in raw_counts_all_samples: KO1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 v2.0.5 was used for genome alignment.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for all samples

source_name: pancreas

extract_protocol:
Cell RNA was harvested with Qiagen Rneasy mini kit.
ABclonal mRNA Library Prep Kit was used for library preparation.

value: pancreas

value: PDAC

value: HuR KO


title: 20220531_hpap_2_Pool_Run2_Well11_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well11_HTO

value: mononuclear cells


title: 20220801_hpap_4_Pool_Well4_HTO, HTO derived library.

description: Library name: 20220801_hpap_4_Pool_Well4_HTO


title: KPC8069_WT_1

description:
Library name: Sample1
Column name in raw_counts_all_samples: WT1

value: WT


title: 20220531_hpap_2_Pool_Run1_Well2_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well2_HTO


title: KPC8069_KO_2

description:
Library name: Sample5
Column name in raw_counts_all_samples: KO2


title: KPC8069_WT_2

description:
Library name: Sample2
Column name in raw_counts_all_samples: WT2


title: KPC8069_WT_3

description:
Library name: Sample3
Column name in raw_counts_all_samples: WT3


title: 20220531_hpap_2_Pool_Run1_Well5_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well5_HTO


title: 20220119_hpap_1_Pool_A4_HTO, HTO derived library.

description: Library name: 20220119_hpap_1_Pool_A4_HTO


title: MAYV Beh407 infected, ipsilateral foot, CD45negative cells, KO2

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Sample_12_KO2_IF_CD45N_12
10Xgenomics

data_processing:
The fastQ files were submitted to Cell Ranger version 7.0.0 ‘mkref’, ‘mkfastq’ and ‘count’ functions with a custom genome of Mus musculus that contain the viral genome as exons (refdata-gex-mm10-2020-A). Mayaro genome acession number - MK573238.
Assembly: Mus musculus (refdata-gex-mm10-2020-A). Mayaro genome acession number - MK573238.
Supplementary files format and content: Tab-separeted values files and matrix files.

source_name: ipsilateral ankle

growth_protocol: N/A - mice used

extract_protocol:
Four-week-old WT or FcRg−/− C57BL/6N were infected subcutaneous in the rear footpad with 103 FFU of MAYV or mock infected with diluent. At 10 dpi, the ipsilateral foot and surrounding skin was enzymatically digested into a single cell suspension and stained for CD45. Viable CD45+ and CD45- cells were sorted
For the preparation of the cDNA and sequencing library generation, we followed manufacturer instructions from the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual index) User Guide with one modification: primers targeting the non-structural and subgenomic RNA were spiked-in during the cDNA synthesis to capture viral RNA (Step 1.1). The virus-specific primer concentration added to each RT reaction was ~15 pmoles. All the other reagents were added according to the protocol, except the nuclease-free water, which was reduced to accommodate the primer spike-in volume. The Illumina library quality, yield, and size distribution was assessed by TapeStation D1000 high sensitivity assay, and by Qubit High Sensitivity dsDNA kit. The molar concentrations of the libraries were determined and diluted for sequencing according to Illumina sequencing protocol. We aimed to sequence each library to achieve >50,000 reads per cell.

treatment_protocol: MAYV Beh407 or Mock infected.

value: ipsilateral ankle

tag: Sex

value: Male

tag: strain

value: FcRg-/-

value: 1000 FFU MAYV BeH407


title: 20220531_hpap_2_Pool_Run2_Well10_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well10_HTO


title: IVC-Dfo_XY_Nr5a1(+)cells_2

description: Library name: Sample5

tag: tissue


title: 20220119_hpap_1_Pool_A2_HTO, HTO derived library.

description: Library name: 20220119_hpap_1_Pool_A2_HTO


title: 20220531_hpap_2_Pool_Run1_Well1_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well1_HTO


title: Naïve, ipsilateral foot, CD45 positive cells, KO

description:
Library name: Sample_16_Na_ve_KO_F_16
10Xgenomics

value: Mock


title: Naïve, ipsilateral foot, CD45 positive cells, WT

description:
Library name: Sample_15_Na_ve_WT_F_15
10Xgenomics


title: 20220119_hpap_1_Pool_A3_HTO, HTO derived library.

description: Library name: 20220119_hpap_1_Pool_A3_HTO


title: 20220531_hpap_2_Pool_Run2_Well9_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run2_Well9_HTO


title: MAYV Beh407 infected, ipsilateral foot, CD45 positive cells, KO2

description:
Library name: Sample_11_KO2_IF_CD45P_11
10Xgenomics


title: MAYV Beh407 infected, ipsilateral foot, CD45 positive cells, KO1

description:
Library name: Sample_7_KO1_IF_CD45P_7
10Xgenomics


title: 20230217_hpap_8_Pool_Well7_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well7_ADT


title: MAYV Beh407 infected, ipsilateral foot, CD45 negative cells, WT2

description:
Library name: Sample_5_WT2_IP_CD45N_5
10Xgenomics


title: 20230217_hpap_8_Pool_Well8_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well8_ADT


title: 20230217_hpap_8_Pool_Well5_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well5_ADT


title: MAYV Beh407 infected, ipsilateral foot, CD45 positive cells, WT2

description:
Library name: Sample_4_WT2_IP_CD45P_4
10Xgenomics


title: MAYV Beh407 infected, ipsilateral foot, CD45 negative cells, KO1

description:
Library name: Sample_8_KO1_IF_CD45N_8
10Xgenomics


title: 20230217_hpap_8_Pool_Well3_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well3_ADT


title: MAYV Beh407 infected, ipsilateral foot, CD45 negative cells, WT1

description:
Library name: Sample_2_WT1_IP_CD45N_2
10Xgenomics


title: MAYV Beh407 infected, ipsilateral foot, CD45 positive cells, WT1

description:
Library name: Sample_1_WT1_IP_CD45P_1
10Xgenomics


title: 20230217_hpap_8_Pool_Well2_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well2_ADT


title: 20230217_hpap_8_Pool_Well1_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well1_ADT


title: S19_Dorl_ctrol3_Tbx18

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: Library name: S19_Dorl_ctrol3_Tbx18

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.99 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization, considering only those genes for which expression was at least 1 count per million (CPM) in at least 3 samples.
Assembly: GRCm38.99
Supplementary files format and content: Normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 3 samples.

source_name: Dorsal epicardium/subepicardium from Tbx18Cre female hearts

extract_protocol:
The epicardium/subepicardium was dissected as previously described (Lioux et al., 2020) and quickly frozen in separate 1.5 ml Eppendorf tubes on dry ice. For mRNA isolation, samples from at least three different litters were used. As low RNA amount from one single epicardial layer was expected, two dissected epicardia of the same genotype were pooled together. Therefore, the three biological replicates per genotype represent six different hearts pooled by pairs. RNA was then purified from each pool using RNeasy Micro kit (Qiagen 74004).
40 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Briefly, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Next, cDNA 3’ ends were adenylated and the adapters were ligated followed by PCR library amplification. Finally, the size of the libraries was checked using the Agilent 2100 Bioanalyzer DNA 1000 chip and their concentration was determined using the Qubit® fluorometer (Life Technologies). Libraries were sequenced on a HiSeq2500 (Illumina) to generate 60 bases single reads and processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).

treatment_protocol: No treatments were applied to the biological material prior to extraction.

value: Dorsal epicardium/subepicardium

value: female


title: S17_Dorl_ctrol1_Tbx18

description: Library name: S17_Dorl_ctrol1_Tbx18


title: 20221004_hpap_7_Pool_Well8_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well8_ADT


title: 20221004_hpap_7_Pool_Well7_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well7_ADT


title: S8_vtrl_ctrol3_Tbx18

description: Library name: S8_vtrl_ctrol3_Tbx18

source_name: Ventral epicardium/subepicardium from Tbx18Cre female hearts

value: Ventral epicardium/subepicardium


title: S7_vtrl_ctrol2_Tbx18

description: Library name: S7_vtrl_ctrol2_Tbx18


title: S6_vtrl_ctrol1_Tbx18

description: Library name: S6_vtrl_ctrol1_Tbx18


title: 20221004_hpap_7_Pool_Well6_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well6_ADT


title: 20221004_hpap_7_Pool_Well5_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well5_ADT


title: KPC8069_KO_3

description:
Library name: Sample6
Column name in raw_counts_all_samples: KO3


title: S8_VC_ventral_ctrol7_Tbx18_macho

description: Library name: S8_VC_ventral_ctrol7_Tbx18_macho

source_name: Ventral epicardium/subepicardium from Tbx18Cre male hearts

value: male


title: 20221004_hpap_7_Pool_Well3_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well3_ADT


title: S6_VC_ventral_ctrol5_Tbx18_macho

description: Library name: S6_VC_ventral_ctrol5_Tbx18_macho


title: 20230217_hpap_8_Pool_Well4_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well4_ADT


title: S5_VC_ventral_ctrol4_Tbx18_macho

description: Library name: S5_VC_ventral_ctrol4_Tbx18_macho


title: 20221004_hpap_7_Pool_Well1_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well1_ADT


title: S4_VC_dorsal_ctrol7_Tbx18_macho

description: Library name: S4_VC_dorsal_ctrol7_Tbx18_macho

source_name: Dorsal epicardium/subepicardium from Tbx18Cre male hearts


title: 20221004_hpap_7_Pool_Well2_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well2_ADT


title: S3_VC_dorsal_ctrol6_Tbx18_macho

description: Library name: S3_VC_dorsal_ctrol6_Tbx18_macho


title: 20221012_hpap_6_Pool_Well8_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well8_ADT


title: S18_Dorl_ctrol2_Tbx18

description: Library name: S18_Dorl_ctrol2_Tbx18


title: 20221012_hpap_6_Pool_Well7_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well7_ADT


title: S2_VC_dorsal_ctrol5_Tbx18_macho

description: Library name: S2_VC_dorsal_ctrol5_Tbx18_macho


title: IVC-Control_XY_Nr5a1(+)cells_2

description: Library name: Sample2


title: 20221012_hpap_6_Pool_Well6_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well6_ADT


title: 20220531_hpap_2_Pool_Run1_Well6_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well6_HTO


title: 20221012_hpap_6_Pool_Well5_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well5_ADT


title: 20221012_hpap_6_Pool_Well3_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well3_ADT


title: 20220531_hpap_2_Pool_Run1_Well8_HTO, HTO derived library.

description: Library name: 20220531_hpap_2_Pool_Run1_Well8_HTO


title: Fetal liver, p-STAT3, ChIP, rep2

city: Suzhou

first: Wen

last: Wei

state: Jiangsu Province

address: No. 199, Ren Ai Road

institute: Soochow University

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.001 as cutoff
Assembly: mm10
Supplementary files format and content: narrowPeak  file were generated using MACS2(2.2.7.1) (except for Input sample)

source_name: E14.5 mouse fetal liver

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: E14.5 mouse fetal liver

tag: chip antibody


title: 20230217_hpap_8_Pool_Well6_ADT, ADT derived library.

description: Library name: 20230217_hpap_8_Pool_Well6_ADT


title: 20221004_hpap_7_Pool_Well4_ADT, ADT derived library.

description: Library name: 20221004_hpap_7_Pool_Well4_ADT


title: Fetal liver, Input, rep1


title: 20221012_hpap_6_Pool_Well4_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well4_ADT


title: S7_VC_ventral_ctrol6_Tbx18_macho

description: Library name: S7_VC_ventral_ctrol6_Tbx18_macho


title: 20221012_hpap_6_Pool_Well2_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well2_ADT


title: Gli2CA + ETC159 Replicate 2 scRNAseq

city: Durham

first: Nicholas

last: DeVito

state: NC

address: 308 Research Drive

institute: Duke University

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the CellRanger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz

source_name: CD45+ cells from tumor

growth_protocol: see manuscript

extract_protocol:
Tumors were mechanically and enzymatically digested, CD45+ cells were selected by magnetic selection using the miltenyi biotec. Fllowing magentic selection, cells were washed and resuspended in 0.04% BSA in PBS prior to cell partitioning and library prep.
Libraries were constructed using 10x Genomics default protocols following the Next GEM Chromium 3' GEX v3.1

treatment_protocol: see manuscript

value: CD45+ cells from tumor

tag: treatment


title: Gli2CA + ETC159 Replicate 1 scRNAseq


title: 20221012_hpap_6_Pool_Well1_ADT, ADT derived library.

description: Library name: 20221012_hpap_6_Pool_Well1_ADT


title: Gli2CA + TPST1495 Replicate 2 scRNAseq


title: S1_VC_dorsal_ctrol4_Tbx18_macho

description: Library name: S1_VC_dorsal_ctrol4_Tbx18_macho


title: 20220923_hpap_5_Pool_Well6_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well6_ADT


title: Gli2CA Replicate 1 scRNAseq

value: IgG


title: Fetal liver, p-STAT3, ChIP, rep1


title: 20220923_hpap_5_Pool_Well7_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well7_ADT


title: Gli2CA + TPST1495 Replicate 1 scRNAseq


title: NTC Replicate 2 scRNAseq


title: 20220923_hpap_5_Pool_Well4_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well4_ADT


title: 20220923_hpap_5_Pool_Well5_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well5_ADT


title: Gli2CA Replicate 2 scRNAseq


title: 20220923_hpap_5_Pool_Well1_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well1_ADT


title: 20220923_hpap_5_Pool_Well3_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well3_ADT


title: Gli2CA Tumor DC3

data_processing:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (NEBNext Ultra™ II RNA Library Prep Kit). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on a Novaseq 6000 (Illumina), according to effective library concentration and data amount. Twenty million reads per sample were acquired at PE150 depth.
Assembly: grcmm39
Supplementary files format and content: xlsx FPKM

source_name: tumor

growth_protocol: NTC and Gli2CA cells were grow in DMEM 10% FBS with 1x AA and 1 ug/mL of puromycin. These were implanted at 1e6 cells per 100 uL (1:1 with matrigel:pbs) into c57 bl/6 mice, and whole tumors were harvested at day d28

extract_protocol:
Tumors were taken at the time of experiment termination and digested in RPMI with collagenase (1 g/100mL HBSS, 10x stock solution, Sigma- Aldrich, C-5138) and DNase (20,000 U/100mL HBSS, 10x stock solution, Sigma-Aldrich, D-5025) at 37°C at 250 rpm in 15 mL conical tubes for 15 minutes. Tumors were processed through a 40 mM cell strainer (Corning, 431750) and CD11c selection was performed using FACS sorting (Sony DH800 Sorter). Selected cells were washed with PBS and lysed with RLT PLUS (QIAGEN, 1053393) with b-mercaptoethanol (VWR, VWRV0482-250ML). RNA was isolated using the RNAeasy Plus Micro kit (QIAGEN, 74034) per the manufacturer’s instructions.
NEBNext Ultra™ II RNA Library Prep Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: tumor

value: dendritic cells


title: 20220801_hpap_4_Pool_Well8_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well8_ADT


title: 20220923_hpap_5_Pool_Well8_ADT, ADT derived library.

description: Library name: 20220923_hpap_5_Pool_Well8_ADT


title: 20220801_hpap_4_Pool_Well7_ADT, ADT derived library.

description: Library name: 20220801_hpap_4_Pool_Well7_ADT


title: NTC tumor DC3

value: NTC