title: AE9a c-kit+ bone marrow cells, C16, rep-1

description: Library name: AE1C16

value: Bone marrow

value: cKit+ bone marrow


title: S14/THP-1_SW620 CM_rep 1

status: Public on Nov 18 2025

type: SRA

city: Taipei

first: Yung-Chi

last: Chang

address: Rm 736, No. 1, Sec. 1, Jei-Ai Rd

department: Microbiology

country: Taiwan

institute: National Taiwan University, College of Medicine

description: Library name: Sample 16

library_source: transcriptomic

data_processing:
Sequencing data were trimmed using Fastp
Assembly: The processed reads were aligned to the human reference genome (GRCh38) using HISAT2 to generate the expression profile
Supplementary files format and content: excel file include counts and TPM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: THP-1-derived macrophage

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 10 mM HEPES, 1 mM sodium pyruvate, 2.5g/L glucose and 0.05 mM 2-mercaptoethanol.

extract_protocol:
Total cellular RNA was extracted using NucleoZol reagent (Macherey-Nagel). 1 mg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA library prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: THP‐1 cells (106 cells/ml) were treated with 100 nM phorbol 12‐myristate 13‐acetate (PMA) for 24 h to induce differentiation into macrophage. THP‐1 cells (106 cells/ml) were treated with 100 nM phorbol 12‐myristate 13‐acetate (PMA) for 24 h to induce differentiation into macrophage.

tag: cell line

value: THP-1-derived macrophage

tag: cell type

value: human monocytic cell line

tag: genotype

value: expressing Siglec-14

tag: treatment

value: 50% SW620 conditioned medium


title: S5/THP-1_SW620 CM_rep 3

description: Library name: Sample 15

value: expressing Siglec-5


title: S14/THP-1_SW620 CM_rep 2

description: Library name: Sample 17


title: S5/THP-1_SW620 CM_rep 1

description: Library name: Sample 13


title: EV/THP-1_SW620 CM_rep 3

description: Library name: Sample 12

value: empty vector control


title: S14/THP-1_SW620 CM_rep 3

description: Library name: Sample 18


title: S5/THP-1_SW620 CM_rep 2

description: Library name: Sample 14


title: EV/THP-1_SW620 CM_rep 1

description: Library name: Sample 10


title: EV/THP-1_SW620 CM_rep 2

description: Library name: Sample 11


title: S14/Mock_rep 3

description: Library name: Sample 9

value: mock


title: Aurka inh_1

status: Public on Nov 19 2025

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

country: Switzerland

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

data_processing:
RNA sequencing reads were aligned to the mouse genome mm10 with STAR aligner with input parameters “--outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts”. Raw counts were extracted from the STAR output using customed script. Principal component analysis and differential expression analysis was performed with raw counts using the R package DESeq2. Genes were considered as deregulated if |log2FC|> 1 and FDR < 0.01 using Benjamini-Hochberge multiple test adjustment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts for each samples
Supplementary files format and content: tab-delimited text files with normalized counts for each samples

organism: Mus musculus

source_name: cell line

growth_protocol: ES cell lines were maintained in the presence of 2i/Lif (0.4 µM PD0325901, 3 µM CHIR99021 and 4 ng/ml Lif), on plastic dishes coated with 0.2% gelatin and passaged at 1:6 ratio using 0.25% Trypsin-EDTA

extract_protocol:
RNA was isolated from cells using the NucleoSpin RNA isolation kit following the manufacturer’s protocol. Samples with RNA integrity number (RIN) above 7 from 1 μg of total RNA were used further.
The mRNA enrichment performed using NEBNext Poly(A) mRNA Magnetic Isolation Module and cDNA library was prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: ES cells were resuspended in matrigel (2000 cells per 1 µl of matrigel) and plated on petri dishes. To solidify the hydrogel, the plate was placed for 5-10 min in a cell culture incubator at 37°C, 5% CO2 atmosphere in air. After that, each well was filled with N2B27 medium supplemented with single or combination of inhibitors inhibitors, 2iLif, FAK, Aurka inh, PD032 or PD032+ Aurka inh.  To isolate ESCs cultured in Matrigel, the Matrigel was incubated in a 1:2 (v/v) mixture of 0.25% trypsin-EDTA and Accutase for 20 min in a cell culture incubator at 37°C, 5% CO2 atmosphere in air. The Matrigel was then broken into pieces by twice manual pipetting. Cells were pelleted by centrifugation (1000rpm/5 min), and the pellet was washed once with PBS.

tag: tissue

value: cell line

value: embryonic stem cells

value: WT

value: E14 ES cells grown in growth factor reduced matrigel


title: NIH03, control, snMultiome [ATAC]

city: Houston

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St.

country: USA

institute: The University of Texas Health Science Center at Houston

description: 10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger ARC (v2.0.2) pipeline was used for aligning the snRNA-seq and snATAC-seq reads from each sample to the GRCh38 genome and quantifying them with ‘cellranger-arc count’.
Assembly: GRCh38
Supplementary files format and content: CellRanger-arc output files: raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

molecule: genomic DNA

source_name: Hippocampus

extract_protocol:
Samples were stored at -80 °C. The nuclei isolation protocol was modified based on a 10x Genomics protocol (CG000375). Briefly, 30 mg of frozen tissue was finely minced on dry ice to the smallest possible size, and then it was homogenized in homogenization buffer on ice within 20 minutes. The homogenized tissue was filtered through a 35 μm cell strainer. Small cell debris were removed by centrifuging at 300g for 3 minutes at 4 °C. The large cell debris was removed by gradient centrifugation using OptiPrep density gradient medium (Sigma, cat#D1556-250ML) at 7200g for 15 minutes at 4 °C. The nuclei pellet was resuspended in a 0.1x lysis buffer. After washing the isolated nuclei in the wash buffer, the nuclei were resuspended in 1x nuclei buffer before single-nuclei Multiome library construction. (UTHealth Cancer Genomic Core)
single-nuclei Multiome sequencing; Single-nuclei libraries were constructed following the 10x Chromium Single Cell Multiome ATAC + Gene Expression protocol (CG000338).

value: Hippocampus

tag: disease state

value: Control

tag: Sex

value: M

tag: age on_death

tag: pmi (hours)


title: S14/Mock_rep 1

description: Library name: Sample 7


title: S5/Mock_rep 3

description: Library name: Sample 6


title: EV/Mock_rep 3

description: Library name: Sample 3


title: S5/Mock_rep 2

description: Library name: Sample 5


title: AE9a c-kit+ bone marrow cells, RE, rep-1

city: Shanghai

first: jiaying

last: xie

address: Dongfang Road

country: China

institute: Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: AE1RE

data_processing:
Raw sequencing reads were quality checked using FastQC (v0.11.9). Adapter and low-quality bases were trimmed using fastp (v0.23.2) with default parameters.
Reads were aligned to the Mouse reference genome (GRCm39) using HISAT2 (v2.1.0) with default settings.
Gene-level counts were obtained using featureCounts (v2.0.3) from the Subread package and TPM was calculated. Only uniquely mapped reads were counted. Raw counts were used for downstream differential expression analysis with DESeq2. No additional normalization was performed for the deposited data.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA extraction was performed by the sequencing service provider (Geneplus technology) using their standard protocols. RNA quality control metrics  were confirmed prior to library construction
RNA-seq library preparation and sequencing were performed by  the sequencing service provider (Geneplus technology, Gene+) following their in-house protocols for MGI platforms

value: RE


title: EV/Mock_rep 1

description: Library name: Sample 1


title: EV/Mock_rep 2

description: Library name: Sample 2


title: VP161 rich media 1

city: Clayton

first: Thomas

middle: R

last: Smallman

state: Victoria

address: 19 Innovation walk

country: Australia

institute: Monash University

description: Library name: L01_VP161_in1_S1_L001_R1_001.fastq.gz

library_source: genomic

data_processing:
Reads quality control checked using FastQC v0.11.9. Checked for presence of the transposon tag in the first 10 bases, and then random genomic DNA afterwars.
Reads were trimmed to remove any adapter sequences using Trimmomatic v0.39
TraDIS data analysis was performed using the Bio-TraDIS toolkit (v1.4.5) (https://github.com/sanger-pathogens/Bio-Tradis). Reads were mapped to the genome using the bacteria_tradis using smalt as the mapper and allowing multimapping reads to be mapped randomly. Insertion site data was combined with the annotation using the tradis_gene_insert_sites, trimming reads in the final 10% of the gene for the rich media analysis, and essential genes identified using tradis_essentiality.R.
Genes important for fitness were identified using tradis_comparison.R (github.com/francesca-short/tradis_scripts).
Assembly: GCF_011390865.1 for VP161 and GCA_002083265.2 for M1404
Supplementary files format and content: Table containing all output data from the Bio-TraDIS pipeline and tradis_comparison.R scripts, shows the number of unique and total insertions per gene, as well as essentiality and fitness calls for all genes.

organism: Pasteurella multocida

source_name: Rich media

growth_protocol: Cells were grown in heart infusion broth overnight, then subcultured into fresh heart infusion broth and grown until mid-exponential phase. Cells were then injected intrapertioneally into BALB/c mice, and when mice reached the humane end point, cells were recovered from the bloodstream by heart puncture, or recovered from the liver and spleen by crushing the tissues in 1 x PBS. Cells were then plated onto heart infusion agar plates and grown overnight.

extract_protocol:
Genomic DNA was extracted using the HiYield Genomic DNA Mini Kit (Real Biotech Corporation) as per the manufacturer's instructions for extraction from Gram-negative bacteria
Genomic DNA was fragmented to ~300 bp using Covaris sonication. The fragment DNA was end-repaired and A-tailed before adapters were ligated onto all fragments. Amplification of transposon-chromosome junctions was performed using Kapa HiFi HotStart ReadyMix, a transposon-specific primer and an adapter-specific primer.

treatment_protocol: No additional treatments

value: Rich media

value: Systemic infection in BALB/c mice

tag: batch


title: CC, day14, graft9

city: New Haven

first: Ryland

last: Mortlock

state: Connecticut

address: 15 York Street, HRT 618C

institute: Yale University

description:
Library name: graft9_d14
Samplename in gene count matrix: graft9_d14

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA3) software.
Primary analysis - sample de-multiplexing and alignment to the human genome - is performed using Illumina's CASAVA 1.8.2 software suite bcl2fastq2/2.20.0-GCCcore-10.2.0.
Assembly: hg38
Supplementary files format and content: gene_count_matrix.csv contains raw, integer read counts for all samples.

source_name: Cultured primary keratinocytes

growth_protocol: After the first passage, keratinocytes were maintained in EpiLife serum-free medium with medium changes every other day. Cultures were passaged at 50-70% confluence.

extract_protocol:
RNA was isolated from 30 mg pieces of each graft using the Qiagen AllPrep DNA/RNA kit and quality was confirmed by measuring RNA concentration and absorbance ratios A260/A230 and A260/A280 using the NanoDrop spectrophotometer.
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352).  Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: After two days in submerged culture, the collagen plugs were lifted onto sterile metal scaffolds and maintained at an air-liquid interface in 6 cm plates with the bottom of the plug exposed to E-medium without EGF. The collagen grafts were then harvested at three different timepoints (3 days, 7 days, and 14 days) measured from when the plug was lifted to the air-liquid interface. To generate HEEs, primary human keratinocytes were seeded onto 1 x 1 cm square pieces of dermis at a cell concentration matching that of the collagen-based model. The constructs were cultured at an air-liquid interface using a sterile metal scaffold and harvested at day three and day seven from seeding.

value: Cultured primary keratinocytes

tag: matrix

value: Contracted collagen


title: CC, day14, graft7

description:
Library name: graft7_d14
Samplename in gene count matrix: graft7_d14


title: CC, day7, graft5

description:
Library name: graft5_d7
Samplename in gene count matrix: graft5_d7


title: CC, day7, graft4

description:
Library name: graft4_d7
Samplename in gene count matrix: graft4_d7


title: ACD, day7, graft6

description:
Library name: ACD_graft6_d7
Samplename in gene count matrix: ACD_graft6_d7

value: Acellular dermis


title: CC, day3, graft3

description:
Library name: graft3_d3
Samplename in gene count matrix: graft3_d3


title: ACD, day3, graft2

description:
Library name: ACD_graft2_d3
Samplename in gene count matrix: ACD_graft2_d3


title: ACD, day7, graft4

description:
Library name: ACD_graft4_d7
Samplename in gene count matrix: ACD_graft4_d7


title: ACD, day3, graft3

description:
Library name: ACD_graft3_d3
Samplename in gene count matrix: ACD_graft3_d3


title: ACD, day7, graft5

description:
Library name: ACD_graft5_d7
Samplename in gene count matrix: ACD_graft5_d7


title: ACD, day3, graft1

description:
Library name: ACD_graft1_d3
Samplename in gene count matrix: ACD_graft1_d3


title: S14/Mock_rep 2

description: Library name: Sample 8

value: THP-1-derived macrophage

value: human monocytic cell line

value: expressing Siglec-14


title: NBH_58-27_120dpi

city: Hamilton

first: cathryn

last: haigh

state: MT

address: 903 S 4th St

institute: NIAID

description:
Library name: NBH_58-27_120dpi
10x Genomics single-cell gene expression

library_source: transcriptomic single cell

data_processing:
Illumina BCL files were converted to FASTQ using bcl2fastq v2.20. Alignment, barcode and UMI processing, and gene counting were performed with Cell Ranger v7.1 (10x Genomics) using the human reference genome GRCh38 (GENCODE v43 annotation). Filtered gene-cell count matrices were generated for downstream analysis. Cell-level data were explored in Loupe Browser (10x Genomics) for clustering and differential expression.
Assembly: GRCh38 (GENCODE v43)
Supplementary files format and content: HDF5 (.h5) files contain filtered gene-cell count matrices (cells × genes) generated by 10x Genomics Cell Ranger, including barcodes, features, and UMI counts per cell.
Supplementary files format and content: FASTQ (.fastq.gz) files contain raw paired-end sequencing reads (Read 1 = cDNA sequence; Read 2 = cell barcode + UMI; I1/I2 = sample index reads).

molecule: polyA RNA

source_name: Cerebrum

growth_protocol: Human induced pluripotent stem cells (hiPSCs) were cultured under feeder-free conditions and differentiated into undirected human cerebral organoids (HuCOs) following established protocols. Organoids were maintained in spinning bioreactors at 37 °C with 5 % CO₂. Culture medium was exchanged every 3–4 days until the desired developmental stage (approximately 120 or 180 days post-infection) was reached.

extract_protocol:
Organoids were washed in PBS and enzymatically dissociated into single-cell suspensions using Accutase or papain digestion. Cell viability (> 85 %) was verified before loading into the 10x Genomics Chromium Controller. Single cells were encapsulated in Gel Bead-in-Emulsions (GEMs) for downstream reverse transcription and barcoding.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 according to the manufacturer’s protocol. cDNA was amplified, fragmented, end-repaired, A-tailed, and adaptor-ligated. Indexed libraries were quantified by Qubit, quality-controlled by Bioanalyzer, pooled, and sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: HuCOs were divided into experimental infection groups (MV1 and MV2) and uninfected controls (NBH). MV1 and MV2 organoids were infected for 5 months prior to harvest. Samples were collected at approximately 120 days post-infection (dpi) and 180 dpi to assess temporal differences in infection and host response. Control NBH organoids were cultured in parallel under identical conditions without viral exposure.

value: Cerebrum

value: Organoid


title: MV1_17-09_120dpi

description:
Library name: MV1_17-09_120dpi
10x Genomics single-cell gene expression


title: MV2_21-09_120dpi

description:
Library name: MV2_21-09_120dpi
10x Genomics single-cell gene expression


title: MV2_21-16_120dpi

description:
Library name: MV2_21-16_120dpi
10x Genomics single-cell gene expression


title: MV1_17-05_120dpi

description:
Library name: MV1_17-05_120dpi
10x Genomics single-cell gene expression


title: S5/Mock_rep 1

description: Library name: Sample 4

value: expressing Siglec-5

value: mock


title: HepG2 RNA-seq, siControl, replicate 2

city: La Jolla

first: Sonia

last: Sharma

state: CA

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute of Immunology

description: Library name: HEPG2_siControl_2

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

source_name: Liver

growth_protocol: HEPG2 cells (ATCC) were maintained in EMEM supplemented with 10% heat-inactivated FBS and 100 U mL⁻¹ penicillin–streptomycin at 37 °C, 5% CO₂, and saturated humidity. Cells were kept between ~30–80% confluence and routinely passaged with Trypsin-EDTA to maintain healthy growth.

extract_protocol:
Total RNA was isolated using the Quick-RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions [with on-column DNase treatment]. RNA quantity was measured by spectrophotometry/fluorometry, and integrity was assessed (Bioanalyzer/TapeStation); only high-quality RNA was used for library prep.
mRNA was enriched by poly(A) selection [or: rRNA depletion—select one], fragmented, and converted to cDNA. Sequencing adapters were ligated and libraries PCR-amplified per the manufacturer’s instructions (kit: [e.g., Illumina TruSeq Stranded mRNA]). Libraries were pooled and sequenced as paired-end reads on an Illumina [model; e.g., NovaSeq/NextSeq] platform with [e.g., 2×75 bp or 2×100 bp] chemistry.

treatment_protocol: Cells were transfected with DGUOK siGENOME siRNA pools (Dharmacon) using Lipofectamine RNAiMAX (Thermo Fisher Scientific) following the UCSF RNAiMAX protocol. For a 24-well format, 6 pmol siRNA was used per well (scaled accordingly for other formats). Non-targeting siRNA served as control (siControl). Cells for RNA-seq were harvested 48 h post-transfection.

value: Liver

value: Hepatocyte (hepatocellular carcinoma derived)

value: 48 h siRNA treatment (siControl)


title: HepG2 RNA-seq, siDGUOK, replicate 1

description: Library name: HEPG2_siDGUOK_1


title: HepG2 RNA-seq, siDGUOK, replicate 3

description: Library name: HEPG2_siDGUOK_3


title: Ctrl_siRNA_4

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: Library name: Ctrl_siRNA_4

data_processing:
100-bp paired-end reads for all samples (4 replicates SPG21 KD, 4 replicates control KD) were trimmed with cutadapt v4.4 using arguments -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim 20 --overlap 6 --minimum-length=25 to remove TruSeq adapters and perform light quality trimming.
Trimmed reads were aligned to the GENCODE v28 human primary assembly using STAR v2.7.10b with parameters recommended by ENCODE for RNA-seq, specifically  –outFilterType BySJout –outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped None
Aligned reads were counted in genes using featureCounts v2.0.3 and the GENCODE v28 GTF primary assembly annotation
Assembly: hg38
Supplementary files format and content: TSV of read counts in each gene for each sample

source_name: Cervical carcinoma

growth_protocol: HeLa were cultured in DMEM supplemented with 10% FBS, 100 IU/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated using Qiagen RNeasy Mini Kit.
5 μl for axon samples and 1 μl for neuron samples were used for synthesizing cDNAs using a SMART-Seq version 4 Ultra Low Input RNA Kit for Sequencing (Takara). A Nextera XT DNA Library Preparation Kit (Illumina) was used to prepare libraries from the cDNA samples using 1 ng of cDNA.

treatment_protocol: siRNA-mediated knockdown was performed using Lipofectamine RNAiMax Transfection Reagent (Invitrogen) and ON-TARGETplus Human SPG21 or non-targeting control pool siRNA (Dharmacon).

value: Cervical carcinoma

value: HeLa

value: Immortalized cell line

value: Control


title: NBH_38-05_120dpi

description:
Library name: NBH_38-05_120dpi
10x Genomics single-cell gene expression


title: HepG2 RNA-seq, siControl, replicate 1

description: Library name: HEPG2_siControl_1


title: HepG2 RNA-seq, siDGUOK, replicate 2

description: Library name: HEPG2_siDGUOK_2


title: CC, day3, graft2

description:
Library name: graft2_d3
Samplename in gene count matrix: graft2_d3

value: Cultured primary keratinocytes


title: HepG2 RNA-seq, siControl, replicate 3

description: Library name: HEPG2_siControl_3


title: Ctrl_siRNA_3

description: Library name: Ctrl_siRNA_3


title: Ctrl_siRNA_2

description: Library name: Ctrl_siRNA_2


title: SPG21_siRNA_3

description: Library name: SPG21_siRNA_3

value: SPG21 knockdown


title: Ctrl_siRNA_1

description: Library name: Ctrl_siRNA_1


title: SPG21_siRNA_2

description: Library name: SPG21_siRNA_2


title: SPG21_siRNA_1

description: Library name: SPG21_siRNA_1


title: MV1_32-11_120dpi

description:
Library name: MV1_32-11_120dpi
10x Genomics single-cell gene expression


title: SPG21_siRNA_4

description: Library name: SPG21_siRNA_4


title: Donor3748_ADT

city: Boston

first: Pablo

last: Argüeso

state: MA

address: 800 Washington St

department: Ophthalmology

institute: Tufts Medical Cener

description:
Library name: Human1_ADT
lectin-derived oligonucleotide (ADT-like)
Donor3748_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds

library_source: other

data_processing:
Raw sequencing data were aligned, filtered, and normalized using Cell Ranger (v7.2.0).
Assembly: GRCh38 - human, mm10 - mice
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5
Supplementary files format and content: Seurat object with merged and processed samples: hCornea.joint.rds
Supplementary files format and content: Seurat object with merged and processed samples: mCornea.joint.rds
Library strategy: CITE-seq

molecule: protein

source_name: Cornea-conjunctiva

extract_protocol:
Human corneal–limbal and conjunctival tissues were incubated separately at 37 °C for 2 hours in DMEM/F12 containing 2.4 IU/mL Dispase II (Thermo Fisher Scientific, Waltham, MA, USA). The epithelia were scraped, collected, and further digested with Gibco™ TrypLE (Thermo Fisher Scientific) for 5 minutes. The remaining stromal and conjunctival fragments were cut into small pieces, placed each in a MACS C tube (Miltenyi Biotec, Bergisch Gladbach, Germany) containing 4 mg/mL collagenase A (Sigma-Aldrich, St. Louis, MO, USA) in DMEM, and digested for 1 hour at 37 °C using a gentleMACS dissociator (Miltenyi Biotec). After digestion, single cells from all individual compartments were pooled, filtered through a 70 µm cell strainer (Miltenyi Biotec), washed in PBS supplemented with 0.04% bovine serum albumin (BSA; Sigma-Aldrich), and counted. Cells were resuspended in cold 0.04% BSA-PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.  Mouse conjunctival and corneal tissues were digested separately in DMEM containing 2 mg/mL collagenase A and 10 mg/mL Dispase II at 37 °C for 1 hour. During digestion, tissues were gently triturated by passing them through a 20G syringe needle five times every 20 minutes. Following enzymatic digestion, samples were rinsed with DMEM and incubated in TrypLE (Thermo Fisher Scientific) for 10 minutes at 37 °C. Cell suspensions were filtered through a 70 µm cell strainer, washed in 0.04% BSA-PBS, and counted. Cells were resuspended in cold 0.04% BSA–PBS, and cold methanol was added dropwise to a final concentration of 80%. Samples were incubated at –20 °C for 30 minutes before storage at –80 °C.
Single-cell suspensions (1 mL, approx. 106 cells/mL) were thawed and washed in wash-resuspension buffer containing 3× SSC, 1 mM DTT, 0.04% ultrapure BSA, and 0.2 U/μL RNase inhibitor. Cells were incubated on ice for 30 minutes with a mixture of DNA-labeled lectins and biotinylated SNA I, each at 0.5 μg/mL (equivalent to 0.05 μg of lectin per million cells). After three washes in wash-resuspension buffer, cells were incubated with TotalSeq™-B0975 Streptavidin (BioLegend, San Diego, CA) at 0.5 μg/mL (0.05 μg per million cells) for 30 minutes on ice. Cells were then washed three times, counted, and adjusted to a final concentration of ~1,000 cells/μL. Single cells were captured using the Chromium Controller, and single-cell RNA sequencing libraries were prepared with the Chromium Next GEM Single Cell 3′ v3.1 Kit and the 3′ Feature Barcode Kit (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions to generate both the gene expression and cell surface feature libraries. For sequencing, gene expression and cell surface feature libraries from each sample were pooled at a 4:1 ratio and sequenced using either the Illumina NovaSeq 6000 or NovaSeq X Plus platforms, targeting 20,000 reads per cell.

value: Cornea-conjunctiva

tag: adt

value: Lectin_MPA, Lectin_PNA, Lectin_ECA, Lectin_AAL, Lectin_MAA-I, Lectin_SNA-I, Lectin_ConA, Lectin_DSA, Lectin_WGA

tag: library type

value: ADT


title: Donor3748_mRNA

description:
Library name: Human1_mRNA
polyA RNA
Donor3748_filtered_feature_bc_matrix.h5
hCornea.joint.paper.clean.rds

value: mRNA


title: Intestinal mucosa,lesions,after IFX treatment,no-response,rep3

city: kunming

first: Zhangqin

last: Li

address: No. 295, Xichang Road, Wuhua District, Kunming City, Yunnan Province

institute: The First Affiliated Hospital of Kunming Medical University

description:
Library name: AM5CS200
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://www.10xgenomics.com/support/software/cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

growth_protocol: All participants were diagnosed with UC according to the Lennard-Jones criteria]. They did not respond to conventional treatments, including 5-Aminosalicylic Acid, anti-hormone drugs, and immunosuppressants.All the patients received IFX treatment for fourteen weeks.

extract_protocol:
Freshly isolated intestinal mucosal specimens were collected and immediately used to prepare their single cell suspension,The library synthesis was conducted in accordance with the instructions of the Chromium Next GEM Single Cell 5′Kit v2 (CG000331,10× GENOMICS). Single cells were processed with the 10X Single-Cell Platform following the manufacturer's protocol with modifications. An appropriate volume of cell suspension with approximately 20,000 cells was loaded in each channel, resulting in the capture of 10,000 cells per sample.
scRNA-seq library preparations were performed according to manufacturer’s standard 10× Genomics protocol(CG000331,10x Genomics). scRNA-seq libraries were sequenced on the Novaseq 6000 platform (Illumina) to a depth of approximately 300 million reads per library with the following read configuration: Read 1: 28 cycles, Read 2: 96 cycles, Index read 1: 8 cycles.

value: Colon

value: After IFX treatment 14 weeks ago (Post-)

value: male

tag: age

tag: sample group


title: Intestinal mucosa,lesions,after IFX treatment,no-response,rep1

description:
Library name: AM5CS317
10X Genomics

treatment_protocol: All participants were diagnosed with UC according to the Lennard-Jones criteria]. They did not respond to conventional treatments, including 5-Aminosalicylic Acid, anti-hormone drugs, and immunosuppressants.All the patients received IFX treatment for fourteen weeks.


title: Intestinal mucosa,lesions,after IFX treatment,response,rep2

description:
Library name: AM5CS318
10X Genomics

value: female


title: Intestinal mucosa,lesions,after IFX treatment,response,rep4

description:
Library name: AM5CS310
10X Genomics


title: Intestinal mucosa,lesions,after IFX treatment,response,rep3

description:
Library name: AM5CS296
10X Genomics


title: Intestinal mucosa,lesions,after IFX treatment,no-response,rep2

description:
Library name: AM5CS364
10X Genomics


title: Intestinal mucosa,lesions,after IFX treatment,no-response,rep4

description:
Library name: AM5CS493
10X Genomics


title: Intestinal mucosa,lesions,before IFX treatment,no-response,rep3

description:
Library name: AM5CS455
10X Genomics

value: Before IFX treatment (Pre-)


title: Intestinal mucosa,lesions,after IFX treatment,response,rep1

description:
Library name: AM5CS255
10X Genomics


title: Intestinal mucosa,lesions,before IFX treatment,no-response,rep2

description:
Library name: AM5CS183
10X Genomics


title: Intestinal mucosa,lesions,before IFX treatment,no-response,rep4

description:
Library name: AM5CS354
10X Genomics


title: Intestinal mucosa,lesions,before IFX treatment,no-response,rep1

description:
Library name: AM5CS149
10X Genomics


title: Unstimulated Donor 5 rep3

city: Cambridge

first: Samir

last: Lal

address: 1 Portland St

institute: Pfizer Inc

description: Library name: RSA-0000111571

data_processing:
Output BCL files were demultiplexed to fastq using Illumina's bcl2fastq2-2.20 tool
The sequencing reads were mapped to the GRCh38 human reference genome using Star v.2.7.3a
gene counts were generated using Salmon v0.14.2
Transcripts were annotated using Ensemble v98
Assembly: GRCh38
Supplementary files format and content: csv.gz file includes raw counts for all samples

source_name: Abdominal Skin

extract_protocol:
Skin explant RNA was isolated using isopropanol
TruSeq Stranded mRNA sample preparation kit

value: Abdominal Skin


title: Intestinal mucosa,lesions,before IFX treatment,response,rep3

description:
Library name: AM5CS170
10X Genomics


title: Intestinal mucosa,lesions,before IFX treatment,response,rep4

description:
Library name: AM5CS182
10X Genomics


title: Unstimulated Donor 5 rep2

description: Library name: RSA-0000111570


title: Unstimulated Donor 4 rep3

description: Library name: RSA-0000111568


title: Unstimulated Donor 5 rep1

description: Library name: RSA-0000111569


title: Intestinal mucosa,lesions,before IFX treatment,response,rep1

description:
Library name: AM5CS126
10X Genomics


title: Unstimulated Donor 4 rep2

description: Library name: RSA-0000111567


title: Unstimulated Donor 1 rep2

description: Library name: RSA-0000111561


title: Unstimulated Donor 1 rep1

description: Library name: RSA-0000111560


title: Unstimulated Donor 4 rep1

description: Library name: RSA-0000111566


title: TH2 Donor 5 rep3

description: Library name: RSA-0000111559

value: TH2 Cytokines


title: Unstimulated Donor 2 rep1

description: Library name: RSA-0000111563


title: Unstimulated Donor 2 rep3

description: Library name: RSA-0000111565


title: Unstimulated Donor 2 rep2

description: Library name: RSA-0000111564


title: TH2 Donor 4 rep3

description: Library name: RSA-0000111556


title: TH2 Donor 4 rep1

description: Library name: RSA-0000111554


title: TH2 Donor 2 rep2

description: Library name: RSA-0000111552


title: Intestinal mucosa,lesions,before IFX treatment,response,rep2

description:
Library name: AM5CS152
10X Genomics


title: TH2 Donor 4 rep2

description: Library name: RSA-0000111555


title: TH2 Donor 5 rep1

description: Library name: RSA-0000111557


title: TH2 Donor 1 rep2

description: Library name: RSA-0000111549


title: TH2 Donor 2 rep3

description: Library name: RSA-0000111553


title: TH2 Donor 1 rep3

description: Library name: RSA-0000111550


title: PF07245303 Donor 5 rep3

description: Library name: RSA-0000111547


title: TH2 Donor 1 rep1

description: Library name: RSA-0000111548


title: PF07245303 Donor 5 rep2

description: Library name: RSA-0000111546


title: PF07245303 Donor 5 rep1

description: Library name: RSA-0000111545


title: PF07245303 Donor 4 rep2

description: Library name: RSA-0000111543


title: PF07245303 Donor 4 rep3

description: Library name: RSA-0000111544


title: PF07245303 Donor 4 rep1

description: Library name: RSA-0000111542


title: PF07245303 Donor 2 rep3

description: Library name: RSA-0000111541


title: PF07245303 Donor 1 rep3

description: Library name: RSA-0000111538


title: PF07245303 Donor 2 rep2

description: Library name: RSA-0000111540


title: Unstimulated Donor 1 rep3

description: Library name: RSA-0000111562


title: PF07245303 Donor 2 rep1

description: Library name: RSA-0000111539


title: TH2 Donor 5 rep2

description: Library name: RSA-0000111558


title: CD4+T cells, SLE4

city: Nanjing

first: Xiaoli

last: Min

address: No.4 Jiang Wang Temple Street

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: Library name: Sample 8

data_processing:
Illumina Novaseq was used for basecalling
The raw data were firstly processed through in-house perl scripts
The RNA-seq data were then mapped to the human reference genome hg38 with Hisat2 v2.0.5
The HERVs were obtained from RepeatMasker for expression analyses by stringtie
The differential analysis was performed using DESeq
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
RNA was harvested using Trizol reagent.RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Cat#FC-122-1001) was used to 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were from SLE and healthy controls

value: PBMC

value: CD4+T cells

value: SLE


title: PF07245303 Donor 1 rep2

description: Library name: RSA-0000111537


title: CD4+T cells, SLE3

description: Library name: Sample 7


title: CD4+T cells, SLE_T2

description: Library name: Sample 10

value: SLE with Prednisone Treatment


title: CD4+T cells, SLE_T1

description: Library name: Sample 9


title: PF07245303 Donor 1 rep1

description: Library name: RSA-0000111536


title: CD4+T cells, SLE2

description: Library name: Sample 6


title: TH2 Donor 2 rep1

description: Library name: RSA-0000111551


title: CD4+T cells, N4

description: Library name: Sample 4

value: HC


title: CD4+T cells, N3

description: Library name: Sample 3


title: CD4+T cells, N2

description: Library name: Sample 2


title: Retinal organoid-1, MS-VUS

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

institute: CMRI

description:
Library name: MSVUS_1
10x Genomics

data_processing:
Basecalling is performed by Illumina RTA software in sequencer, further demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information, the number of reads and quality score(Q30) are counted as well.
Sequencing data were processed using CellRanger v3.1 (10x Genomics) with default parameters to extract genomic reads which were aligned against annotated human genome, including the protein and non-coding transcripts (GRCh38, GENCODE v27). The reads with the same cell barcode and unique molecular identifier were collapsed to a unique transcript, generating the count matrix where columns correspond to single cells and rows correspond to transcripts. To remove potentially empty droplets with ambient RNA, the emptyDrops function from the DropletUtils package was used.
Assembly: GRCh38, GENCODE v27
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retinal organoid

growth_protocol: Retinal organoids were differentiated from iPSCs as per protocol from Gonzalez-Cordero et al., Stem cell reports 9, 820-837 (2017) and West et  al., Stem cell reports 17, 775-788 (2022).

extract_protocol:
Retinal organoids were dissociated into single cells using the Neurosphere Dissociation Kit (P) (Miltenyi Biotec), as per manufacturer’s protocol and processed by 10X Chromium Single Cell 3' Gene Expression - 1 reaction provided to the Single Cell Analytics Facility at CMRI for portioning into single cells and library construction using the Chromium Next GEM Single cell 3’ kit (10x Genomics).
Library was performed accroding to the manufacturer's protocol for the 10X Genomics Chromium Single Cell 3' Gel Bead and Library kit (v3.1) at one reaction per retinal organoids single cell suspension (10,000 cells input).

treatment_protocol: No treatment was given to retinal organoids

value: Retinal organoid

value: MS-VUS

value: Retinal cells

value: RPGRIP1 (NM_020366.4):c.2108T>C p.(Ile703Thr), homozygous


title: Retinal organoid-3, MS-VUS

description:
Library name: MSVUS_3
10x Genomics


title: Retinal organoid-1, LCA-1

description:
Library name: LCA1_1
10x Genomics


title: Retinal organoid-2, MS-VUS

description:
Library name: MSVUS_2
10x Genomics


title: Retinal organoid-3, Control-1

description:
Library name: Control1_3
10x Genomics

value: WT


title: Retinal organoids, LCA-1, rep 3

description:
Library name: LCA1_3
Column name in dedup_countTable_geneName.tsv.gz LCA1_3

data_processing:
Starting with Illumina GA Pipeline v1.8 (currently v1.9), base quality scores range from 0 to 41.
Raw fastq files were quality checked by FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Trimming of adapters and quality filtering were then performed by AdapterRemoval (version 2.3.2)
Trimmed and quality filtered paired-end reads were aligned to the human GRCh38 reference genome using STAR (version 2.7.9a) with default parameters.
Gene expression was quantified by counting the number of reads aligned to each Ensembl gene model using featureCounts (version 2.0.1).
The Trimmed Mean of M-values (TMM) normalisation method from edgeR package in R (version 3.36.0) was applied to normalise read counts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Retinal organoids

extract_protocol:
Total RNA was extracted from at least 3 retinal organoids pooled per sample using the QIAzol and RNeasy Micro kit (Qiagen). The yield and integrity were determined by Tapestation analysis (Agilent).
Library preparation with poly A selection (non-strand specific) (VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina) was performed by Azenta (Suzhou, China) as per manufacturer's protocol.

value: Retinal organoids

tag: time

value: Day 210


title: Retinal organoids, MS-VUS, rep 1

description:
Library name: MSVUS_1
Column name in dedup_countTable_geneName.tsv.gz MSVUS_1


title: Retinal organoids, MS-VUS, rep 2

description:
Library name: MSVUS_2
Column name in dedup_countTable_geneName.tsv.gz MSVUS_2


title: Retinal organoids, MS-VUS, rep 3

description:
Library name: MSVUS_3
Column name in dedup_countTable_geneName.tsv.gz MSVUS_3


title: Retinal organoids, Control-1, rep 2

description:
Library name: Control1_2
Column name in dedup_countTable_geneName.tsv.gz Control1_2


title: Retinal organoids, LCA-1, rep 2

description:
Library name: LCA1_2
Column name in dedup_countTable_geneName.tsv.gz LCA1_2


title: Retinal organoids, Control-1, rep 1

description:
Library name: Control1_1
Column name in dedup_countTable_geneName.tsv.gz Control1_1


title: Retinal organoids, Control-1, rep 3

description:
Library name: Control1_3
Column name in dedup_countTable_geneName.tsv.gz Control1_3


title: PBMCs patient pair_11, indolent stage T-PLL

city: Koeln

first: Linus

last: Wahnschaffe

address: Kerpener Str. 62

department: Department I of Internal Medicine, Center for Integrated Oncology Aachen-Bonn-Cologne-Duesseldorf (CIO ABCD)

country: Germany

institute: University hospital of Cologne

description:
Library name: pair_11_indolent
demultiplexed

data_processing:
Sequencing with 29+89bp read length
Demultiplexing, alignment, filtering, and counting, using the 10x Genomics Cell Ranger 6.1.2 pipeline at default parameters.
Assembly: GRCh38-2020-A reference genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
After sampling, peripheral blood mononuclear cells (PBMCs) were isolated via density gradient centrifugation (Histopaque, Sigma-Aldrich). Cryo-preserved PBMCs were transferred to the Cologne Center for Genomics (CCG, Cologne) and CeMM-Biomedical Sequencing Facility (BSF, Vienna) for sequencing. Removal of dead cells was accomplished using a Dead Cell Removal Kit (Miltenyi Biotec) or by FACS sorting of DAPI-negative cells.
Single-cell suspensions were processed with the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics) with dual indices according to the manufacturer’s instructions, using either one reaction per sample or multiplexing two to three samples with the Cell Multiplexing technology option. In short, cells and the appropriate master mix were loaded on a Chromium Next GEM Chip G and processed on the Chromium Controller to generate Gel Bead-In-Emulsions (GEMs). After the creation of barcoded full-length cDNA by incubation with cell lysate, primers, and a reverse transcription master mix, GEMs were broken, and the pooled fractions were recovered. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post-GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon. Library construction was performed, including end repair, A-tailing, adaptor ligation, and PCR. The final libraries were quantified (Qubit), pooled, and the pool was quantified using the Peqlab KAPA Library Quantification kit and the Applied Biosystems 7900HT Sequence Detection System.

value: peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

value: indolent stage T-PLL

tag: number of_cells_detected_by_cellranger


title: PBMCs patient pair_11, active stage T-PLL

description:
Library name: pair_11_active
demultiplexed

value: active stage T-PLL


title: PBMCs patient pair_9, indolent stage T-PLL

description: Library name: pair_9_indolent


title: PBMCs patient pair_9, active stage T-PLL

description: Library name: pair_9_active


title: PBMCs patient pair_8, indolent stage T-PLL

description: Library name: pair_8_indolent


title: PBMCs patient pair_10, indolent stage T-PLL

description:
Library name: pair_10_indolent
demultiplexed


title: CD4+T cells, SLE1

description: Library name: Sample 5


title: PBMCs patient pair_8, active stage T-PLL

description: Library name: pair_8_active


title: CD4+T cells, N1

description: Library name: Sample 1


title: PBMCs patient pair_10, active stage T-PLL

description:
Library name: pair_10_active
demultiplexed


title: Retinal organoid-2, LCA-1

description:
Library name: LCA1_2
10x Genomics

tag: cell line


title: Polysomes OGFOD1 OE U937

first: Christina

last: Mayerhofer

address: 185 Cambridge St.

department: Center for Regenerative Medicine

institute: MGH, Simches building

description: Library name: U937_OEP

data_processing:
Transcriptome RNASeq data was processed according to the recommendation of the manufacturer (Smart-Seq v4, Takara Bio USA) . Reads were trimmed with cutadapt in paired-end read mode with parameters: -j 4 --trim-n --match-read-wildcards -a CTGTCTCTTATACACATCT -a AAAAAAAAAAA -A CTGTCTCTTATACACATCT -A AAAAAAAAAAA --nextseq-trim 20 -m 10. Reads were then aligned using STAR to GRCh38 release 113 reference genome in paired-end read mode with parameters --sjdbOverhang 150. Finally, featureCounts was used to detect gene counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

molecule: other

source_name: hematopoietic

growth_protocol: Human AML cell lines were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin, 100 μg/ml streptomycin, 2mM L-glutamine.

extract_protocol:
AML cells were treated with 100 μg/ml cycloheximide in cold PBS and lysed in 350 μl ice-cold polysome lysis buffer (10 mM Tris–HCl pH 7.4, 100 mM KCl, 5 mM MgCl2, 2 mM DTT, 100 μg/ml CHX, 1% Triton X-100; 1mM PMSF, 100 U/ml RNAse Inhibitor) for 20 min on ice. The lysates were clarified for 10 min at 10,000 rpm at 4°C. Using 7% and 53% sucrose in 10 mM Tris–HCl pH 7.4, 100 mM KCl, 5 mM MgCl2, 2 mM DTT, 100 μg/ml CHX, a sucrose gradient is made on a Gradient Master (Biocomp) in a 13.2 ml ultra-clear tube. Lysates were overlaid onto the sucrose gradient for 1h 30 h at 36,000 rpm, 4°C with low deceleration in SW 41 Ti rotor in Beckman Coulter XPN-100 ultracentrifuge. Samples are run on a Piston Gradient Fractionator (Biocomp) to obtain polysome data and fractions stored -80°C. mRNA sequencing was performed of the fractions obtained from polysome profiling as described previously (PMID:39143206). Following the polysome sucrose gradient fractioning of U937 and Molm13 with OGFOD1 OE or control, two samples were pooled with 50 μl of each fraction of free ribonucleoproteins (RNPs), monosomes (80S), and disomes (1), and heavy polysomes containing all fractions with 3+ ribosomes (2).
RNA was extracted using Trizol and libraries prepared with the Smart-seq kit.

treatment_protocol: OGFOD1 was overexpressed in leukemia cell lines through lentivirus-carrying overexpression vector.

value: hematopoietic

tag: cell type

value: Acute myeloid leukemia

value: OGFOD1 OE


title: PBMCs patient single_indolent_5, indolent stage T-PLL

description:
Library name: single_indolent_5
demultiplexed


title: Polysomes ctrl U937

description: Library name: U937_ScrP

tag: genotype

value: control


title: Retinal organoids, LCA-1, rep 1

description:
Library name: LCA1_1
Column name in dedup_countTable_geneName.tsv.gz LCA1_1


title: RNP+M+D ctrl U937

description: Library name: U937_ScrM


title: RNP+M+D OGFOD1 OE U937

description: Library name: U937_OEM


title: Polysomes OGFOD1 OE Molm13

description: Library name: Molm13_OEP


title: Polysomes ctrl Molm13

description: Library name: Molm13_ScrP


title: RNP+M+D OGFOD1 OE Molm13

description: Library name: Molm13_OEM


title: RNP+M+D ctrl Molm13

description: Library name: Molm13_ScrM


title: IP_Z22_raw_MYC_ab_2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

description: Library name: IP_Z22_raw_MYC_ab_2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) merged with D. melanogaster genome (dm6) using Bowtie2 (version 2.4.2).
PCR duplicates were removed using MarkDuplicates tool of Picard (version 2.23.3)  with the parameter ‘--REMOVE DUPLICATES = true’.
Genome coverage bigwig files were generated by BEDtools (version 2.29.2) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 1,000,000/ (the number of reads mapped to dm6 genome)’.
Assembly: hg19
Supplementary files format and content: BigWig files

extract_protocol:
Cells for ChIP-seq were crosslinked with 1% paraformaldehyde for 10 min and then quenched in 125 mM glycine for 5 min at room temperature with rotation. After washed with cold PBS, cells were lysed in lysis buffer (10 mM Tris_x0002_HCl, pH 7.5, 10 mM NaCl, and 0.5% NP-40) on ice for 10 min. The nuclei were spun down and then resuspended in 500 µl 1XChIP-seq buffer(50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, and 0.1% sodium deoxycholate). Sonication was per_x0002_formed for 5 cycles of 30 s on and 30 s off in Bioruptor. After centrifuged at 15,000 × g at 4 °C for 10 min, the supernatant was used for chromatin immunoprecipitation. Same amounts of Drosophila S2 cell chromatin were spiked in for normalization, 1% for input. 10 µg of Z22 antibodies was added into each sample and rocked at 4 °C overnight. Protein A beads were added and incubated for 3 h. After the beads were extensively washed, the bound DNA was eluted by elution buffer (10 mM Tris-HCl, pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, and 1% SDS). Reverse_x0002_crosslinked at 65 °C overnight. The eluted DNA was treated with proteinase K and RNase A, and then purified with the Min-Elute PCR purification kit (Qiagen, Cat.#28006).
Sample extracted was subjected to library preparation with VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat. #ND607-1) following the manufacturer’s instructions.

value: osteosarcoma cell line

value: Zab + MYC O/E


title: IP_Z22_raw_MYC_ab_1

description: Library name: IP_Z22_raw_MYC_ab_1


title: IP_Z22_raw_CT_2

description: Library name: IP_Z22_raw_CT_2


title: IP_Z22_raw_ab_2

description: Library name: IP_Z22_raw_ab_2

value: Zab


title: IP_Z22_raw_ab_1

description: Library name: IP_Z22_raw_ab_1


title: Input_raw_MYC_ab_1

description: Library name: Input_raw_MYC_ab_1


title: Input_raw_MYC_1

description: Library name: Input_raw_MYC_1

value: MYC O/E


title: Input_raw_CT_1

description: Library name: Input_raw_CT_1


title: Input_raw_ab_2

description: Library name: Input_raw_ab_2


title: Input_raw_MYC_ab_2

description: Library name: Input_raw_MYC_ab_2


title: rnaseq_MYC_ab_1

description: Library name: rnaseq_MYC_ab_1

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) merged with D. melanogaster genome (dm6) using STAR mapper (version 2.7.7a).
Tag directories were generated using HOMER (version 4.11.1) makeTagDirectory, and expression matrixes were counted by analyzeRepeats.pl with the parameter ‘-raw’, and further scaled by the reads of dm6.
Assembly: hg19
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample of RNA-seq

extract_protocol:
RNA was extracted with Trizol.
RNA-Seq was performed by RNA-seq library prep kit (Abclonal Cat. # RK20306) following the manufacturer’s instructions.


title: IP_Z22_raw_MYC_1

description: Library name: IP_Z22_raw_MYC_1


title: IP_Z22_raw_CT_1

description: Library name: IP_Z22_raw_CT_1


title: rnaseq_MYC_2

description: Library name: rnaseq_MYC_2


title: rnaseq_MYC_1

description: Library name: rnaseq_MYC_1


title: rnaseq_CT_2

description: Library name: rnaseq_CT_2


title: rnaseq_ab_2

description: Library name: rnaseq_ab_2


title: Input_raw_CT_2

description: Library name: Input_raw_CT_2


title: rnaseq_CT_1

description: Library name: rnaseq_CT_1


title: IP_Z22_raw_MYC_2

description: Library name: IP_Z22_raw_MYC_2


title: rnaseq_zdna4_CL_2

description: Library name: rnaseq_zdna4_CL_2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) merged with double-length Z-SCPs sequences and D. melanogaster genome (dm6) using STAR mapper (version 2.7.7a).
Genome coverage bigwig files were generated by BEDtools (version 2.29.2) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-split -scale 1,000,000/ (the number of reads mapped to dm6 genome)’.
The double-length Z-SCPs signals were ultimately converted into signals of single length.
Assembly: hg19
Supplementary files format and content: Matrix table with normalized counts for every gene and every sample of RNA-seq


title: rnaseq_zdna4_CC_2

description: Library name: rnaseq_zdna4_CC_2


title: rnaseq_zdna4_CL_1

description: Library name: rnaseq_zdna4_CL_1


title: rnaseq_zdna3_CL_1

description: Library name: rnaseq_zdna3_CL_1


title: rnaseq_zdna4_CC_1

description: Library name: rnaseq_zdna4_CC_1


title: rnaseq_zdna3_CC_2

description: Library name: rnaseq_zdna3_CC_2


title: rnaseq_zdna3_CC_1

description: Library name: rnaseq_zdna3_CC_1


title: rnaseq_zdna2_CL_2

description: Library name: rnaseq_zdna2_CL_2


title: Input_raw_MYC_2

description: Library name: Input_raw_MYC_2


title: rnaseq_zdna2_CL_1

description: Library name: rnaseq_zdna2_CL_1


title: rnaseq_zdna2_CC_2

description: Library name: rnaseq_zdna2_CC_2


title: Input_raw_ab_1

description: Library name: Input_raw_ab_1


title: rnaseq_MYC_ab_2

description: Library name: rnaseq_MYC_ab_2


title: rnaseq_zdna2_CC_1

description: Library name: rnaseq_zdna2_CC_1


title: rnaseq_zdna1_CL_2

description: Library name: rnaseq_zdna1_CL_2


title: rnaseq_zdna1_CC_2

description: Library name: rnaseq_zdna1_CC_2


title: cuttag_SSRP1_MYC_ab_2

description: Library name: cuttag_SSRP1_MYC_ab_2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) merged with D. melanogaster genome (dm6) using Bowtie2 (version 2.4.2).
Genome coverage bigwig files were generated by BEDtools (version 2.29.2) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-scale 1,000,000/ (the number of reads mapped to dm6 genome)’.
Assembly: hg19
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag

extract_protocol:
10^5 cells were harvested in NE buffer (20 mM HEPES-KOH, pH 7.5, 0.5 mM spermidine, 10 mM KCl, 0.1% TritonX-100, 10% Glycerol, 1 mM PMSF) and on ice for 10 min.
10 µl ConA beads were added to each sample and incubated at room temperature for 10 min. The beads were washed with washing buffer (20 mM HEPES-KOH, pH 7.5, 0.5 mM spermidine, 150 mM NaCl, 0.1% BSA) and resuspended in blocking buffer (20 mM HEPES KOH, pH 7.5, 0.5 mM spermidine, 150 mM NaCl, 0.1% BSA, 2 mM EDTA) at room temperature for 5 min. Primary antibodies were added by 1:100 dilution and incubated at room temperature for 2 h. After washed with washing buffer, secondary antibodies were added by 1:100 dilution and incubated at room temperature for 30 min. 1.2 µl PA-Tn5 transposomes were added to sample extracted and incubated at room temperature for 30 min.  Beads were resuspended in 30 µl washing buffer with 10 mM MgCl2 and incubated at 37 °C for 1 h. Reactions were stopped by adding 5.5 µl stop buffer (2.25 μl of 0.5 M EDTA, 2.75 μl of 10% SDS and 0.5 μl of 20 mg/ml Proteinase K) and incubated at 55 °C for 30 min, and then 70 °C for 20 min to inactivate Proteinase K. 0.9X of VAHTS DNA clean beads (VAHTS, Cat. #N411-03) were added to each sample to extract the tagmentated DNA.


title: cuttag_SSRP1_MYC_ab_1

description: Library name: cuttag_SSRP1_MYC_ab_1


title: cuttag_SSRP1_MYC_1

description: Library name: cuttag_SSRP1_MYC_1


title: rnaseq_zdna1_CC_1

description: Library name: rnaseq_zdna1_CC_1


title: cuttag_SSRP1_MYC_2

description: Library name: cuttag_SSRP1_MYC_2


title: cuttag_SSRP1_CT_2

description: Library name: cuttag_SSRP1_CT_2


title: rnaseq_ab_1

description: Library name: rnaseq_ab_1


title: rnaseq_zdna3_CL_2

description: Library name: rnaseq_zdna3_CL_2


title: cuttag_SSRP1_CT_1

description: Library name: cuttag_SSRP1_CT_1


title: cuttag_pol2_MYC_ab_2

description: Library name: cuttag_pol2_MYC_ab_2


title: cuttag_SSRP1_ab_2

description: Library name: cuttag_SSRP1_ab_2


title: cuttag_pol2_MYC_2

description: Library name: cuttag_pol2_MYC_2


title: cuttag_pol2_MYC_ab_1

description: Library name: cuttag_pol2_MYC_ab_1


title: cuttag_pol2_CT_2

description: Library name: cuttag_pol2_CT_2


title: cuttag_pol2_ab_1

description: Library name: cuttag_pol2_ab_1


title: cuttag_myc_MYC_ab_2

description: Library name: cuttag_myc_MYC_ab_2


title: cuttag_myc_MYC_ab_1

description: Library name: cuttag_myc_MYC_ab_1


title: cuttag_myc_MYC_2

description: Library name: cuttag_myc_MYC_2


title: rnaseq_zdna1_CL_1

description: Library name: rnaseq_zdna1_CL_1


title: cuttag_myc_MYC_1

description: Library name: cuttag_myc_MYC_1


title: cuttag_myc_CT_2

description: Library name: cuttag_myc_CT_2


title: cuttag_myc_CT_1

description: Library name: cuttag_myc_CT_1


title: cuttag_myc_ab_2

description: Library name: cuttag_myc_ab_2


title: cuttag_myc_ab_1

description: Library name: cuttag_myc_ab_1


title: ttseq_MYC_ab_2

description: Library name: ttseq_MYC_ab_2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) merged with D. melanogaster genome (dm6) using STAR mapper (version 2.7.7a).
Sense reads were obtained using the parameters ‘-f 128 -F 16’ and ‘-f 64 -f 16’ with samtools (version 1.11), while antisense reads were obtained using the parameters ‘-f 128 -f 16’ and ‘-f 64 -F 16’.
Genome coverage bigwig files were generated by BEDtools (version 2.29.2) genomecov and bedGraphToBigWig (version 4) with the parameter ‘-split -scale 1,000,000/ (the number of reads mapped to dm6 genome)’.
Assembly: hg19
Supplementary files format and content: Matrix table with normalized sense counts for every gene and every sample of TT-seq

extract_protocol:
RNA labeled with 4-SU was extracted with Trizol.
Sample extracted was subjected to library preparation with RNA-seq library prep kit(Abclonal Cat. # RK20306) following the manufacturer’s instructions.


title: ttseq_MYC_ab_1

description: Library name: ttseq_MYC_ab_1


title: cuttag_SSRP1_ab_1

description: Library name: cuttag_SSRP1_ab_1


title: ttseq_MYC_2

description: Library name: ttseq_MYC_2


title: ttseq_ab_2

description: Library name: ttseq_ab_2


title: ttseq_MYC_1

description: Library name: ttseq_MYC_1


title: ttseq_ab_1

description: Library name: ttseq_ab_1


title: MNase_MYC_ab_2

description: Library name: MNase_MYC_ab_2

data_processing:
Raw reads were trimmed to remove adapters and low-quality sequences using Trim Galore (version 0.6.6) with the parameters ‘-q 20 --paired’.
Then trimmed reads were uniquely mapped to the human reference genome (hg19) using Bowtie2 (version 2.4.2).
PCR duplicates were removed using MarkDuplicates tool of Picard (version 2.23.3) with the parameter ‘--REMOVE DUPLICATES = true’.
Mononucleosomal DNA fragments (141–180 nt) were extracted for further analysis.
Genome coverage bigwig files were generated by deepTools (version 3.5.0) bamCoverage with the parameter ‘--MNase --binSize 1 –smoothLength 40 --scaleFactor 10,000,000/ (the number of reads within ±1 kb of the TSS)’.
Assembly: hg19
Supplementary files format and content: bigWig files for nucleosome occupancy

extract_protocol:
Cells for Mnase-seq were crosslinked with 1% paraformaldehyde for 10 min and then quenched in 125 mM glycine for 5 min at room temperature with rotation. After washed with cold PBS, cells were lysed in lysis buffer (10 mM Tris_x0002_HCl, pH 7.5, 10 mM NaCl, and 0.5% NP-40) on ice for 10 min. The nuclei were spun down and then digested in 500 µL MNase digestion buffer (20 mM Tris-HCl pH 7.5, 15 mM NaCl, 60 mM KCl, and 1 mM CaCl2) with 1000 units of MNase (NEB, Cat. #M0247S) by incubating at 37 °C for 20 min. The reaction was stopped by adding 2X STOP buffer (100 mM Tris-HCl pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, and 0.2% sodium deoxycholate). After centrifuged at 15,000 × g at 4 °C for 10 mins, the supernatant was collected, adding the same amounts of Drosophila S2 cell chromatin as spike-in for normalization.  The sample was then treated with proteinase K and RNase A, and purified with the Min-Elute PCR purification kit (Qiagen, Cat. #28006).
Sample extracted was subjected to library preparation with VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat. #ND607-1) following the manufacturer’s instructions.


title: MNase_MYC_ab_1

description: Library name: MNase_MYC_ab_1


title: cuttag_pol2_CT_1

description: Library name: cuttag_pol2_CT_1


title: cuttag_pol2_MYC_1

description: Library name: cuttag_pol2_MYC_1


title: MNase_CT_2

description: Library name: MNase_CT_2


title: MNase_MYC_1

description: Library name: MNase_MYC_1


title: MNase_MYC_2

description: Library name: MNase_MYC_2


title: MNase_CT_1

description: Library name: MNase_CT_1


title: cuttag_pol2_ab_2

description: Library name: cuttag_pol2_ab_2


title: MNase_ab_2

description: Library name: MNase_ab_2


title: MNase_ab_1

description: Library name: MNase_ab_1


title: naive_poly_4

description: Library name: Sample 8

data_processing:
Illumina Novaseq was used for basecalling
The raw data were firstly processed through in-house perl scripts
The RNA-seq data were then mapped to the human reference genome hg38 with Hisat2 v2.0.5
The differential analysis was performed using DESeq
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: PBMC

value: CD4+T cells

tag: treatment

value: poly


title: naive_poly_3

description: Library name: Sample 7

tag: tissue


title: naive_poly_2

description: Library name: Sample 6


title: RNAseq Ba/F3 Rps15 H137Y/H137Y #2

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

description:
Library name: RNA_Rps15H137Y_021
ColName in RawCounts.xlsx : RNA_Rps15H137Y_021

data_processing:
For RNA-seq of total RNA, SeqPurge (v2.0.1) was used for trimming sequence adapters
For footprinting, Adaptor sequence ‘TGGAATTCTCGGGTGCC’ was clipped and sequences were trimmed based on sequencing quality in all datasets with the FASTX toolset (0.0.14). Sequences shorter than 20 nucleotides were hereby discarded and the quality threshold was set at 28
All contaminant PhiX, rRNA, snRNA, sn-o-RNA and tRNA sequences were filtered using a reference information for prefiltering purposes including: (i) the PhiX bacteriophage genome from ftp.ncbi.nih.gov, (ii) mouse rRNA nucleotide sequences from ncbi.nlm.nih.gov/nuccore (obtained using the search term ‘biomol_rrna’), (iii) mouse sn-RNA and sn-o-RNA sequences from Biomart (obtained using the gene type filters for ‘sn-RNA’ and ‘sn-o-RNA’) and (iv) mouse tRNA sequences from gtrnadb.ucsc.edu
Pre -processed trimmed reads from total RNA-seq and ribosomes-protected fragments were aligned using the nf-core/rnaseq (v3.0) to the reference genome using STAR aligner (v.2.6.1d)
Quantification was performed by Salmon (v.1.4.0) using the star_salmon option
Differential expression analysis was performed on the triplicates of two groups (WT and mutant) using the package DESeq2 (v.1.30) in the R environment
Assembly: Mus musculus (GRCm38, release 102) reference genome
Supplementary files format and content: RawCounts.csv: Comma separated file containing all raw read counts for each sample, including RNA and RIBO samples (RPFs)
Supplementary files format and content: DifferentialRNA.xlsx: Excel file containing DeSeq2 results analysing differential RNA expression when comparing experimental conditions (one tab per comparison). This was calculated by using RNA samples read counts only.
Supplementary files format and content: DifferentialRIBO.xlsx: Excel file containing DeSeq2 results analysing differential RIBO (RPFs) expression when comparing experimental conditions (one tab per comparison). This was calculated by using RIBO samples read counts only.
Supplementary files format and content: DifferentialTE.xlsx: Excel file containing DeSeq2 results analysing differential Translation Efficiencies (TE) when comparing experimental conditions (one tab per comparison). This was calculated by using both RNA and RIBO samples read counts.

growth_protocol: 10 – 50 million cells cultured in RPMI‐1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS, Gibco) and with 1 ng/mL interleukin‐3 (IL‐3, Miltenyi Biotec)

extract_protocol:
Cell pellets were lysed in 750 μl of ice-cold Lysis buffer supplemented with 100mg/ml cycloheximide. After debris removal, the lysate was divided for total RNA purification and for subsequent footprinting. For RNA-seq of total RNA, RNA was purified from the lysate with the RNA Clean and Concentrator-5 kit (Zymo Research), followed by NEBnext polyA mRNA magnetic isolation. For footprinting, 10 μg of lysate was digested for 45 min with RNase I at 21°C, and the reaction was stopped by adding SuperaseIn RNase Inhibitor (Thermofisher). Digested lysate was purified on a MicroSpin S-400 HR Sephacryl column (GE Healthcare), and flow through was purified with the RNA Clean and Concentrator-5 (ZymoResearch). Ribosome protected fragments (RPFs) corresponding to 28-30 nt were excised after gel electrophoresis on a Novex TBE-Urea gel (15%) (Thermofisher), and excised gel fragments were incubated overnight in molecular grade water supplemented with ammonium acetate at 4°C. The slurry was transferred to CoStar filter tubes and centrifuged, and flow through was incubated at -80°C for 2 hrs with glycogen and isopropanol. Following centrifugation, the pellet was washed with ice-cold 80% EtOH, dried and resuspended in molecular grade water.
For RNA-seq of total RNA, mRNA where processed with the NEBNext Ultra II directional RNA library prep kit (NEB) in combination with NEBNext Multiplex Oligos for Illumina (Dual Index Primer pairs). For Footprinting, RPFs were 3’ dephosphorylated with T4 PNK (New England Biolabs) and purified using the Oligo Clean and Concentrator kit (ZymoResearch). The 3’ adapter was ligated and fragments were purified using the Small RNA Library prep kit (Lexogen). After 5’ phosphorylation of the RPFs and purification with the Oligo Clean and Concentrator kit, 5’ adapter ligation and first strand cDNA synthesis was performed according to the Small RNA Library prep kit manual. Ribosomal RNA (rRNA) was depleted by adding LNA probes from the QIAseq FastSelect rRNA HMR kit (Qiagen) during the cDNA synthesis reaction. In the indexing PCR amplification step (Small RNA Library prep kit), index primers (Lexogen) were added at both ends of the fragments. Library products were purified with AMPure XP beads, and  adapter dimers and excess index primers were removed by running the samples on a Novex TBE gel (8%) (Thermofisher), the gel part corresponding to the correct library products was excised and purified. Quality of the final libraries was determined on the Agilent Bioanalyzer with the High Sensitivity DNA kit.

treatment_protocol: Cells were treated for 1 min with 0.1 mg/ml cycloheximide prior harvesting


title: RNAseq Ba/F3 WT #2

description:
Library name: RNA_WT_023
ColName in RawCounts.xlsx : RNA_WT_023

value: WT


title: RNAseq Ba/F3 Rps15 H137Y/H137Y #6

description:
Library name: RNA_Rps15H137Y_020
ColName in RawCounts.xlsx : RNA_Rps15H137Y_020


title: RNAseq Ba/F3 WT #3

description:
Library name: RNA_WT_022
ColName in RawCounts.xlsx : RNA_WT_022


title: RNAseq Ba/F3 WT #1

description:
Library name: RNA_WT_024
ColName in RawCounts.xlsx : RNA_WT_024


title: ttseq_CT_1

description: Library name: ttseq_CT_1


title: RNAseq Ba/F3 Rps15 H137Y/H137Y #16

description:
Library name: RNA_Rps15H137Y_019
ColName in RawCounts.xlsx : RNA_Rps15H137Y_019


title: ttseq_CT_2

description: Library name: ttseq_CT_2


title: RNAseq Ba/F3 Rpl10 R98S/R98S #A34

description:
Library name: RNA_Rpl10_018
ColName in RawCounts.xlsx : RNA_Rpl10_018

value: Rpl10 R98S/R98S


title: RNAseq Ba/F3 Rpl10 R98S/R98S #A29

description:
Library name: RNA_Rpl10_017
ColName in RawCounts.xlsx : RNA_Rpl10_017


title: naive_poly_1

description: Library name: Sample 5


title: RNAseq Ba/F3 Rpl10 R98S/R98S #A30

description:
Library name: RNA_Rpl10_016
ColName in RawCounts.xlsx : RNA_Rpl10_016


title: naive_mock_3

description: Library name: Sample 3

value: mock


title: naive_mock_4

description: Library name: Sample 4


title: RNAseq Ba/F3 Rpl5 +/- #68

description:
Library name: RNA_Rpl5_015
ColName in RawCounts.xlsx : RNA_Rpl5_015


title: RNAseq Ba/F3 Rpl5 +/- #76

description:
Library name: RNA_Rpl5_014
ColName in RawCounts.xlsx : RNA_Rpl5_014


title: RNAseq Ba/F3 Rpl5 +/- #80

description:
Library name: RNA_Rpl5_013
ColName in RawCounts.xlsx : RNA_Rpl5_013


title: RNAseq Ba/F3 Rpl22 +/- #60

description:
Library name: RNA_Rpl22het_012
ColName in RawCounts.xlsx : RNA_Rpl22het_012


title: HC3

description: Library name: WC_L4

value: HC


title: HC5

description: Library name: LLN_L2


title: naive_mock_1

description: Library name: Sample 1


title: RNAseq Ba/F3 Rpl22 +/- #13

description:
Library name: RNA_Rpl22het_010
ColName in RawCounts.xlsx : RNA_Rpl22het_010


title: naive_mock_2

description: Library name: Sample 2


title: HC4

description: Library name: HXL_L2


title: HC2

description: Library name: ZYE_L2


title: RNAseq Ba/F3 Rpl22 +/- #16

description:
Library name: RNA_Rpl22het_011
ColName in RawCounts.xlsx : RNA_Rpl22het_011


title: HC1

description: Library name: ZML_L4


title: RNAseq Ba/F3 Rps15 P131S #63

description:
Library name: RNA_Rps15P131S_008
ColName in RawCounts.xlsx : RNA_Rps15P131S_008


title: SLE5

description: Library name: FRRL192012701-1a_L3

value: SLE


title: SLE4

description: Library name: FRRL192012699-1a_L2


title: RNAseq Ba/F3 Rpl11 +/- #406

description:
Library name: RNA_Rpl11_004
ColName in RawCounts.xlsx : RNA_Rpl11_004


title: SLE3

description: Library name: FRRL192012698-1a_L3


title: RNAseq Ba/F3 Rpl11 +/- #22

description:
Library name: RNA_Rpl11_006
ColName in RawCounts.xlsx : RNA_Rpl11_006


title: SLE1

description: Library name: FRRL192012695-1a_L2


title: RNAseq Ba/F3 Rps15 P131S #24

description:
Library name: RNA_Rps15P131S_007
ColName in RawCounts.xlsx : RNA_Rps15P131S_007


title: RNAseq Ba/F3 Rpl11 +/- #414

description:
Library name: RNA_Rpl11_005
ColName in RawCounts.xlsx : RNA_Rpl11_005


title: RNAseq Ba/F3 Rpl22 -/- #776

description:
Library name: RNA_Rpl22hom_003
ColName in RawCounts.xlsx : RNA_Rpl22hom_003


title: SLE2

description: Library name: FRRL192012697-1a_L2


title: 1167 Cell Line,120h,Replicate 2 ,Illumina

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample35
1167_120h_2

data_processing:
RNA Sequencing (both short and long reads) was performed at the National Institute on Aging. Nanopore was base-called using Guppy v. 6.0.1. Short-read data were processed by checking quality (FastQC v. 0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trimming (BBDuk, https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), and mapping to the human genome 38 and annotation version 104 using STAR (v. 2.7.10a). Minimap version 2.17 was used for mapping long-read data.
Stringtie2 (v. 2.2.1) was used for quantification and assembly.
Assembly: HG38 v. 104
Supplementary files format and content: Data at the isoform level generated by stringtie2.
Supplementary files format and content: Tab delimited .txt file containing counts for all samples.

growth_protocol: Human myoblast cell lines AB1167 and AB678 were cultured in Hamm's F10 media with 20% fetal bovine serum (FBS) and Promocell Skeletal Muscle Cell Growth Medium. AB678 and AB1167 myoblasts were cultured in proliferative conditions (day 0).

extract_protocol:
RNA was collected every 24 hours over the 5-day differentiation period. Total RNA collection included a digestion step using DNase I, extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research). RNA quality and quantity were checked using Agilent RNA Screen Tape on the Agilent Tapestation.
For Illumina (short-read) sequencing libraries were prepared from 150 ng RNA, using an Illumina TruSeq Stranded mRNA Library prep kit following the manufacturer’s protocol (Illumina, Cat#20020594). For Nanopore (long-read) sequencing, 75 ng of RNA were used to prepare the sequencing library using a cDNA-PCR Sequencing Kit (SQK-PCS109) following the manufacturer’s protocol (Oxford Nanopore).

treatment_protocol: This study has no chemical treatment to the cells. However, in this study we investigated molecular processes during muscle differentiation , therefore the intervention applied was aimed to differentiate the cell lines. We induced AB678 and AB1167 myoblasts to differentiate by culturing them to high density and replacing the growth medium with differentiation medium, Dulbecco’s modified Eagle medium, (DMEM) containing 2% horse serum.

value: Muscle


title: 1167 Cell Line,120h,Replicate 3 ,Illumina

description:
Library name: Sample36
1167_120h_3


title: 1167 Cell Line,120h,Replicate 1 ,Illumina

description:
Library name: Sample34
1167_120h_1


title: RNAseq Ba/F3 Rpl22 -/- #649

description:
Library name: RNA_Rpl22hom_001
ColName in RawCounts.xlsx : RNA_Rpl22hom_001


title: 1167 Cell Line,96h,Replicate 3 ,Illumina

description:
Library name: Sample33
1167_96h_3


title: RNAseq Ba/F3 Rpl22 -/- #30

description:
Library name: RNA_Rpl22hom_002
ColName in RawCounts.xlsx : RNA_Rpl22hom_002


title: KO 5

city: New York

first: Ankit

last: Gilani

state: New York

address: 413E 69th Street

institute: Weill Cornell Medical College

description: Library name: Sample 10

data_processing:
CLC Genomics workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each samples

source_name: Inguinal SVF

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 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 using manufacturer's protocols.

value: Inguinal SVF

value: Primary Adipocytes

value: Adipogenic differentiation'


title: KO 3

description: Library name: Sample 8


title: RNAseq Ba/F3 Rps15 P131S #20

description:
Library name: RNA_Rps15P131S_009
ColName in RawCounts.xlsx : RNA_Rps15P131S_009


title: KO 2

description: Library name: Sample 7


title: 1167 Cell Line,72h,Replicate 3 ,Illumina

description:
Library name: Sample30
1167_72h_3


title: KO 4

description: Library name: Sample 9


title: 1167 Cell Line,96h,Replicate 1 ,Illumina

description:
Library name: Sample31
1167_96h_1


title: 1167 Cell Line,72h,Replicate 2 ,Illumina

description:
Library name: Sample29
1167_72h_2


title: Control 5

description: Library name: Sample 5


title: 1167 Cell Line,72h,Replicate 1 ,Illumina

description:
Library name: Sample28
1167_72h_1


title: Control 4

description: Library name: Sample 4


title: Control 3

description: Library name: Sample 3


title: Control 2

description: Library name: Sample 2


title: 1167 Cell Line,48h,Replicate 3 ,Illumina

description:
Library name: Sample27
1167_48h_3


title: 1167 Cell Line,24h,Replicate 3 ,Illumina

description:
Library name: Sample24
1167_24h_3


title: 1167 Cell Line,48h,Replicate 1 ,Illumina

description:
Library name: Sample25
1167_48h_1


title: 1167 Cell Line,48h,Replicate 2 ,Illumina

description:
Library name: Sample26
1167_48h_2


title: 1167 Cell Line,24h,Replicate 2 ,Illumina

description:
Library name: Sample23
1167_24h_2


title: 1167 Cell Line,24h,Replicate 1 ,Illumina

description:
Library name: Sample22
1167_24h_1


title: 1167 Cell Line,0h,Replicate 3 ,Illumina

description:
Library name: Sample21
1167_0h_3


title: KO 1

description: Library name: Sample 6


title: 1167 Cell Line,96h,Replicate 2 ,Illumina

description:
Library name: Sample32
1167_96h_2


title: liver, Rougan Keli dosing group, 3

first: xujing

last: Gu

address: Xianlin Street, Qixia District, Nanjing, Jiangsu Province, China

institute: Nanjing Unicersity of Chinese Medicine

description: Library name: Sample3

data_processing:
Raw datas (fastq format) of single-cell 3’ transcriptome were pre-analyzed by MobiVision (version 3.0, MobiDrop), and reads were aligned to  reference genome. Filtered cell-gene matrix was obtained with MobiVision.
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: liver

extract_protocol:
At the end of the animal experiment,  the liver was taken, weighed, and an appropriate amount of liver tissue was placed in 4% formaldehyde, 2.5% glutaraldehyde fixative, or stored in a refrigerator at -80°C, respectively.
Then cells were loaded into microfluidic chip of Chip A Single Cell Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., cat. no. S050100301) to generate droplets with MobiNova-100(MobiDrop(Zhejiang) Co., Ltd., cat. no.A1A40001). Each cell was involved into a droplet which contained a gel bead linked with up to millions oligos (cell unique barcode). After encapsulation, droplets suffer light cut by MobiNovaSP-100(MobiDrop (Zhejiang) Co., Ltd., cat. no.A2A40001) while oligos diffuse into reaction mix. The mRNAs were captured by cell barcodes with cDNA amplification in droplets. Following reverse transcription, cDNAs with barcodes were amplified, and a library was constructed using the High Throughput Single-Cell 3' Transcriptome Kit v2.1 (MobiDrop (Zhejiang) Co., Ltd., cat. no. S050200301) and the 3' Dual Index Kit(MobiDrop (Zhejiang) Co., Ltd., cat. no.S050300301)

value: liver

value: 6 weeks old

value: male

tag: condition

value: liver cirrhosis

value: Rougan Keli


title: 1167 Cell Line,0h,Replicate 1 ,Illumina

description:
Library name: Sample19
1167_0h_1


title: AngII+HS_28days

city: Beijing

first: xianxian

last: Wu

address: Building 5, Panjiayuan Nanli, Chaoyang District, Beijing

institute: Institute of Laboratory Animal Science: Beijing, CN

description:
Library name: Sample2
10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were processed using the Cell Range software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Table separated values files and matrix files

source_name: Abdominal aorta

extract_protocol:
Mouse suprarenal abdominal aortas from one control mouse and two AngII plus salt induce mice were cut and digested in a mixed enzyme solution [450 U/mL collagenase type I (Gibco, cat# 17100-017), 125 U/mL collagenase type XI (Millipore Sigma, cat# C7657), 60 U/mL hyaluronidase type I-s (Millipore Sigma, cat# H3506), and 60 U/mL DNase I (Millipore Sigma, cat# DN25)] for 0.5 h at 37℃. The cell suspension was strained through a 40 μm filter and washed twice with PBS, followed by centrifugation at 500g for 5 minutes. The cells were resuspended in DMEM containing 10% FBS, and were subsequently subjected to sc-RNA seq only when the cell viability was greater than 80%.
10× Genomics Cell Ranger software was used to process the raw single-cell RNA-seq data. After finishing the performance of demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression information production for each cell, the downstream analysis (mainly including quality control, Uniform Manifold Approximation and Projection (UMAP) dimensional reduction, clustering analysis) were carried out Seurat R package (version 4.0.5).

value: Abdominal aorta

value: AngII+HS


title: Control_28days

description:
Library name: Sample1
10× Genomics

value: Normal saline


title: 678 Cell Line,120h,Replicate 2 ,Illumina

description:
Library name: Sample17
678_120h_2


title: 1167 Cell Line,0h,Replicate 2 ,Illumina

description:
Library name: Sample20
1167_0h_2


title: M13 Tgfbr2 cKO E2/MPA

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Library name: Sample 13

data_processing:
Raw sequencing reads were preprocessed for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using HISAT2 Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include normalized gene counts for each Sample

source_name: Endometrium

extract_protocol:
Trizol extracted, purified with Direct-zol RNA Purification Kit from ZYMO Research.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina NovaSeq 6000.

treatment_protocol: After two days of culture, organoids were treated with either vehicle (6 days) or 10 nM E2 (2 days) + 10 nM E2/1 µM MPA (4 days).

value: Endometrium

value: Epithelial

value: Tgfbr2 cKO (Tgfbr2 PRcre+)


title: 678 Cell Line,120h,Replicate 1 ,Illumina

description:
Library name: Sample16
678_120h_1


title: M12 control E2/MPA

description: Library name: Sample 12

value: Control (Tgfbr2 FF)


title: 678 Cell Line,96h,Replicate 3 ,Illumina

description:
Library name: Sample15
678_96h_3


title: M14 Tgfbr2 cKO E2/MPA

description: Library name: Sample 14


title: M15 Tgfbr2 cKO E2/MPA

description: Library name: Sample 15


title: liver, model group, 3

description: Library name: Sample2

tag: Sex

value: no


title: M10 control E2/MPA

description: Library name: Sample 10


title: M11 control E2/MPA

description: Library name: Sample 11


title: Control 1

description: Library name: Sample 1


title: 678 Cell Line,96h,Replicate 2 ,Illumina

description:
Library name: Sample14
678_96h_2

value: Muscle


title: 678 Cell Line,120h,Replicate 3 ,Illumina

description:
Library name: Sample18
678_120h_3


title: M16 Tgfbr2 cKO E2/MPA

description: Library name: Sample 16


title: 678 Cell Line,96h,Replicate 1 ,Illumina

description:
Library name: Sample13
678_96h_1


title: 678 Cell Line,72h,Replicate 3 ,Illumina

description:
Library name: Sample12
678_72h_3


title: M9 control E2/MPA

description: Library name: Sample 9


title: M8 Tgfbr2 cKO veh

description: Library name: Sample 8

value: vehicle


title: 678 Cell Line,72h,Replicate 1 ,Illumina

description:
Library name: Sample10
678_72h_1


title: M6 Tgfbr2 cKO veh

description: Library name: Sample 6


title: M7 Tgfbr2 cKO veh

description: Library name: Sample 7


title: 678 Cell Line,48h,Replicate 3 ,Illumina

description:
Library name: Sample9
678_48h_3


title: 678 Cell Line,48h,Replicate 2 ,Illumina

description:
Library name: Sample8
678_48h_2


title: M4 control veh

description: Library name: Sample 4


title: M5 Tgfbr2 cKO veh

description: Library name: Sample 5


title: M3 control veh

description: Library name: Sample 3


title: 678 Cell Line,24h,Replicate 3 ,Illumina

description:
Library name: Sample6
678_24h_3


title: 678 Cell Line,24h,Replicate 2 ,Illumina

description:
Library name: Sample5
678_24h_2


title: M2 control veh

description: Library name: Sample 2


title: 678 Cell Line,24h,Replicate 1 ,Illumina

description:
Library name: Sample4
678_24h_1


title: M1 control veh

description: Library name: Sample 1


title: WT BMDMs, R848-treated, Replicate 4

city: Minneapolis

first: Anders

middle: John

last: Lindstedt

state: MN

address: 2101 6th Street SE

department: Department of Pharmacology

institute: University of Minnesota

description: Library name: WT4_R848

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36.
Trimmed sequence reads mapped to the Mus musculus GRCm38 reference genome on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were determined using featureCounts from the Subread package v.1.5.2, generating the raw_counts.csv file.
Pre-filtering was done in R to identify genes with at least 10 hit counts in at least 3 of 4 samples within a genotype-treatment group.
DESeq2 in R was used on pre-filtered hit counts and variance-stablizing transformation was applied on gene hit counts, generating the normalized expression values in vst_normalized_counts.csv file.
Assembly: GRCm38
Supplementary files format and content: The raw_counts.csv file includes the raw hit counts of all detected transcripts for every sample.
Supplementary files format and content: The vst_normalized_counts.csv file includes the variance-stablizing transformed hit counts for every sample.

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow was isolated from femurs and tibiae of mice, and erythrocytes were lysed with a hypotonic solution of ammonium-chloride-potassium. For BMDM generation, 8x106 cells were seeded in 150mm untreated, polystyrene plates and cultured in 30mL of Dulbecco’s modified Eagle’s medium (DMEM) with a final concentration of 10% heat-inactivated fetal bovine serum (FBS), 1mM sodium pyruvate, 6mM L-glutamine, 1% Penicillin-Streptomycin (179mM-172mM), and 5% CMG14-12 cell-conditioned medium as a source of M-CSF, at 37 °C, 10% CO2.

extract_protocol:
Cell-culture supernatants were aspirated, cells were washed briefly in phosphate-buffered saline (PBS), and then lysed in TRIzol. RNA was isolated by chloroform extraction followed by the use of an RNeasy Mini Kit.
RNA samples were enriched for mRNA via poly-A tail selection and were sequenced with Illumina NovaSeq (2 x 150bp), generating paired-end reads, with a read depth ranging 17.5M to 27M reads per sample and a mean Q-score ranging from 37.92 to 38.64. Files labeled R1 are in the forward orientation and R2 are in the reverse-complement orientation.

treatment_protocol: BMDMs were resuspended in M-CSF-free DMEM containing 10% heat-inactivated FBS, plated at 1x106 cells/well in untreated, polystyrene 6-well plates, and rested overnight at 37 °C, 10% CO2. After resting, cells were treated 2h with M-CSF-free media alone (NT) or media containing 2 ng/mL LPS from S. Minnesota R595 or 20 ng/mL R848.

value: Bone marrow-derived macrophages

value: WT

value: Female


title: 678 Cell Line,0h,Replicate 1 ,Illumina

description:
Library name: Sample1
678_0h_1


title: WT BMDMs, LPS-treated, Replicate 4

description: Library name: WT4_LPS

value: LPS


title: WT BMDMs, Non-treated, Replicate 4

description: Library name: WT4_NT

value: Non-treated


title: 678 Cell Line,72h,Replicate 2 ,Illumina

description:
Library name: Sample11
678_72h_2


title: IgG ChIPseq ΔCISTR rep1+2

city: Toronto

first: Philipp

last: Maass

state: Ontario

address: 686 Bay St

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

description: Library name: IgG ChIPseq ΔCISTR rep1+2

data_processing:
Details on data processing are described in the manuscript.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: RPMI 2650

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus UCD300 sonicator (Diagenode).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit.

value: RPMI 2650

value: nasal epithelial

value: CISTR

value: IgG ChIP from  ΔCISTR cell lysate


title: IgG ChIPseq WT rep1+2

description: Library name: IgG ChIPseq WT rep1+2

value: IgG ChIP from wildtype cell lysate


title: WT BMDMs, LPS-treated, Replicate 3

description: Library name: WT3_LPS


title: WT BMDMs, Non-treated, Replicate 3

description: Library name: WT3_NT


title: WT BMDMs, R848-treated, Replicate 2

description: Library name: WT2_R848

value: Male


title: FOSL2 ChIPseq ΔCISTR rep2

description: Library name: FOSL2 ChIPseq ΔCISTR rep2

value: FOSL2 ChIP from  ΔCISTR cell lysate


title: WT BMDMs, Non-treated, Replicate 2

description: Library name: WT2_NT


title: FOSL2 ChIPseq ΔCISTR rep1

description: Library name: FOSL2 ChIPseq ΔCISTR rep1


title: FOSL2 ChIPseq WT rep2

description: Library name: FOSL2 ChIPseq WT rep2

value: FOSL2 ChIP from wildtype cell lysate


title: 678 Cell Line,48h,Replicate 1 ,Illumina

description:
Library name: Sample7
678_48h_1


title: 678 Cell Line,0h,Replicate 2 ,Illumina

description:
Library name: Sample2
678_0h_2


title: WT BMDMs, LPS-treated, Replicate 2

description: Library name: WT2_LPS


title: 678 Cell Line,0h,Replicate 3 ,Illumina

description:
Library name: Sample3
678_0h_3


title: WT BMDMs, R848-treated, Replicate 3

description: Library name: WT3_R848


title: 10% input FOSL2 ChIPseq ΔCISTR rep1+2

description: Library name: 10_ input FOSL2 ChIPseq ΔCISTR rep1+2

value: Input from ΔCISTR cell lysate


title: WT BMDMs, Non-treated, Replicate 1

description: Library name: WT1_NT


title: 10% input FOSL2 ChIPseq WT rep1+2

description: Library name: 10_ input FOSL2 ChIPseq WT rep1+2

value: Input from wildtype cell lysate


title: WT BMDMs, LPS-treated, Replicate 1

description: Library name: WT1_LPS


title: eVON, WTC

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

description:
Library name: Sample 3
10X genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (version 8.0.0), which included read alignment to the human reference genome, filtering of empty droplets and generation of gene-cell count matrices.
Assembly: GRCh38 (Human Reference 2024-A - GENCODE v44/Ensembl 110)
Supplementary files format and content: Filtered count matrices in mtx format, gzipped
Supplementary files format and content: Feature and barcode tab-separated values files, gzipped

extract_protocol:
In order to obtain a single-cell suspension, mature eVON were cut into 4 parts with a disposable scalpel and incubated with a digestion buffer containing 0.3% collagenase II (Worthington, LS004176) and 0.2% collagenase IV (Worthington, LS0004186) in PBS on a mini rocker shaker at 37ºC (400 rpm) for 30 min. Digestion reaction was blocked with a sequencing buffer containing PBS (without Ca2+ and Mg2+), 2% FBS and 0.5% EDTA 0.5M. The samples were then filtered through 40mm strainers (Falcon, 352340) and centrifuged for 4 min at 1500 rpm at room temperature. Cells were then resuspended in a sequencing buffer, counted and stored at 4ºC until loading on a 10X Genomics microfluidic chip.
The single-cell experiment was performed with the 10x Chromium Single Cell 3’ v3.1 kit according to manufacturer’s instructions. Briefly, cells combined with reverse transcription mix, gel beads, and oil were loaded onto a 10x microfluidic chip to form nanodroplets (GEMs). Each GEM contained a cell where first-strand cDNA synthesis occurred, tagging each mRNA with a unique molecular identifier  (UMI) and a cell-specific barcode. Droplets were broken, fractions were pooled and purified using Dynabeads MyOne Silane, and cDNA was amplified with PCR. Single-cell libraries were prepared through fragmentation, end repair, A-tailing, and double-sided size selection with SPRIselect Reagent. P5 and P7 adapters were ligated, and individual sample indices from Dual Index Plate were added for pooling and later demultiplexing of libraries. Library quality and quantity were checked with high-sensitivity DNA assays on an Agilent Bioanalyzer and Fragment Analyzer.

value: hiPSC

value: male


title: LynKO BMDMs, R848-treated, Replicate 4

description: Library name: LynKO4_R848

value: Bone marrow-derived macrophages

value: LynKO


title: MHU4_GC5_1G

type: RNA

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

hyb_protocol: The arrays were incubated for 16 h (60 rpm) at 45 °C in a GeneChip™ Hybridization Oven 645 (Thermo Fisher Scientiﬁc) and washed with a GeneChip™ Fluidics Station 450 (Thermo Fisher Scientiﬁc) according to the manufacturer’s protocol.

scan_protocol: The samples were scanned using a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientiﬁc). We analyzed the results via the Transcriptome Analysis Console (Thermo Fisher Scientiﬁc).

data_processing: The data was analyzed with Transcriptome Analysis Console (TAC) 4.0.3.

label: biotin

source_name: Mandible, C57BL/6J male, JAXA

label_protocol: We produced fragmented and labeled cDNA from 50 ng of total RNA with a GeneChip™ 3' IVT Pico Kit (Thermo Fisher Scientiﬁc).

growth_protocol: Six mice in the transportation cage unit (TCU) were launched aboard SpX-17 on May 7, 2019, from the NASA Kennedy Space Center (KSC) and were then transported to the ISS. To determine the effects of different gravitational forces on mice during spaceflight, the mice were maintained on the ISS for approximately one month.

extract_protocol: RNA was extracted from the samples via a miRNeasy® FFPE Kit (QIAGEN, Hilden, Germany), RNase Free DNase Set (QIAGEN), NanoDrop TM One (Thermo Fisher Scientific, MA, USA) and an Agilent RNA 6000 Nano Kit (Agilent Technologies, Inc., Santa Clara, California, USA), and the quality was assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, California, USA).

treatment_protocol: Gravity was set to 1/6G (0.167 g = lunar gravity = partial gravity) to mimic the gravity of the moon, as the most feasible future missions are to explore the moon. Habitat cage units (HCUs) were placed on the floor, each housing six mice, and a short radius centrifuge (MARS-S) was used to generate 1/6G. In contrast, the mice in the 1G group were housed on Earth and in the same MHU as those in the 1/6G group were.

value: Mandible

tag: strain

value: wild type


title: eVON, WiBJ

description:
Library name: Sample 2
10X genomics

source_name: WiBJ

value: WiBJ

value: female


title: MHU4_GC6_1G


title: LynKO BMDMs, LPS-treated, Replicate 4

description: Library name: LynKO4_LPS

value: LPS

value: Female


title: FOSL2 ChIPseq WT rep1

description: Library name: FOSL2 ChIPseq WT rep1

value: RPMI 2650

value: nasal epithelial

value: WT


title: eVON, 409B2

description:
Library name: Sample 1
10X genomics


title: LynKO BMDMs, Non-treated, Replicate 4

description: Library name: LynKO4_NT

value: Non-treated


title: U87 cells, U2

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

description: Library name: U87 cells-U2

data_processing:
Raw data were processed with Cutadapt.
The clean reads were aligned to the reference Database of miRBase22.1, piRNABank and RfamV14.1
The UMI Counts of miRNA ,piRNA and SmallRNA were calculated by perl.
The expression of miRNA ,piRNA and SmallRNA was normalized to CPM
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text file includes row counts for each Sample

extract_protocol:
Small RNAs were extracted from Ac4ManNAz-labeled U87, LN229, and Hela cells by using RNAzol RT kit (Molecular Research Center, RN-190). The extracted small RNAs were treated with DBCO-biotin and then purified through Zymo columns. The MyOne C1 Streptavidin magnetic beads (Thermo Fisher Scientific, REF: 65001) were utilized to enrich Ac4ManNAzlabeled glycoRNAs. MyOne C1 streptomycin avidin magnetic beads containing 50 ng/mL glycogen were incubated in 500 μL Biotin Wash Buffer at 25 ℃ for 1h, then centrifuged at 3000 rpm at 4℃ for 2 min, and the supernatant was discarded. The magnetic beads were re-suspended in 500 μL Biotin Wash Buffer, added into small RNAs, rotated and mixed at 4 ℃ for 2 h, and centrifuged at 3000 rpm for 2 min. The supernatant was collected, and purified using Zymo columns. The magnetic beads and the small RNAs bound to them were re-suspended in solution containing 0.75M NaCl, 10 mM EDTA, and 10 mM Tris-Cl (pH 7.4) and incubated at 22 °C for 5 min. The above mixture was mixed with 1× volume of 5% B-mercaptoethanol (BME) solution, incubated at 22 °C for 5 min, and centrifuged at 3000 rpm for 2 min. The glycoRNA-rich supernatant was collected and purified by Zymo columns.
RNA quality was checked using Agilent 4200 TapeStation (Agilenttechnologies, Santa Clara, CA, US) according to standard procedures. Sequencing libraries were constructed by QIAseq miRNA Library Kit for Illumina (Cat #331505, Qiagen) according to manufacturer's instructions. The sequencing was performed on an Illumina NovaSeq platform (Illumina, San Diego, CA, USA).


title: LynKO BMDMs, Non-treated, Replicate 3

description: Library name: LynKO3_NT


title: WT BMDMs, R848-treated, Replicate 1

description: Library name: WT1_R848

value: Male


title: LynKO BMDMs, R848-treated, Replicate 3

description: Library name: LynKO3_R848