title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 2

description:
417_KO_CD4_2_S39_R1_001_bio_2
Library #56


title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 2, replicate 1

status: Public on Jul 09 2025

type: SRA

city: Baltimore

first: Brian

last: Mog

state: MD

address: 1650 Orleans street, CRB1 room 520

country: USA

institute: Ludwig Center at Johns Hopkins

description:
417_KO_CD4_1_S31_R1_001_bio_2
Library #55

library_source: transcriptomic

data_processing:
FASTQ files were demultiplexed and only reads containing the 5’ unique molecular identifiers (UMIs: ATTGCGCAATGNNNNNNNNGGGGG) were retained after trimming adapters and extracting the UMI. Reads were aligned to hg38 with RNA STAR using gencode release 44 comprehensive gene annotation followed by UMI deduplication using UMI-tools. Gene-counts of unique reads were generated with HTseq. Differentially expressed genes were identified with DEseq2 and defined as genes with adjusted p-value less than 0.05, base-mean expression greater than 4, and absolute value of fold change greater than 1.2. Heatmaps were Z-score scaled by row on variance stabilizing transformations of the normalized count matrix produced by DEseq2. Pathway analysis was performed using the STRING tool on differentially expressed genes and Reactome gene sets were reported. The strength of enrichment was calculated with the following expression: log10(observed number of genes/expected number of genes).
Assembly: hg38
Supplementary files format and content: Individual tabular processed data files are the count outputs from the program htseq-count on samples after UMI de-deuplication. These files were the input into the DEseq2 differential expression analysis.
Supplementary files format and content: The file "DEseq2_Normalized_Counts_Unedited_STAR-3_Co-STAR-1_Co-Cultures.tabular" contains the normalized counts for each sample after DEseq2 analysis.

molecule: polyA RNA

organism: Homo sapiens

source_name: T cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque PLUS (Cytiva, 17144002) gradient centrifugation from healthy donor leukopaks (StemCell and Charles River). CD3+ T cells were isolated by negative selection (StemCell Technologies, 17951) and activated with Dynabeads Human T-Activator CD3/CD28 (Thermo Fisher Scientific, 11132D) at a 1:1 bead-to-cell ratio in T cell media, which consisted of RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (Cytiva, SH30070.03), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15140163), 100 IU/mL recombinant human IL-2 (Proleukin, Prometheus Laboratories), and 5 ng/mL recombinant human IL-7 (BioLegend, 581908). After 48-56 hours of activation, T cells were separated from CD3/CD28 beads by two passes over a magnet and allowed to rest while CRISPR reagents were prepared. For each electroporation condition of simultaneous TRAC knock-in and TRBC knock-out, 50 pmols of each crRNA were independently mixed with 25 pmols of Alt-R A.s. Cas12a (Cpf1) Ultra (IDT, 10001273) and 37.5 pmols of Alt-R Cpf1 Electroporation Enhancer (IDT, 1076301) in a total volume of 1.27 µl of Nuclease Free Duplex Buffer (IDT, 11-01-03-01) for at least 15 minutes before combining the two RNPs at a 1:1 volume ratio. The TRAC and TRBC RNPs were then mixed with 0.5 µg HDRT diluted in 2.4 uL OptiMEM for a final volume of 5 µL per electroporation condition. Immediately prior to electroporation, T cells were centrifuged at 90g for 10 minutes, then resuspended at 0.75-1.25 x 106 T cells in 20 µl P3 buffer (Lonza, V4XP-3032) and combined with the 5uL Cpf1 RNP and HDRT mixture. Cells were nucleofected in 16-well cuvettes (Lonza, V4XP-3032) with a 4D Nucleofector X-Unit (Lonza, AAF-1003X) using pulse code EH115. After nucleofection, 80 µl pre-warmed cytokine free T cell media was added to cells and the cuvette strip was placed in a 37 °C incubator for 20 min. The cells were then diluted in 1 mL of T cell media and transferred to a 24-well plate. T cell media was changed every 3 days until functional assays on days 11 or greater after initial activation. STAR-3 and Co-STAR-1 T cells were generated using CRISPR-HDR as described above. On days 8-9 after activation, knock-in+ T cells were isolated using the EasySep™ Release Human PSC-Derived Neural Crest Cell Positive Selection Kit (StemCell, 100-0047).

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions and quantified by RNA ScreenTape (Agilent, 5067-5576).
The SMART-Seq mRNA LP (with UMIs) kit (Takara, 634765) and the Unique Dual Index Kit (1–96) (Takara, 634752) were used to generate cDNA and prepare sequencing libraries from two independent batches of T cells, with 3 independent cDNA libraries per condition. Libraries were sequenced on a NovaSeq 6000 (Illumina) using the 100 cycle single-end configuration at approximately 25 million reads per technical replicate.

treatment_protocol: On days 13-14 after activation, unedited, STAR-3, or Co-STAR-1 T cells were cocultured with KMS26-MUT, KMS26-NULL, or no target cells at an E:T ratio of 1:5 for 18 hours followed by flow sorting of CD4+ and CD8+ T cells into RNAprotect Tissue Reagent (Qiagen, 76104).

tag: cell type

value: T cell

tag: susbet

tag: receptor

tag: co-culture condition

tag: biological replicate

tag: technical replicate


title: H3K4me3, SP, ND, rep3

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E Superior St

department: Department of Medicine

institute: Northwestern University

library_source: genomic

data_processing:
none provided
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: kidney

extract_protocol: none provided

treatment_protocol: SGTL2 WT and MT mice were fed with HFD for 18 weeks. Single nuclei was isolated from renal cortex.

tag: tissue

value: kidney

tag: chip antibody

tag: genotype

value: Sglt2 mutant

tag: treatment

value: normal diet


title: H3K27me3, WT, HFD, Placebo, rep5

treatment_protocol: SGTL2 MT mice were fed with HFD for 8 weeks. Then, MAT2Ai (10 mg/kg BW) was injected into intraperitoneal cavity for eight weeks.

value: WT

value: high-fat diet, Placebo


title: H3K4me3, SP, ND, rep2


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 2

description:
Mock_T_Only_CD8_2_S32_R1_001_bio_1
Library #53

value: Unedited

value: No target cells


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 3

description:
Mock_T_Only_CD8_3_S33_R1_001_bio_1
Library #54


title: H3K4me3, WT, HFD, rep1

value: high-fat diet


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 3

description:
Mock_T_Only_CD4_3_S27_R1_001_bio_1
Library #51


title: Unedited T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 1

description:
Mock_T_Only_CD8_1_S31_R1_001_bio_1
Library #52


title: H3K4me3, WT, ND, rep3


title: H3K4me3, WT, ND, rep2


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 2

description:
Mock_T_Only_CD4_2_S26_R1_001_bio_1
Library #50


title: H3K4me3, WT, ND, rep1


title: Unedited T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 1

description:
Mock_T_Only_CD4_1_S25_R1_001_bio_1
Library #49


title: H3K27me3, SP, HFD, rep3


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
Mock_Parental_CD8_3_S9_R1_001_bio_1
Library #48


title: H3K27me3, SP, HFD, rep2


title: H3K27me3, SP, ND, rep3


title: H3K27me3, SP, HFD, rep1


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
Mock_Parental_CD8_2_S8_R1_001_bio_1
Library #47


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 2, replicate 1

description:
417_KO_CD8_1_S32_R1_001_bio_2
Library #58


title: H3K27me3, SP, ND, rep2


title: Unedited T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
Mock_Parental_CD8_1_S7_R1_001_bio_1
Library #46


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
Mock_Parental_CD4_3_S3_R1_001_bio_1
Library #45


title: H3K27me3, WT, HFD, rep3


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
Mock_Parental_CD4_1_S1_R1_001_bio_1
Library #43


title: Unedited T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
Mock_Parental_CD4_2_S2_R1_001_bio_1
Library #44


title: H3K4me3, WT, HFD, rep2


title: H3K27me3, SP, ND, rep1


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
Mock_KO_CD8_2_S20_R1_001_bio_1
Library #41


title: H3K27me3, WT, HFD, rep2


title: H3K27me3, WT, HFD, rep1


title: H3K27me3, WT, ND, rep3


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
Mock_KO_CD8_1_S19_R1_001_bio_1
Library #40


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
Mock_KO_CD4_3_S15_R1_001_bio_1
Library #39


title: Unedited T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
Mock_KO_CD8_3_S21_R1_001_bio_1
Library #42


title: H3K27me3, WT, ND, rep1


title: H3K27me3, WT, ND, rep2


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
Mock_KO_CD4_1_S13_R1_001_bio_1
Library #37


title: SP, Mat2ai, kidney, rep5

molecule: total RNA

source_name: Kidney

treatment_protocol: SGTL2 WT and MT mice were fed with HFD for 8 weeks, then they were treated with placebo (DMSO) or (E)-4-(2-Chloro-6-fluorostyryl)-N-methylaniline (MAT2Ai, 10 mg/kg BW) through the intraperitoneal route three times per week for 8 weeks.  Single nuclei was isolated from renal cortex.

value: Kidney

value: Mat2a inhibitor


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 2

description:
566_T_Only_CD8_2_S35_R1_001_bio_1
Library #35


title: SP, Mat2ai, kidney, rep4


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 3

description:
566_T_Only_CD8_3_S36_R1_001_bio_1
Library #36


title: SP, Placebo, kidney, rep5

value: Placebo


title: SP, Mat2ai, kdiney, rep3


title: SP, Placebo, kidney, rep3


title: Co-STAR-1 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 1

description:
566_T_Only_CD8_1_S34_R1_001_bio_1
Library #34


title: SP, Mat2ai, kidney, rep2


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 3

description:
566_T_Only_CD4_3_S30_R1_001_bio_1
Library #33


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 1

description:
566_T_Only_CD4_1_S28_R1_001_bio_1
Library #31


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
566_Parental_CD8_3_S12_R1_001_bio_1
Library #30


title: Co-STAR-1 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 2

description:
566_T_Only_CD4_2_S29_R1_001_bio_1
Library #32


title: Unedited T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
Mock_KO_CD4_2_S14_R1_001_bio_1
Library #38


title: SP, Placebo, kidney, rep2


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
566_Parental_CD8_2_S11_R1_001_bio_1
Library #29


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
566_KO_CD8_2_S23_R1_001_bio_1
Library #23


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
566_Parental_CD4_3_S6_R1_001_bio_1
Library #27


title: SP, Placebo, kidney, rep1


title: WT, Mat2ai, kidney, rep2


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
566_Parental_CD8_1_S10_R1_001_bio_1
Library #28


title: SP, Mat2ai, kidney, rep1


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
566_Parental_CD4_2_S5_R1_001_bio_1
Library #26


title: WT, Mat2ai, kidney, rep1


title: SP, Placebo, kidney, rep4


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
566_KO_CD8_3_S24_R1_001_bio_1
Library #24


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
566_KO_CD4_3_S18_R1_001_bio_1
Library #21


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
566_Parental_CD4_1_S4_R1_001_bio_1
Library #25


title: WT, Mat2ai, kidney, rep5


title: WT, Placebo, kidney, rep5


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
566_KO_CD4_2_S17_R1_001_bio_1
Library #20


title: WT, Mat2ai, kidney, rep4


title: WT, Placebo, kidney, rep3


title: Co-STAR-1 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
566_KO_CD8_1_S22_R1_001_bio_1
Library #22


title: Co-STAR-1 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
566_KO_CD4_1_S16_R1_001_bio_1
Library #19


title: WT, Placebo, kidney, rep2


title: cardiac fibroblasts, OE_Tfap4, repilcate 2

city: Wuhan

first: jie

last: liu

state: Hubei

address: Fruit Lake Street

country: China

institute: Wuhan university

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Mus musculus from GRCM38/mm10 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample.

source_name: heart

extract_protocol:
Total RNAs were harvested using TRIzol Reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA library for RNA-seq were prepared using KCTM Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: heart

tag: cell line

value: primary cell

value: fibroblasts

value: TFAP4 overexpression


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 2

description:
417_T_Only_CD8_2_S57_R1_001_bio_1
Library #17


title: cardiac fibroblasts, OE_Tfap4, repilcate 1


title: cardiac fibroblasts, OE_LacZ, repilcate 2

value: control


title: WT, Mat2ai, kidney, rep3


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 2

description:
417_T_Only_CD4_2_S54_R1_001_bio_1
Library #14

value: T cell


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 1

description:
417_T_Only_CD4_1_S53_R1_001_bio_1
Library #13


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
417_Parental_CD8_3_S45_R1_001_bio_1
Library #12


title: 20m_WT_5

city: Paris

first: Isadora

last: Lenoel

address: 47 Boulevard de l'hopital

country: France

institute: Paris Brain Institute

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting cd  raw counts and TPM

source_name: Spinal Cord

extract_protocol:
Motor neuron laser-microdissection was performed as previously described (Lobsiger et al., 2007). Briefly, lumbar spinal cords were rapidly recovered, rinsed and frozen in -40°C Isopentane in HistoPrep OCT compound (Fisher Scientific International), cryosectioned (16 μm) and sections mounted on RNase-free PENfoil covered glass slides (Leica Microsystems). Sections were fixed for 60 s in 75% EtOH and stained for 30 s in 4% cresyl-violet acetate/0.3% acetic-acid (Sigma) to identify motor neurons, dehydrated in graded solutions of ethanol (70%, 95%, 100%) and dehydrated for 1 h before laser-microdissection (Leica LMD-7000). From one spinal cord, 200 large (diameter ≥ 25 μm) ventral horn motor neurons of the lumbar L4–L6 region were collected dryly, then immediately lysed in lysis buffer (NucleoSpin RNA XS Kit, Machery-Nagel) and the lysate stored at -80°C. Approximately 10 ng of total RNA can be recovered per 200 laser-microdissected motor neurons (NucleoSpin RNA XS Kit; with DNase treatment)
Since the RNAconcentration was too low to be detected using a Nanodrop, test samples were used to assess  RIN quality. Since the same number of motor neurons were taken per sample, the same volume of RNA was used (10µL).cDNA synthesis was performed using the Smartseq V4 TAKARA kit with linear pre-amplification.
Library preparation was made with amplified cDNA for every sample using the Nextera XT DNA Library Preparation Kit (Illumina). 47 samples were run with a 1600 million cartridge to reach an average coverage of 34 million reads per sample (100bp, paired-ends). Sequencing was performed using the Novaseq 6000 sequencer (Illumina). Library preparations and sequencing were performed by the ICM iGenSeq core facility.

value: Spinal Cord

value: Motor neurons

tag: age

value: 20 months


title: 20m_WT_4

value: WT


title: WT, Placebo, kidney, rep4


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
417_Parental_CD8_1_S43_R1_001_bio_1
Library #10


title: 20m_WT_3


title: STAR-3 T cells,CD8 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
417_Parental_CD8_2_S44_R1_001_bio_1
Library #11


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 3

description:
417_Parental_CD4_3_S39_R1_001_bio_1
Library #9


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 1

description:
417_Parental_CD4_1_S37_R1_001_bio_1
Library #7


title: STAR-3 T cells,CD4 subset, cultured with KMS26-MUT, experiment 1, replicate 2

description:
417_Parental_CD4_2_S38_R1_001_bio_1
Library #8


title: WT, Placebo, kidney, rep1


title: 20m_WT_2


title: 20m_WT_1


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
417_KO_CD8_3_S52_R1_001_bio_1
Library #6


title: 20m_KO_6

value: KO


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 1

description:
417_T_Only_CD8_1_S56_R1_001_bio_1
Library #16


title: 20m_KO_4


title: STAR-3 T cells,CD8 subset, cultured with No target cells, experiment 1, replicate 3

description:
417_T_Only_CD8_3_S58_R1_001_bio_1
Library #18


title: STAR-3 T cells,CD4 subset, cultured with No target cells, experiment 1, replicate 3

description:
417_T_Only_CD4_3_S55_R1_001_bio_1
Library #15


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
417_KO_CD8_1_S50_R1_001_bio_1
Library #4


title: 20m_KO_2


title: STAR-3 T cells,CD8 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
417_KO_CD8_2_S51_R1_001_bio_1
Library #5


title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 2

description:
417_KO_CD4_2_S48_R1_001_bio_1
Library #2


title: 20m_KO_3


title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 3

description:
417_KO_CD4_3_S49_R1_001_bio_1
Library #3


title: cardiac fibroblasts, OE_LacZ, repilcate 1


title: 20m_WT_6


title: 20m_KO_1


title: STAR-3 T cells,CD4 subset, cultured with KMS26-NULL, experiment 1, replicate 1

description:
417_KO_CD4_1_S47_R1_001_bio_1
Library #1


title: 4_WT_5

source_name: Brain

extract_protocol:
Microglial isolation was performed as previously described (Hammond et al.). Mice were all females and were deeply anesthetized using xylazine (Rompun 0.2%) and ketamine (Imalgene 500) and transcardially perfused with ice-cold 0.1 M PBS and whole brains were collected. Brains were Dounce homogenized in ice cold Hank’s balanced salt solution (HBSS) 10 times with the loose and 5 times with tight pestles. Tissues were passed through a 70-μm cell strainer (Corning). Cells were pelleted by centrifugation (300g, 5 minutes), resuspended in 40% Percoll solution (GE Healthcare), HBSS and centrifugated (30 minutes, 500g, 4°C). Myelin was then removed with the Percoll. Cell pellet was washed in HBSS and resuspended in PBS/2mM EDTA (Life Technologies).  Cells were stained with Zombie Green (1/1000, Biolegend) for 15 minutes at 4°C. All samples were then washed and resuspended in ice cold FACS buffer (5% FCS, 2mM EDTA, in 1x PBS) with TruStain FcX (Biolegend) for 10 minutes. Antibodies were then added Cd11b (PE, 1/100, Biolegend 101207), CD45 (SBB700, 1/20, Biorad, MCA1031) and incubated for 20 minutes at 4°C. Finally, cells were sorted using Biorad S3 cell sorter. Approximately 10000 to 30000 cells were isolated per sample and directly lysed with RNA lysis buffer (RNeasy micro kit, Qiagen). Lysates were stored at -80°C before RNA extraction according to manufacturer’s protocol (RNeasy micro kit, Qiagen). Quantity of RNA used for sequencing was adjusted to the number of cells sorted, and 2500 to 5000 cells were sequenced.
Since the RNAconcentration was too low to be detected using a Nanodrop, test samples were used to assess  RIN quality. RNA quantity sequenced was adjusted to the number of FAC-sorted cells, to sequence between 2500 and 5000 cells per sample.cDNA synthesis was performed using the Smartseq V4 TAKARA kit with linear pre-amplification.
Library preparation was made with amplified cDNA for every sample using the Nextera XT DNA Library Preparation Kit (Illumina). 47 samples were run with a 1600 million cartridge to reach an average coverage of 34 million reads per sample (100bp, paired-ends). Sequencing was performed using the Novaseq 6000 sequencer (Illumina). Library preparations and sequencing were performed by the ICM iGenSeq core facility.

value: Brain

value: Microglial cells

value: 4 months


title: 4_WT_4


title: not_migrated_R8

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Raw reads were assessed for quality by FastQC (v.0.12.0, Babraham Institute Cambridge, UK) and pre-processed with FASTQ Toolkit v.2.2.5 for adapter trimming and low quality (Q<30) filtering of the reads.
Trimmed sequence reads were aligned to the reference Genome assembly GRCh38 and GENCODE Gene Set v.38 for gene annotation using salmon aligner (v.1.5) using a decoy-aware transcriptome index with k-mers of length 31 and normalizing for local GC content.  Transcripts were merged to genes using Bioconductor R (v.4.3.1) package tximport (v1.28.0). Gene-level normalization and identification of differentially expressed genes (DEGs) were performed with R package DESeq2 v.1.40.2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized values (by DESeq2) for each Sample

source_name: blood

extract_protocol:
RNA from migrated and non-migrated CD8+ T cells of eight patients with AS was iextracted using the QIAGEN's RNeasy Plus Micro Kit, according to the manufacturer's instructions.
Ovation SoLo RNA-seq Library Preparation kit (Tecan Genomics, Redwood city, CA) was used for library preparation following the manufacturer’s instructions. After quantification, RNA samples quality was tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). The libraries were sequenced on paired-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA).

value: blood

value: isolated CD8+ cells

tag: Sex

value: male

tag: disease state

value: radiographic axial Spondyloarthritis


title: 4_WT_6


title: not_migrated_R7

value: female


title: 4_WT_3


title: not_migrated_R6


title: not_migrated_R5


title: 4_WT_2


title: 20m_KO_5


title: not_migrated_R4


title: 4_WT_1


title: 4_KO_4


title: not_migrated_R2


title: not_migrated_R3


title: 4_KO_5


title: migrated_R8


title: 4_KO_2


title: not_migrated_R1


title: 4_KO_3


title: migrated_R7


title: migrated_R6


title: 4_HET_5

value: HET


title: migrated_R4


title: 4_HET_4


title: migrated_R3


title: 4_HET_3


title: 4_HET_1


title: migrated_R2


title: migrated_R1


title: 22_WT_7

value: 22 months


title: IMR-32_PTC-028_3

city: Nagoya

first: Hiromasa

last: Aoki

address: 3-1 Tanabe-dori, Mizuho-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Nagoya City University

data_processing:
Data processing was conducted on RaNA-seq (https://ranaseq.eu), a rapid analytical platform on a web browser utilizing salmon.
Assembly: GRCh38
Supplementary files format and content: Excel file containing the TPM for each gene.

growth_protocol: IMR-32 cellswere cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 mg/ml streptomycin at 37°C in a 5% CO2 environment.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. This process was performed by novogene.

treatment_protocol: IMR-32 cells were seeded in a 6-well plate at 2.0×10^5 cells/well and cultured for 24 h at 37°C, 5% CO2. After 24 hours, cells were treated with DMSO or PTC-028 (25 nM) for another 24 h.

value: Cancer cells


title: 22_WT_6


title: 22_WT_5


title: 22_WT_3


title: IMR-32_PTC-028_1


title: IMR-32_PTC-028_2


title: 22_WT_4


title: IMR-32_CTRL_3

value: DMSO


title: IMR-32_CTRL_1


title: 22_WT_2


title: IMR-32_CTRL_2


title: 4_KO_1


title: MGG8 scRNAseq

city: Orsay

first: Giorgio

last: Seano

address: Bâtiment 110, Rue Henri Becquerel

department: INSERM U1021 - CNRS UMR3347

institute: Institut Curie

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcodes processing, gene counting, and aggregation were performed using CellRanger v3.0.1 on hg38
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: brain

growth_protocol: cells were maintained in neurospheres using NeuroCult basal medium with NeuroCult proliferation supplement (STEMCELL technologies, #05751), 20ng/ml EGF, 20ng/ml bFGF, 5ug/ml heparin (STEMCELL Technologies, #07980) and gentamycin (Sigma) (NC complete media) in low attachment flasks (Corning, #3814)

extract_protocol:
MGG8 cells were dissociated as described, washed and dead cells were removed using the dead cell removal kit (Miltenyi Biotech, #130-090-101). Briefly, cells were incubated for 15min at room temperature with dead cell removal microbeads, then diluted in 1X binding buffer and loaded in the column. Effluent contained live cells and the column was washed with 1X binding buffer in order to maximize efficiency. Live cells were centrifuged, resuspended in 1X PBS BSA 0.04%, counted and resuspended at 106 cells/ml.
Chromium Single Cell 3’ v3.1 Library and Gel Bead kit (PN-1000121) and Chromium Next GEM Chip G Single Cell Kit (PN-1000127) were used according to the manufacturer’s instructions. 3000 cells were loaded on the chip, then 10X capture and library protocol was used without modification and samples were sequenced on the Illumina Novaseq 6000

value: brain

value: patient-derived glioblastoma cell line


title: GB-Hybrid_H3K27me3

data_processing:
scChIPseq data were processed using the pipeline scChIP-inDrop v1.1.0 (https://doi.org/10.5281/zenodo.10523263) based on Prompsy et al. Nat Comm 2020 and Grosselin et al. Nat Genet 2019.
Briefly, reads were aligned to the hg38 reference genome with STAR (v2.7.8a) and PCR and RT duplicates were removed to produce 50kb binned count matrices.
Assembly: hg38
Supplementary files format and content: Tab-seperated value files and matrix files

extract_protocol:
Full single cell ChIP-seq protocol has been previously described in (Grosselin, 2019). Briefly, 1M cells were labeled by 20 min incubation of 1 μM CellTrace solution (CellTrace CFSE, Thermo Scientific, C34554) at room temperature. Cells were then washed and incubated in culture medium for 15 minutes to allow the CellTrace reagent to undergo acetate hydrolysis. Labeled cells were resuspended in a suspension mix (PBS supplemented with 30% Percoll, 0.1% Pluronic F-68, 25 mM HEPES pH 7.4 and 50 mM NaCl) and encapsulated in 45pL droplets with a digestion mix (0,1 M Tris-HCl pH 7.4, 0,3 M NaCl, 2,15% Tritonx100, 0,22% NaDoc, 0,01 M CaCl2, 0,2 U/µl Micrococcale Nuclease (Thermo Scientific, EN0181), 1x Protease Inhibitor Cocktail and 2µM Sulforhodamine B). Once encapsulated, cells droplets are collected and incubated at 37°C for 20 minutes for cellular lysis and chromatin digestion. In parallel, beads with unique double-stranded barcodes were encapsulated in 100pL droplets with a ligation mix (0,1 M EGTA, 2 mM ATP, 2 μM Sulforhodamine B, 0,38 U/μL Fast link DNA ligase (Lucigen, LK0750H)) and a repair mix (4 mM dNTP, 2 μM Sulforhodamine B, 0,1 x End-it Repair mix (Lucigen, ER81050), 0,1 U/μL Fast link DNA ligase (Lucigen, LK0750H)). Beads droplets and cells droplets were then fused with a 1:1 ratio by electrocoalescence and counted by laser detection as previously described (Grosselin, 2019).  Double-stranded DNA barcodes were released in fused droplets by UV exposure (1 min, 230mW/cm2) and ligated to nucleosomes during an overnight incubation at 16°C. Immunoprecipitation of barcoded nucleosomes associated with H3K27me3 histone mark (Antibody Cell Signaling Technology, 9733-C36B11, 1/200) or H3K4me3 histone mark (Antibody Cell Signaling Technology, 9751-C42D8, 1/200) was performed overnight at 4°C on a rotating wheel.
DNA amplification and library preparation were performed as described in (Grosselin, 2019). Libraries were then sequenced on the NovaSeq 6000 in PE100, with a coverage of 100,000 reads per cell.

tag: antibody


title: 22_WT_1


title: 22_KO_6


title: 22_KO_5


title: migrated_R5


title: GBH-neg_H3K27me3

value: Antibody Cell Signaling Technology, 9733-C36B11


title: 4_HET_2


title: GB-Hybrid_H3K4me3

value: Antibody Cell Signaling Technology, 9751-C42D8


title: 22_KO_4

value: KO


title: 22_KO_3

value: Brain


title: MGG8_bulk_3

description:
D1342T006
MGG8_GB-Hybrid_2_tpm.csv

data_processing:
The reads obtained were processed using the Curie Institute Nextflow RNA-seq analysis pipeline
reads quality was assessed using FastQC and mapped to the reference genome (hg38) using STAR software
raw reads count tables were generated using STAR
Software versions and full pipelines are available at https://github.com/bioinfo-pf-curie/RNA-seq/
Assembly: hg38
Supplementary files format and content: Matrix table with TPM gene counts for every gene and every sample (.csv)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using 100ng to 1ug of RNA using Illumina library structure (Stranded mRNA Library preparation, Illumina), according to the manufacturer’s instructions. Samples were sequenced as 100bp paired-end runs on the Novaseq 6000 (Illumina).

treatment_protocol: In-vitro cells were treated with 5Gy of irradiation using a gamma ray irradiator 5 days before RNA extraction. For population-based RNA sequencing of MGG4 and MGG8, cells were sorted based on fluorescent intensity of reporters.


title: GBH-neg_H3K4me3


title: MGG8_GB-Hybrid_3

description:
D1342T005
MGG8_GB-Hybrid_2_tpm.csv


title: 22_KO_1

value: Microglial cells


title: 22_HET_6


title: MGG8_bulk_2

description:
D1342T004
MGG8_GB-Hybrid_2_tpm.csv


title: MGG8_GB-Hybrid_2

description:
D1342T003
MGG8_GB-Hybrid_2_tpm.csv


title: 22_HET_4


title: 22_HET_5


title: 22_HET_3


title: MGG8_GB-Hybrid_1

description:
D1342T001
MGG8_GB-Hybrid_2_tpm.csv


title: MGG4_GBH-neg_003

description:
D1151T143
MGG4_GB-Hybrid_tpm.csv


title: 22_HET_2


title: 22_HET_1


title: KO_IL4_5

source_name: Microglial cells

growth_protocol: Primary microglial cells were cultured in DMEM, 10% FCS, 50μM ß-mercaptoethanol for 16h after purification, before stimulation

extract_protocol:
After 24h of stimulation, medium was removed, and cells were lysed in lysis buffer RLT from  Rneasy mico kit (Qiagen) and preserved at -80°C until further use. RNA was then extracted using the Rneasy micro kit (qiagen) with final RNA elution in 14µL.
RNA concentration was determined using a nanodrop, and 300ng were used to prepare RNA-seq libraries, using the Kapa mRNA Hyperprep kit (Roche).

treatment_protocol: Culture medium of primary microglial cells was replaced 16h after plating with fresh medium (untreated, UT), or medium plus stimuli: Lipopolysaccharide (LPS, 100ng/mL), or Interleukin-4 (IL-4, 20ng/mL); and incubated for 24h (37°C, 5%CO2)


title: MGG4_GBH-neg_002

description:
D1151T141
MGG4_GB-Hybrid_tpm.csv


title: KO_LPS_5

value: LPS


title: MGG4_GB-Hybrid_002

description:
D1151T140
MGG4_GB-Hybrid_tpm.csv


title: MGG8_bulk_1

description:
D1342T002
MGG8_GB-Hybrid_2_tpm.csv


title: HET_IL4_5


title: MGG4_GB-Hybrid_001

description:
D1151T138
MGG4_GB-Hybrid_tpm.csv


title: 22_KO_2


title: MGG8_GB-Hybrid_003

description:
D1103T536
MGG8_GB-Hybrid_1_tpm.csv


title: MGG8_MES_002

description:
D1103T530
MGG8_GB-Hybrid_1_tpm.csv


title: MGG4_GBH-neg_001

description:
D1151T139
MGG4_GB-Hybrid_tpm.csv


title: HET_LPS_5


title: WT_IL4_5

value: WT


title: MGG8_GB-Hybrid_001

description:
D1103T528
MGG8_GB-Hybrid_1_tpm.csv


title: WT_LPS_5


title: MGG8_GBH-neg_002

description:
D1103T529
MGG8_GB-Hybrid_1_tpm.csv


title: KO_IL4_4


title: MGG8_MES_003

description:
D1103T534
MGG8_GB-Hybrid_1_tpm.csv


title: KO_LPS_4


title: Sample 12 Control, Ventral, 8 month

city: Moscow

first: Vasiliy

last: Akimov

email: VAkimov@cspfmba.ru, vasoakim@gmail.com

address: Pogodinskaya Street, 10, bld. 1

country: Russia

institute: Centre for Strategic Planning of FMBA of Russia

description:
Library name: Sample 12
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ventral part of the hippocampus

extract_protocol:
Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.).
snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample.

value: ventral part of the hippocampus

value: Hippocampal cells

value: 8 month old

value: Wild type


title: WT_nIgG_3

city: Kanazawa

first: Sotaro

last: Fujisawa

state: Ishikawa

address: 13-1 Takara-machi

institute: Kanazawa University

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using Bowtie v2.3.5.
Unmapped, unpaired, low-quality reads, and mitochondrial reads were removed using samtools.
ENCODE blacklist regions were removed, and PCR duplicates were removed using Picard.
BED file was created using bamtobed function of BedTools.
Data were normalized by mapping the reads to E. coli DNA, the carry-over from purification of pAG-MNase (Meers et al., 2019) and normalized bigwig files were created using deepTools bamCoverage
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

source_name: CD8+ T cells

extract_protocol:
DNA fragment of TF-bound regions were extracted using pAG-MNase.
Sequence libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina

value: CD8+ T cells

value: Rabbit IgG (Invitrogen, 02-6102)


title: KO_UT_4

value: UT


title: HET_IL4_4

value: HET


title: WT_nIgG_1


title: Sample 2 Control, Ventral, 8 month

description:
Library name: Sample 2
10x Genomics

value: male


title: MGG8_GBH-neg_001

description:
D1103T525
MGG8_GB-Hybrid_1_tpm.csv

value: brain

value: patient-derived glioblastoma cell line


title: MGG8_PN_001

description:
D1103T527
MGG8_GB-Hybrid_1_tpm.csv


title: MGG8_PN_003

description:
D1103T535
MGG8_GB-Hybrid_1_tpm.csv


title: BatfKO_FoxO1_2

value: BatfKO

value: FoxO1 (CST, C29H4)


title: KO_UT_5

value: KO


title: HET_LPS_4

value: Microglial cells


title: WT_FoxO1_1


title: MGG8_GBH-neg_003

description:
D1103T533
MGG8_GB-Hybrid_1_tpm.csv


title: BatfKO_FoxO1_1


title: HET_UT_4


title: BatfKO_JunD_2

value: JunD (CST, D17G2)


title: MGG8_PN_002

description:
D1103T531
MGG8_GB-Hybrid_1_tpm.csv


title: WT_JunD_2

value: WT


title: WT_IL4_4


title: MGG8_MES_001

description:
D1103T526
MGG8_GB-Hybrid_1_tpm.csv


title: HET_UT_5


title: BatfKO_JunD_1


title: WT_LPS_4

value: LPS


title: MGG4_GB-Hybrid_003

description:
D1151T142
MGG4_GB-Hybrid_tpm.csv


title: WT_JunD_1


title: MGG8_GB-Hybrid_002

description:
D1103T532
MGG8_GB-Hybrid_1_tpm.csv


title: WT_nIgG_2


title: BatfKO_JunB_1

value: JunB (CST, C37F9)


title: WT_UT_4


title: KO_IL4_3


title: BatfKO_Tbet_2

value: Tbet (CST, E4I2K)


title: P3-vitro-IR-002

description:
D211T39
MGG8_P3_IR_tpm.csv

value: irradiation, 5Gy


title: BatfKO_Tbet_1

value: CD8+ T cells


title: P3-vitro-IR-001

description:
D211T38
MGG8_P3_IR_tpm.csv


title: KO_LPS_3


title: WT_FoxO1_2


title: WT_Tbet_2


title: WT_Tbet_1


title: KO_UT_3


title: BatfKO_IRF4_2

value: IRF4 (SantaCruz, E-7)


title: WT_IRF4_2


title: HET_IL4_3


title: P3-vitro-CTL-002

description:
D211T36
MGG8_P3_IR_tpm.csv


title: BatfKO_JunB_2


title: WT_BATF_1

value: BATF (Brookwood Biomedical, PAB4003)


title: WT_IRF4_1


title: MGG8-vitro-IR-003

description:
D211T28
MGG8_P3_IR_tpm.csv


title: P3-vitro-IR-003

description:
D211T40
MGG8_P3_IR_tpm.csv


title: HET_UT_3

value: HET

value: UT


title: WT_BATF_2


title: WT_JunB_2


title: HET_LPS_3


title: P3-vitro-CTL-001

description:
D211T35
MGG8_P3_IR_tpm.csv

value: brain


title: ABE-corrected hiPSC-SMCs, bio rep 2

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description:
Library name: Sample 11
1COR1-2_S5

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (GRCH38) or mouse genome (mm10) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package. Low-expressed genes (genes with the expression value of 0 in more than 30% of samples) were removed before any subsequent analysis. Gene expression was normalized using the Voom method from the R package limma (v 3.50.3). Differentially expressed genes were then identified using the same package. Gene Set Enrichment Analysis (GSEA) for the DEGs was performed using R package clusterProfiler (v4.2.2).
Assembly: hg38
Supplementary files format and content: raw counts in tsv file

source_name: ABE-corrected hiPSC-SMCs

extract_protocol:
Total RNA from iPSC-SMCs was extracted by using TRIzol (Thermo Fisher Scientific). RNeasy Mini Kit (Qiagen) was used to purify RNA following the manufacturer’s recommendations.
RNA sequencing libraries were prepared using the KAPA mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's instructions.

value: ABE-corrected hiPSC-SMCs

value: human induced pluripotent stem cell-derived smooth muscle cells

value: ABE-corrected


title: ACTA2R179H/R179H hiPSC-SMCs, bio rep 3

description:
Library name: Sample 9
1HOM-3_S14

source_name: ACTA2R179H/R179H hiPSC-SMCs

value: ACTA2R179H/R179H hiPSC-SMCs


title: ABE-corrected hiPSC-SMCs, bio rep 3

description:
Library name: Sample 12
1COR1-3_S6


title: WT_IL4_3

value: Microglial cells


title: P3-vitro-CTL-003

description:
D211T37
MGG8_P3_IR_tpm.csv

value: patient-derived glioblastoma cell line


title: ACTA2R179H/R179H hiPSC-SMCs, bio rep 2

description:
Library name: Sample 8
1HOM-2_S13


title: MGG8-vitro-IR-001

description:
D211T26
MGG8_P3_IR_tpm.csv


title: WT_LPS_3

value: WT


title: WT_UT_3


title: MGG8-vitro-IR-002

description:
D211T27
MGG8_P3_IR_tpm.csv


title: TCells_WT, scRNAseq

city: Milwaukee

first: Anthony

middle: Elston

last: Zamora

state: Wisconsin

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

description:
WT_Tcells
instrument model: G4 sequencer from Singular Genomics
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v.7.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: T-Cells

extract_protocol:
Cells were isolated from the colons of mice, sorted for the live cells, resuspended in PBS with 2% BSA at a concentration of 700-800 cells per microliter and used as input for a target recovery of 5000 cells.
Library was performed according to Chromium Next GEM Single Cell 5' Reagent kits v3 and Chromium GEM Single Cell 3' Reagent kit v3.

value: T-Cells


title: ACTA2R179H/R179H hiPSC-SMCs, bio rep 1

description:
Library name: Sample 7
1HOM-1_S12


title: MGG8-vitro-CTL-003

description:
D211T25
MGG8_P3_IR_tpm.csv


title: KO_IL4_2

value: KO


title: TCells_IL34-/-, scRNAseq

description:
IL34KO_Tcells
instrument model: G4 sequencer from Singular Genomics
10x Genomics


title: ACTA2R179H/+ hiPSC-SMCs, bio rep 3

description:
Library name: Sample 6
1HET-3_S11

source_name: ACTA2R179H/+ hiPSC-SMCs

value: ACTA2R179H/+ hiPSC-SMCs


title: MGG8-vitro-CTL-002

description:
D211T24
MGG8_P3_IR_tpm.csv


title: Macrophages_IL34-/-, scRNAseq

description:
IL34KO_MACS
instrument model: G4 sequencer from Singular Genomics
10x Genomics

source_name: Macrophages

value: Macrophages


title: KO_LPS_2

value: LPS


title: ACTA2R179H/+ hiPSC-SMCs, bio rep 2

description:
Library name: Sample 5
1HET-2_S10


title: ACTA2R179H/+ hiPSC-SMCs, bio rep 1

description:
Library name: Sample 4
1HET-1_S9


title: KO_UT_2


title: Macrophages_GVHD, scRNAseq

description:
GVHD_MACS
instrument model: G4 sequencer from Singular Genomics
10x Genomics


title: MGG8-vitro-CTL-001

description:
D211T23
MGG8_P3_IR_tpm.csv


title: Macrophages_WT, scRNAseq

description:
WT_MACS
instrument model: G4 sequencer from Singular Genomics
10x Genomics


title: MGG4-vitro-CTL-003

description:
D1025T51
MGG4_NS_IR_tpm.csv


title: HET_IL4_2


title: WT_JunB_1

value: CD8+ T cells

value: JunB (CST, C37F9)


title: Macrophages_BM, scRNAseq

description:
BM _MACS
instrument model: G4 sequencer from Singular Genomics
10x Genomics


title: ABE-corrected hiPSC-SMCs, bio rep 1

description:
Library name: Sample 10
1COR1-1_S4


title: WT hiPSC-SMCs, bio rep 3

description:
Library name: Sample 3
1WT-3_S3

source_name: WT iPSC-SMCs

value: WT iPSC-SMCs


title: HET_LPS_2

value: HET


title: WT hiPSC-SMCs, bio rep 2

description:
Library name: Sample 2
1WT-2_S2


title: MGG4-vitro-IR-003

description:
D1025T52
MGG4_NS_IR_tpm.csv

value: brain

value: irradiation, 5Gy


title: WT hiPSC-SMCs, bio rep 1

description:
Library name: Sample 1
1WT-1_S1

value: human induced pluripotent stem cell-derived smooth muscle cells


title: SI_WT_4

city: Nanjing

first: Ming

last: Xiao

address: 101 Longmian Avenue

institute: NMU

description: Library name: SI_WT_4

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: medial prefrontal cortex

extract_protocol:
The medial prefrontal cortex were isolated.RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA library was constructed using the Illumina platform according to the manufacturer’s instruction

value: medial prefrontal cortex

tag: batch


title: HET_UT_2

value: UT


title: MGG4-vitro-IR-002

description:
D1025T50
MGG4_NS_IR_tpm.csv


title: MGG4-vitro-IR-001

description:
D1025T48
MGG4_NS_IR_tpm.csv


title: SI_WT_3

description: Library name: SI_WT_3


title: MGG4-vitro-CTL-002

description:
D1025T49
MGG4_NS_IR_tpm.csv


title: SI_WT_2

description: Library name: SI_WT_2


title: WT_IL4_2

value: Microglial cells


title: WT_LPS_2


title: HASMC, 100 mmHg, 3

city: Beijing

first: Jun

last: Cai

state: --- Select One ---

institute: Fuwai Hospital

description: Library name: low3

data_processing:
Read quality was assessed with FastQC. Samples that did not pass half of the 12 assessed quality control (QC) statistics were eliminated. Reads were aligned to the human genome version GRCh37.75 using TopHat v2.1.0. Raw counts were processed in R (version 3.4.4) using edgeR (version 3.20.9) to generate normalized counts.
Assembly: GRCh37.75

source_name: HASMC

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, 15596018) according to the manufacturer’s instructions.
For the library preparation, the Illumina TruSeq Stranded mRNA Library Prep Kit High Throughput was used according to the manufacturer’s instructions.

value: HASMC


title: HASMC, 100 mmHg, 2

description: Library name: low2


title: MGG4-vitro-CTL-001

description:
D1025T47
MGG4_NS_IR_tpm.csv

value: patient-derived glioblastoma cell line


title: WT_UT_2

value: WT


title: GH_WT_4

description: Library name: GH_WT_4


title: KO_IL4_1

value: KO


title: HASMC, 100 mmHg, 1

description: Library name: low1


title: T-2465, ST

city: New York

first: Osama

last: Al Dalahmah

state: NY

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description: 10X Visium

data_processing:
The spatial transcriptomics (ST) samples were prepared using 10X Genomics Space Ranger (version 2.1.0) count commands, accompanied by Hematoxylin & Eosin (H&E) images in TIF format and a manually-aligned JSON file, generated from Loupe Browser (v7.0) with raw TIF images of the tissue. The loupe alignment JSON file was inputted into the loupe-alignment argument in Space Ranger along with its respective TIF image file, FASTQ reads, and slide numbers. The reference genome used for alignment was built using the Space Ranger function spaceranger mkgtf with GRCh38 as the assembly and Ensemble 91 for the transcript annotations. All other parameters set to default settings.
Count matrices were generated from BAM files using default parameters of the DropEst pipeline.
Spots with 0 reads were removed. Normalization of counts was done using the SCTransform function in Seurat
Assembly: GRCh38
Supplementary files format and content: .txt files represent the raw counts matrix
Supplementary files format and content: manual alignment file (json)
Library strategy: Spatial transcriptomics (ST)

source_name: Substantia Nigra

extract_protocol:
Following 10x Visium Spatial Protocols – Tissue Preparation Guide (CG000240), OCT embedded tissue was scored to the size of the capture area targeting the SN. One 10 µm section was mounted on each capture area of the Visium slide. Tissues on the slides were fixed using a methanol-containing buffer as per the 10X Visium manual, stained with H&E or antibodies NeuN, GFAP, and DAPI as per the 10X protocol for Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312), and then imaged. Imaging of whole slides was done at 20X magnification on a Leica DMI8 Thunder microscope. After imaging, the slides were de-cover-slipped and the tissue was permeabilized for 11 minutes (which was empirically determined to yield best results based on the Visium Spatial Tissue Optimization Slide & Reagent Kit PN-1000193, as detailed in the protocol provided in document CG000238_RevD available in 10X demonstrated protocols).
libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit, 16 reactions (PN-1000184). Visium Spatial Gene Expression Reagent Kits user guide (CG000239 Rev G) was followed.

value: Substantia Nigra

value: F

tag: condition

value: Control


title: HASMC, 200 mmHg, 3

description: Library name: high3


title: T-3799, ST

description: 10X Visium


title: T-4424, ST

description: 10X Visium

value: M

value: PD


title: GH_WT_2

description: Library name: GH_WT_2


title: GH_WT_3

description: Library name: GH_WT_3


title: HASMC, 200 mmHg, 1

description: Library name: high1


title: T-5359, ST

description: 10X Visium


title: KO_LPS_1

tag: cell type

value: LPS


title: BatfKO_IRF4_1

value: CD8+ T cells

value: BatfKO

value: IRF4 (SantaCruz, E-7)


title: HET_IL4_1

value: HET


title: GH_WT_1

description: Library name: GH_WT_1

value: medial prefrontal cortex


title: T-4839, ST

description: 10X Visium


title: SI_EE_4

description: Library name: SI_EE_4

value: EE


title: A431, p53 ctrl, rep 3

city: Durham

first: Patricia

last: Muller

address: Stockton Road

country: United Kingdom

institute: Durham University

description: Library name: S9_p53_ctrl_3_S8

data_processing:
Paired-end 75bp sequencing was carried out by clustering 1.8 pM of the pooled libraries on a NextSeq 500 sequencer (Illumina Inc.)
RNA-Seq reads were quality checked by FASTQC programme (248) and aligned in paired-end mode to the human genome assembly (GRCh38) using the STAR aligner v.2.5.1b (249) with the default parameter setting
Mapped data were converted to gene level integer read counts by featureCounts (250) using the Ensemble gene annotation (Homo_sapiens.GRCh38.85.gtf).
Assembly: GRCh38
Supplementary files format and content: raw_counts.csv - normalised counts of RNA-Seq data. Rownames contain Ensembl ID and gene symbols and column names contain sample names.

growth_protocol: Cells were grown under normal conditions of DMEM, 10% FBS at 37 degrees and 5% CO2.

extract_protocol:
Cell lysis and RNA isolation was done using Norgen’s total RNA purification kit (#17200, Norgen Biotek)
Indexed PolyA RNA-Seq libraries were prepared using 200ng of total RNA and 14 cycles of amplification with the Agilent SureSelect Strand Specific RNA Library Prep Kit for Illumina Sequencing (Agilent Technologies, Inc., Cat No: G9691A). Libraries were quality checked by Bioanalyzer (Agilent) and quantified by qPCR using a Kapa Library Quantification Kit (Kapa Biosystems Inc., Cat No: KK4835).

treatment_protocol: Cells were grown as single colonies and once stabolised grown in 6 well plates and harvested 48 hrs after settling.

value: p53 ctr


title: HET_LPS_1

value: Microglial cells


title: A431, p53 ctrl, rep 2

description: Library name: S8_p53_ctrl_2_S4


title: T-5498, ST

description: 10X Visium


title: HET_UT_1

value: UT


title: SI_EE_3

description: Library name: SI_EE_3


title: A431, p53 ctrl, rep 1

description: Library name: S7_p53_ctrl_1_S1


title: SI_EE_2

description: Library name: SI_EE_2


title: T-2791, ST

description: 10X Visium


title: SI_WT_1

description: Library name: SI_WT_1

value: WT


title: WT_IL4_1


title: HASMC, 200 mmHg, 2

description: Library name: high2

value: HASMC


title: SI_EE_1

description: Library name: SI_EE_1


title: T-3870, ST

description: 10X Visium

value: Substantia Nigra


title: A431, p53 KO, rep 2

description: Library name: S5_p53_KO_2_S14

value: p53 KO


title: WT_LPS_1


title: A431, p53 KO, rep 3

description: Library name: S6_p53_KO_3_S9


title: KO_UT_1

value: KO


title: GH_EE_3

description: Library name: GH_EE_3


title: WNV, liver, 7 dpi, r10

city: Madrid

first: Miguel A.

last: Martín-Acebes

state: Madrid

address: Ctra. de La Coruña, km 7, 5

country: Spain

institute: INIA-CSIC

data_processing:
Average base quality was determined by Fastqc
Sequence reads were trimmed using trimmomatic to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed sequence reads were mapped to mm10 using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Known genes and transcripts were assembled with StringTie based on reference genome model. After assembly, abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library. RLE normalized count was adopted for negative binomial Wald Test(nbinomWaldTest) in DESeq2.
Statistical analysis is performed using Fold Change, nbinomWaldTest using DESeq2 per comparison pair. Significant results are selected on conditions of |fc|>=2 & nbinomWaldTest raw p-value<0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including gene ID, gene symbol, log2 fold change (FC), raw pvalue, bh corrected pvalue (benjamini hochberg), expression level (normalized value), raw reads counts, FPKM and TMP values for each group comparison

source_name: Liver

growth_protocol:
Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC)
Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 3, 7 and 10 days post-infection.

extract_protocol:
Total liver RNA was extracted from tissue samples using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol:
Mice were infected intraperitoneally (i.p.) with 10e4 plaque forming units (PFU) of WNV in 200 µL of Minimum Essential Medium Eagle (Corning) mock-infected animals were also inoculated i.p. with 200 µL of culture media
Mock-infected animals were also inoculated i.p. with 200 µL of culture media

value: Liver

value: WNV infection

tag: time

value: Day 07


title: GH_EE_4

description: Library name: GH_EE_4


title: T-4515, ST

description: 10X Visium

value: M

value: PD


title: A431, p53 KO, rep 1

description: Library name: S4_p53_KO_1_S10


title: A431, parental, rep 3

description: Library name: S3_P3_S6

value: parental


title: MB248_10xATAC

city: Baden-Württemberg - Heidelberg

first: Piyush

last: Joshi

state: BW

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

data_processing:
Demultiplexing sequencing output was done by cellranger. Alignment to GRCh38 genome assembly was done using cellranger arc count for snATAC-seq reads.
Assembly: GRCh38, gencodegenes.org
Supplementary files format and content: Fragment data and filtered barcode for snATAC-seq data. Output of cellranger arc count alignment.

source_name: Cerebellar tumor

extract_protocol:
Frozen tumor tissue was homogenized on ice in 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl (pH 8), 0.1% IGEPAL, 1 µM DTT, 0.4 U/µl Murine RNase Inhibitor. Cellular debris post homogenization was removed by pelleting at 100g for 1 min. Cloudy supernantant was again centrifuged at 400g for 4 minutes to pellet the nuclei. Pelleted nuclei were resuspended in homogenization buffer and pelleted again. Pellted nuclei was now resuspended in Nuclei buffer (10x genomics). Extracted nuclei were processed for single-cell multi-ome, RNA-seq or ATAc-seq run as per manufacturer's recommendation.
Single-cell multiome: Chromium Single Cell Multiome ATAC + Gene Expression. Single-cell ATAC: Chromium Single Cell ATAC Reagent Kits, V1.1

value: Cerebellar tumor

value: Brain tumor


title: A431, parental, rep 2

description: Library name: S2_P2_S15


title: GH_EE_2

description: Library name: GH_EE_2

value: medial prefrontal cortex

value: EE


title: WNV, liver, 7 dpi, r7


title: WNV, liver, 7 dpi, r6


title: A431, parental, rep 1

description: Library name: S1_P1_S7


title: T-0081, ST

description: 10X Visium

value: F


title: GH_EE_1

description: Library name: GH_EE_1


title: WNV, liver, 7 dpi, r5


title: INF_R_637_10xATAC


title: MB272_R_10xATAC


title: INF_P_637_10xATAC


title: SI_Con_4

description: Library name: SI_Con_4

value: SI


title: SI_Con_3

description: Library name: SI_Con_3


title: PSEK-1574 and Healthy Control Data

city: New Haven

first: Ryland

last: Mortlock

state: Connecticut

address: 15 York Street, HRT 618C

institute: Yale University

description:
Library name: TMA02_50077958
Formalin-fixed paraffin-embedded spatial transcriptomic sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline (version 3.0.1) to generate FASTQ files
Sequences were aligned to the reference transcriptome GRCh38-2020-A using default settings in the Space Ranger software
Gene expression levels were quantified using Space Ranger's default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene names
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: tissue_positions.csv.gz: list of spatial barcodes and coordinates specifying spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue and spots
Supplementary files format and content: tissue_lowres_image.png.gz: image of tissues and spots
Supplementary files format and content: sample_labels.csv.gz: listing of the sample label (PSEK-1574 or HC) for each barcode
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Samples were formalin-fixed and paraffin-embedded, and arranged onto a tissue microarray. 5 μm sections were hematoxylin and eosin stained, imaged, and placed onto the Visium HD slide using the CytAssist instrument.
Spatial transcriptomic sequencing libraries were prepared with 10X Genomics Visium HD Spatial Gene Expression Slides & Reagent kits for FFPE tissue according to manufacturer instructions (Visium HD v1 - FFPE chemistry with Visium Human Transcriptome Probe Set v2.0).

value: Skin


title: INF_R_1237_10xATAC


title: RNAseq, PANC-1 cell, shSTYK1-3

city: WuHan

first: Cefan

last: Zhou

state: HuBei

address: Hubei University of Technology, 28 NanLi Road, Wuhan, Hubei, China

institute: Hubei University of Technology

description: Library name: A2-3

data_processing:
RSEM was used to quantify gene abundance. Essentially, differential expression was analysed using DESeq2 or DEGseq. Significantly differentially expressed genes were those with |log2FC|≧1,FDR≤0.05 (DESeq2) or FDR≤0.001 (DEGseq). In addition, we performed functional enrichment analyses, including GO and KEGG, to determine which DEGs were significantly enriched in GO terms and metabolic pathways, with a Bonferroni-corrected p-value of ≤0.05 compared to the whole transcriptome background.Goatools and KOBAS were performed to analysis GO functional enrichment and KEGG pathways, respectively.
Assembly: GRCh38, hg38

extract_protocol:
Total RNA was extracted using Trizol, and an Oligo(dT) magnetic beads  were used to isolate mRNA. ThismRNA was fragmented and synthesized into a one-stranded cDNA using random primers for reverse synthesis, followed by two-stranded synthesis to form a stable duplex structure. After end repair, ligation of adapters, fragment screening and library enrichment, followed by on-board sequencing.
mRNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

value: Human pancreatic cancer


title: WNV, liver, 7 dpi, r2

value: WT


title: WT_UT_1

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting cd  raw counts and TPM

value: Microglial cells

value: UT


title: INF_R_46_10xATAC


title: SI_Con_2

description: Library name: SI_Con_2


title: SI_Con_1

description: Library name: SI_Con_1


title: N4059_22_10xATAC


title: Mock, liver, 7 dpi, r10

value: Liver

value: Mock


title: RNAseq, PANC-1 cell, control-3

description: Library name: A1-3


title: GH_Con_4

description: Library name: GH_Con_4

value: control


title: MB292_10xATAC


title: RNAseq, PANC-1 cell, shSTYK1-1

description: Library name: A2-1


title: GH_Con_3

description: Library name: GH_Con_3


title: RNAseq, PANC-1 cell, control-2

description: Library name: A1-2


title: Mock, liver, 7 dpi, r6

value: Day 07


title: MB129_10xATAC


title: GH_Con_2

description: Library name: GH_Con_2


title: MTHFD, scRNAseq

city: Chicago

first: Yalu

address: 303 E Superior St

institute: Northwestern University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: kidney

extract_protocol:
Kidneys from male SGLT2 WT/MT mice fed with ND or HFD for 8 weeks were harvested. Kidneys were minced with a sterile razor blade into small pieces (< 1 mm in diameter) after removing capsule. Approximately 65 mg tissue was digested in 1.5 ml digestion buffer including liberase TM (0.3 mg/mL, Sigma), hyaluronidase (10 μg/mL, Sigma,) and DNase I (20 μg/mL, Roche) at 37°C for 40 min on shaker (300rpm). After centrifugation, cell pellet was resuspended in 2ml red blood cell lysis buffer (eBioscience) and incubate for 2 min at room temperature. Cells were then further digested with 5ml 0.25% trypsin EDTA (Gibco) at 37°C for 30 min on shaker (100rpm) after washing with 0.04% bovine serum albumin (BSA) in PBS 3 times. Trypsin was inactivated using 2ml 10% FBS in PBS after digestion. Cells were then washed with 10% FBS twice and 0.04% BSA twice followed by being resuspended in ice-cold PBS supplemented with 0.04% BSA. After filtration through a 40 μm strainer, cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method
Ten thousand cells for each group were loaded into the Chromium Controller (10X Genomics) on a Chromium Next GEM Chip G (10X Genomics), and processed to generate single cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10X Genomics) and Single Index Kit T Set A (10X Genomics) according to the manufacturer’s manual. Quality control for constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively.

value: kidney

tag: strain

value: 18 weeks old age


title: MB294_10xATAC

value: Cerebellar tumor


title: WNV, liver, 7 dpi, r4

value: WNV infection


title: Mock, liver, 7 dpi, r3


title: INF_R_447_10xATAC

value: Brain tumor


title: Mock, liver, 7 dpi, r5


title: RNAseq, PANC-1 cell, control-1

description: Library name: A1-1


title: GH_Con_1

description: Library name: GH_Con_1

value: medial prefrontal cortex


title: Mock, liver, 7 dpi, r4


title: VHD_scPrint1-HE

city: Portland

first: Luiz

middle: E

last: Bertassoni

state: OR

address: 2720 S Moody Ave

department: Knight Cancer Institute

institute: Oregon Health and Science University

description:
Library name: VHD_scPrint1
Fixed in place, no embedding or sectioning. Spatial transcriptomic sequencing. Visium HD library.

data_processing:
Raw FASTQ files were processed using the 10x Genomics Space Ranger 3.1.3 pipeline to generate the spatial gene expression matrix, filtered and raw feature matrices, image-linked outputs, spatial metadata, and quality control metrics. Sequences were aligned to the Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A reference transcriptome and the refdata-gex-GRCh38-2020-A reference genome using Space Ranger v3.1.3 default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: image of tissue and spots
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: scPrint1_IF.tif: live cell image with transduced reporters to aid annotation
Supplementary files format and content: scPrint1_VHD_HE_HighRes.tif: full resolution HE image
Library strategy: Spatial Transcriptomics

source_name: Engineered in vitro model

growth_protocol: A comination of primary human cells (mammary eptithelial cells, mammary myoepithelial cells, mammary fibroblasts, umbilical vein endothelial cells, and macrophages) and human cell lines (MDA-MB-231 and MCF10A) were patterned onto a collagen coated glass microscope slide using a single-cell bioprinter. The cells were cultured in M87 media for 24 hours before being fixed with 4% PFA and permeabilized with 100% methanol. The Visium HD spatial transcriptomics protocol was then followed to generate the data deposited here.

extract_protocol:
Cells were fixed and place and permeabilized with 100% methanol. The sample was not embedded or sectioned.
Visium HD Spatial Gene Expression (10x Genomics) library was constructed according to manufacturer's instruction.

value: Engineered in vitro model

value: MDA-MB-231, MCF10A

value: Human Mammary Epithelial Cells (HMEC), Human Mammary Myoepithelial Cells, Hummary Mammary Fibroblasts (HMF), Human Umbilical Vein Endothelial Cells (HUVEC), Human Macrophage, Breast Cancer Cell Line


title: RNAseq, PANC-1 cell, shSTYK1-2

description: Library name: A2-2

value: Human pancreatic cancer


title: MB110_10xATAC


title: MB272_10xATAC


title: MT, scRNAseq

description: 10x Genomics


title: WTHFD, scRNAseq

description: 10x Genomics


title: AML7 LR scRNA-Seq technical rep1

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Library name: AML7-rep1
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 7 (primative/monocytic LSC from Xenograft)

data_processing:
Full-length isoform sequences were derived using the SMRT Link cloud service with generated hg38 genome aligned isoform GFF and single-cell sparse matrix files retained for analysis in AltAnalyze version 3, using the long-read automated workflow vignette and default options (AltAnalyze-LR, https://github.com/SalomonisLab/altanalyze3). We used the corresponding previously produced CITE-Seq cell barcode-to-cluster associations, to annotate bone marrow cell-populations, in AltAnalyze-LR. This workflow produces single-cell and cell population pseudobulk exon-exon and exon-intron junction counts, isoform counts for downstream integrated differential isoform and splicing analyses.
Note: Cell barcodes are reverse complemented from the original matching Illumina CITE-Seq libraries (use reverse complement option in AltAnalyze3).
Assembly: hg38
Supplementary files format and content: GFF format isoform models for each library
Supplementary files format and content: seurat_info.tar.gz is sparse matrix and single-cell molecule information per cell barcode.

source_name: Bone marrow

extract_protocol:
cDNA from 10x Genomics 3' v3.1 libraries were obtained from a prior analysis from study (GSE245108).
PacBio Kinnex (103-072-200) library generation protocol to cDNA from three previously described AML bone marrow biopsies, captured using 10x Genomics 3′ version 3.1 Chromium chemistry. These total mononuclear cells consist of two samples with functionally defined primitive-LSCs and one with mixed primitive and monocytic LSCs. In brief, 75ng cDNA were used as input with 5,000-7,000 profiled cells per sample using the Kinnex library preparation kit. The Kinnex protocol produces 10-15kb containing 16 concatenated single-cell cDNA segments. These long-read libraries were sequenced using a PacBio Revio SMRT Cell, producing 80-100 million initial UMI reads per library, with an average of ~1kb long reads. These libraries were sequenced as technical or quadruplicate replicates to increase sequencing depth.

value: Bone marrow

value: AML biopsy


title: WNV, brain, 7 dpi, r10

growth_protocol:
Experimental infections in mice were performed in the biosafety level 3 (BSL-3) facilities at Centro de Investigación en Sanidad Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (CISA, INIA-CSIC)
Animals were kept with ad libitum access to food and water and were anesthetized under isoflurane and humanely sacrificed at 7 days post-infection.

extract_protocol:
Total brain RNA was extracted from tissue samples using Ribopure following manufacturer's protocols
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: Brain

value: WT


title: Mock, liver, 7 dpi, r7

value: Liver

value: Mock


title: WNV, brain, 7 dpi, r7

value: Day 07


title: AML14 LR scRNA-Seq technical rep2

description:
Library name: AML14-rep2
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 14 (primative/monocytic LSC from Xenograft)


title: MB164_10xATAC


title: WT, scRNAseq

description: 10x Genomics

value: kidney


title: WNV, brain, 7 dpi, r6


title: AML14 LR scRNA-Seq technical rep1

description:
Library name: AML14-rep1
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 14 (primative/monocytic LSC from Xenograft)


title: Skin9, LE, biol rep4

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: s_9462LE

data_processing:
The output data (FASTQ files) are mapped to the target genome using the STAR aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used). After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases. The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw HTseq counts
Supplementary files format and content: tab-delimited text file with normalized counts

extract_protocol:
20-30mg frozen tissue was homogenized in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) using the QIAGEN TissueLyser at 15Hz for 2-3 minutes with a Stainless Steel Bead (QIAGEN catalog # 69989). Phase separation was induced with 200 µL chloroform. RNA was precipitated from the aqueous phase with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in 13 µL nuclease-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.7-1 µg of total RNA with DV200 percentages varying from 70-88% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina). On average, 46 million paired reads were generated per sample and 26% of the data mapped to the transcriptome.

value: Skin

value: Human skin cells

value: Lymphedema affected


title: Skin5, LE, biol rep3

description: Library name: s_5290LE


title: WNV, brain, 7 dpi, r4

value: WNV infection


title: MB249_10xATAC

value: Cerebellar tumor

value: Brain tumor


title: Skin9, Normal, biol rep4

description: Library name: s_9462Normal

value: control


title: MB86_10xATAC


title: AML12 LR scRNA-Seq technical rep4

description:
Library name: AML12-rep4
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 12 (primative LSC from Xenograft)


title: AML12 LR scRNA-Seq technical rep1

description:
Library name: AML12-rep1
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 12 (primative LSC from Xenograft)


title: AML7 LR scRNA-Seq technical rep2

description:
Library name: AML7-rep2
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 7 (primative/monocytic LSC from Xenograft)


title: MB96_10xATAC


title: AML12 LR scRNA-Seq technical rep3

description:
Library name: AML12-rep3
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 12 (primative LSC from Xenograft)


title: Mock, brain, 7 dpi, r7


title: Skin5, Normal, biol rep3

description: Library name: s_5290Normal


title: Mock, brain, 7 dpi, r6


title: MB90_10xATAC


title: WNV, brain, 7 dpi, r5


title: MB38_10xATAC


title: Skin4, Normal, biol rep2

description: Library name: s_4664Normal


title: MB177_10xATAC


title: Mock, brain, 7 dpi, r5


title: DSS T748A Rep5

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

description: Library name: DSS T748A Rep5

data_processing:
Sequence reads were mapped to the mm10 genome using HISAT2
Mapped reads on each gene were counted using featureCounts with default setting
Differential expression analysis was performed using DESeq2
Assembly: mm10
Supplementary files format and content: tabular file including normalized counts of each transcript

source_name: Colon

extract_protocol:
A total of 2–5 × 10⁵ cells per condition were lysed in 0.5 mL of TRIzol Reagent (Thermo Fisher) following the indicated treatments. Total RNA was extracted, and RNA-seq analysis was performed by the Genome Information Research Center (GIRC) at Osaka University.
cDNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, Cat. No. 20020594) according to the manufacturer’s instructions. Sequencing was conducted on an Illumina HiSeq 2500 platform using 75-base single-end reads. Base calling was performed with Illumina Casava v1.8.2 software. Sequenced reads were aligned to the mouse reference genome (mm10/GRCm38) using TopHat v2.0.13 with Bowtie2 v2.2.3 and SAMtools v0.1.19. Gene expression levels were quantified as fragments per kilobase of exon per million mapped reads (FPKM) using Cuffnorm v2.2.1. Further data processing and analysis were conducted on the Galaxy platform (https://usegalaxy.org/). Read quality was assessed using FastQC (v0.73), and adaptor sequences were trimmed prior to alignment with HISAT2 (v2.2.1) using default parameters. Gene counts were generated with featureCounts (v2.0.3), and differential expression analysis was performed using DESeq2 (v2.11.40.7). Visualization of results, including volcano plots and heatmaps, was performed using Volcano Plot (v0.0.5) and heatmap2 (v3.1.3), respectively. Gene ontology enrichment and pathway analysis were conducted using the PANTHER GO-Slim Biological Process database (v17.0, released 2022/02/22).

treatment_protocol: Briefly, IECs were isolated from Wt and Stat1T748A littermate mice at basal level and following DSS treatment.

value: Colon

value: Intestinal epithelial cells

value: Stat1 T748A/T748A

value: DSS


title: DSS T748A Rep4

description: Library name: DSS T748A Rep4


title: DSS T748A Rep3

description: Library name: DSS T748A Rep3


title: MB98_10xATAC


title: MB134_10xATAC


title: Skin2, LE, biol rep1

description: Library name: s_2907LE


title: WNV, brain, 7 dpi, r2

value: Brain


title: Mock, brain, 7 dpi, r10

value: WT


title: Skin4, LE, biol rep2

description: Library name: s_4664LE


title: AML12 LR scRNA-Seq technical rep2

description:
Library name: AML12-rep2
long-read (kinnex) single-cell RNA-Seq of a diagnosis AML bone marrow biopsy from patient AML 12 (primative LSC from Xenograft)

value: Bone marrow

value: AML biopsy


title: DSS T748A Rep2

description: Library name: DSS T748A Rep2


title: Mock, brain, 7 dpi, r4

value: Mock

value: Day 07


title: MDSL-PRT543-Sample-5

description:
Library name: MDSL-PRT543-Sample-5
PRMT5 inhibition MDS-L cells

data_processing:
The FASTQ files were aligned to the human genome (h19) using STAR. Splicing quantification was performed in AltAnalyze version 2.1.4 using the Ensembl72 reference database and MultiPath-PSI.
Assembly: hg19
Supplementary files format and content: PSI_EventAnnotation-Ens72.txt, splicing event quantification from MultiPath-PSI
Supplementary files format and content: gene-RPKM-PRMT5-Ens72.txt, gene level RPKM values (Ensembl 72 IDs)

growth_protocol: MDS-L cells were seeded in a 6 well plate at a density of 100,000 cells.

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini kit (Life Technologies).
Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies) and paired-end stranded RNA-Seq using an Illumina HiSeq 4000.

treatment_protocol: PRT543 treatment at a concentration of 300nM

value: MDS-L


title: MB165_10xATAC


title: Mock, brain, 7 dpi, r3


title: DSS T748A Rep1

description: Library name: DSS T748A Rep1


title: MDSL-PRT543-Sample-4

description:
Library name: MDSL-PRT543-Sample-4
PRMT5 inhibition MDS-L cells


title: MB166_10xATAC


title: Bdh1KO, Input, Rep1&2

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

data_processing:
Fastq files for each sample were concatenated across flowcells and aligned to the mm10 genome (GRCm38.p6; GENCODE release M24) using Bowtie2 v2.3.5 with the parameters, '-p 20 -I 0 -X 700 --end-to-end --sensitive'.
SAM output from bowtie2 was converted to BED format using a custom AWK script.
IP samples and their corresponding input samples were processed using the siQ-ChIP workflow (https://github.com/BradleyDickson/siQ-ChIP; https://www.biorxiv.org/content/10.1101/2022.08.09.503331v1).
Assembly: mm10
Supplementary files format and content: Bigwig files showing abundance as calculated by the siQ-ChIP workflow.

source_name: CD8+ T cell

extract_protocol:
Cells were cross-linked in 0.75% formaldehyde for 5 minutes. After quencing and lysis, lysates were treated with MNase.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit (v 9.20). Libraries were amplified using 12 cycles on the thermocycler.

value: CD8+ T cell


title: DSS Wt Rep5

description: Library name: DSS Wt Rep5

value: Stat1 +/+


title: wt, Input, Rep2&3

value: Control


title: DSS Wt Rep4

description: Library name: DSS Wt Rep4


title: MB5_10xATAC

value: Cerebellar tumor


title: MDSL-CTL-Sample-2

description:
Library name: MDSL-CTL-Sample-2
DMSO MDS-L cells


title: MDSL-CTL-Sample-1

description:
Library name: MDSL-CTL-Sample-1
DMSO MDS-L cells


title: Skin2, Normal, biol rep1

description: Library name: s_2907Normal

value: Skin

value: Human skin cells


title: DSS Wt Rep3

description: Library name: DSS Wt Rep3

value: Colon


title: MB279_10xATAC

value: Brain tumor


title: wt, Input, Rep1


title: Whole fish, endothelial pulldown, biol rep 3

city: Bethesda

first: Gennady

last: Margolin

address: 9000 Rockville Pike

institute: National Institutes of Health

library_source: other

data_processing:
lcdb-wf pipeline (https://github.com/lcdb/lcdb-wf, v1.9rc)
zebrafish genome assembly version GRCz11/danRer11 and ENSEMBL gene annotation version 99.
R and packages DESeq2, clusterProfiler and GeneTonic
Assembly: danRer11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: other

organism: Danio rerio

growth_protocol: Tg(kdrl:egfp-2a-rpl10a3xHA)y530 transgenic zebrafish were  housed in a large recirculating aquaculture facility.  Fry were fed rotifers and adults were fed Gemma Micro 300 (Skretting).

extract_protocol:
RNA from either total lysate or immunoprecipitated samples was harvested using RNeasy Micro Plus Kit (Qiagen #74034) with RNA-only ß-Mercaptoethanol supplementation in the RLT buffer
RNA libraries for RNA-seq were prepared by Novogene using SMART-seq V4 Ultra Low Input RNA kit & non-directional library


title: MB99_10xATAC


title: Bdh1KO, H3K27ac, Rep2

value: H3K27ac (Active Motif, 39133)


title: Whole fish, endothelial pulldown, biol rep 2


title: MB297_10xATAC


title: DSS Wt Rep1

description: Library name: DSS Wt Rep1

value: Intestinal epithelial cells

value: DSS


title: Bdh1KO, H3K27ac, Rep1


title: Whole fish, endothelial pulldown, biol rep 1


title: wt, H3K27ac, Rep3


title: MB26_10xATAC


title: Skin, endothelial pulldown, biol rep 3

source_name: skin

value: skin


title: wt, H3K27ac, Rep2


title: wt, H3K27ac, Rep1


title: Untreated T748A Rep3

description: Library name: Untreated T748A Rep3

value: Stat1 T748A/T748A


title: Skin, endothelial pulldown, biol rep 1


title: Untreated T748A Rep2

description: Library name: Untreated T748A Rep2


title: Untreated Wt Rep3

description: Library name: Untreated Wt Rep3


title: MB89_10xATAC


title: OFC astrocytes, OE_Z8

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
OE_ZBT.peaks.annotated.txt
OE_Z8_A_S12_L001

data_processing:
Raw sequencing reads from mice were aligned to mm10 reference genome using HISAT2.
MACS was utilized to obtain sites of chromatin openness in samples.
diffReps was utilized to find differential sites between groups ZBT vs GFP in OE condition and ZBT-STRESS vs ZBT-CON, ZBT-STRESS vs GFP-STRESS, ZBT-CON vs GFP-CON, GFP-STRESS vs GFP-CON in KD condition.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing peaks

source_name: OFC astrocytes

extract_protocol:
50,000 sorted nuclei were centrifuged at 500 ×g
for 10 min, 4°C. Pellets were resuspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Samples were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204) according to the manufacturer's instructions.
Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute for a total of 5 cycles. In order to prevent saturation due to over-amplification, a 5µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 13–19 cycles, followed by bead purification with Ampure XP beads (Beckman Coulter).

value: OE

tag: virus

value: ZBT

tag: group

value: OFC astrocytes


title: Untreated T748A Rep1

description: Library name: Untreated T748A Rep1


title: Muscle, endothelial pulldown, biol rep 2

source_name: muscle

value: muscle


title: MB278_10xATAC


title: Muscle, endothelial pulldown, biol rep 3


title: DSS Wt Rep2

description: Library name: DSS Wt Rep2


title: Untreated Wt Rep2

description: Library name: Untreated Wt Rep2


title: INF_R_63_10xRNA

data_processing:
Demultiplexing sequencing output was done by cellranger. Alignment to GRCh38 genome assembly was done by STARsolo for snRNA-seq reads.
Assembly: GRCh38, gencodegenes.org
Supplementary files format and content: Raw gene expression matrix for snRNA-seq data. Output of STARsolo alignment.

extract_protocol:
Frozen tumor tissue was homogenized on ice in 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl (pH 8), 0.1% IGEPAL, 1 µM DTT, 0.4 U/µl Murine RNase Inhibitor. Cellular debris post homogenization was removed by pelleting at 100g for 1 min. Cloudy supernantant was again centrifuged at 400g for 4 minutes to pellet the nuclei. Pelleted nuclei were resuspended in homogenization buffer and pelleted again. Pellted nuclei was now resuspended in Nuclei buffer (10x genomics). Extracted nuclei were processed for single-cell multi-ome, RNA-seq or ATAc-seq run as per manufacturer's recommendation.
Single-cell multiome: Chromium Single Cell Multiome ATAC + Gene Expression. Single-cell RNA: Chromium Single Cell 3' Reagent Kits, V3.1.


title: Muscle, endothelial pulldown, biol rep 1


title: OFC astrocytes, OE_Z7

description:
OE_ZBT.peaks.annotated.txt
OE_Z7_A_S10_L001


title: OFC astrocytes, OE_Z6

description:
OE_ZBT.peaks.annotated.txt
OE_Z6_A_S8_L001


title: INF_P_63_10xRNA


title: Untreated Wt Rep1

description: Library name: Untreated Wt Rep1


title: MB18_10xATAC


title: MB183_10xATAC


title: MB272_R_10xRNA


title: Whole fish, tissue input, biol rep 2


title: Whole fish, tissue input, biol rep 3


title: OFC astrocytes, OE_Z2

description:
OE_ZBT.peaks.annotated.txt
OE_Z2_A_S4_L001


title: INF_R_12_10xRNA


title: OFC astrocytes, OE_Z5

description:
OE_ZBT.peaks.annotated.txt
OE_Z5_A_S6_L001


title: Spinal cord, 50 days, wild type, rep8

city: Zaragoza

first: Janne

middle: M

last: Toivonen

address: Miguel servet 177

department: Departamento de Anatomía, Embriología y Genética Animal

institute: Universidad de Zaragoza

description: Library name: WT_3619

data_processing:
Seq Quality Control (FastQC),  removal of adapter sequences,  reads with N>10% and  reads with a quality value sQ <= 5 and the number of bases accounting for more than 50% of the entire read.
Reference mapping
circRNA identification (CircExplorer)
Readcount (HTSeq)
Reads only observed in one mouse and those where average read count across all samples was less than one were filtered out.
Assembly: GRCm38.p6 (mmu)
Supplementary files format and content: tab-delimited text file includes raw read counts after last data procesing step

source_name: Spinal cord

extract_protocol:
Spinal cord  tissues were homogenized with QIAzol Lysis Reagent (Qiagen) using the TissueLyser LT (Qiagen). RNA was isolated with Direct-zol RNA Miniprep (Zymo Research) according to the manufacturer’s instructions.
Ribosomal RNA depletion, RNase R digestion , double-stranded cDNA synthesis, adapter ligation (Illumina), second-strand cDNA elimination, first-strand cDNA purification for PCR.

value: Spinal cord

value: male

value: Wild type


title: INF_R_46_10xRNA

value: Cerebellar tumor


title: Skin, tissue input, biol rep 3


title: Spinal cord, 50 days, wild type, rep7

description: Library name: WT_3600


title: N4059_22_10xRNA


title: OFC astrocytes, OE_G8

description:
OE_GFP.peaks.annotated.txt
OE_G8_A_S11_L001

value: GFP


title: OFC astrocytes, OE_G7

description:
OE_GFP.peaks.annotated.txt
OE_G7_A_S9_L001


title: Skin, tissue input, biol rep 1


title: Whole fish, tissue input, biol rep 1


title: MB292_10xRNA


title: Spinal cord, 50 days, wild type, rep5

description: Library name: WT_3567


title: Muscle, tissue input, biol rep 3


title: OFC astrocytes, OE_G6

description:
OE_GFP.peaks.annotated.txt
OE_G6_A_S7_L001


title: OFC astrocytes, OE_Z1

description:
OE_ZBT.peaks.annotated.txt
OE_Z1_A_S2_L001


title: Spinal cord, 50 days, wild type, rep4

description: Library name: WT_3566


title: INF_R_44_10xRNA


title: Muscle, tissue input, biol rep 2


title: MB1947_10xRNA


title: OFC astrocytes, OE_G5

description:
OE_GFP.peaks.annotated.txt
OE_G5_A_S5_L001


title: Spinal cord, 50 days, wild type, rep3

description: Library name: WT_3550


title: Spinal cord, 50 days, wild type, rep2

description: Library name: WT_3540


title: MB1935_10xRNA


title: Spinal cord, 50 days, wild type, rep1

description: Library name: WT_3520


title: OFC astrocytes, OE_G2

description:
OE_GFP.peaks.annotated.txt
OE_G2_A_S3_L001


title: Muscle, tissue input, biol rep 1


title: Spinal cord, 50 days, wild type, rep6

description: Library name: WT_3579


title: OFC astrocytes, OE_G1

description:
OE_GFP.peaks.annotated.txt
OE_G1_A_S1_L001


title: MB279_10xRNA


title: Brain, endothelial pulldown, biol rep 3

source_name: brain

value: brain


title: Brain, endothelial pulldown, biol rep 2


title: OFC astrocytes, KD_ZS5

description:
KD_ZBT_STRESS.peaks.annotated.txt
KD_ZS5_A_S32_L001

value: KD

value: STRESS


title: MB249_10xRNA

value: Brain tumor


title: MB129_10xRNA


title: Brain, endothelial pulldown, biol rep 1


title: Spinal cord, 50 days, transgenic, rep6

description: Library name: G93A_3578

value: ALS model SOD1G93A


title: Heart, endothelial pulldown, biol rep 3

source_name: heart

value: heart


title: MB99_10xRNA


title: OFC astrocytes, KD_ZS3

description:
KD_ZBT_STRESS.peaks.annotated.txt
KD_ZS3_A_S26_L001


title: Spinal cord, 50 days, transgenic, rep5

description: Library name: G93A_3569


title: OFC astrocytes, KD_ZS2

description:
KD_ZBT_STRESS.peaks.annotated.txt
KD_ZS2_A_S24_L001


title: Spinal cord, 50 days, transgenic, rep4

description: Library name: G93A_3568


title: Spinal cord, 50 days, transgenic, rep3

description: Library name: G93A_3548


title: Heart, endothelial pulldown, biol rep 2


title: Heart, endothelial pulldown, biol rep 1


title: OFC astrocytes, KD_ZS1

description:
KD_ZBT_STRESS.peaks.annotated.txt
KD_ZS1_A_S22_L001


title: Liver, endothelial pulldown, biol rep 3

source_name: liver

value: liver


title: OFC astrocytes, KD_ZC5

description:
KD_ZBT_CON.peaks.annotated.txt
KD_ZC5_A_S30_L001

value: CON


title: MB26_10xRNA


title: Spinal cord, 50 days, transgenic, rep2

description: Library name: G93A_3537


title: Spinal cord, 50 days, transgenic, rep8

description: Library name: G93A_3617


title: Liver, endothelial pulldown, biol rep 2


title: OFC astrocytes, KD_ZC4

description:
KD_ZBT_CON.peaks.annotated.txt
KD_ZC4_A_S20_L001


title: MB110_10xRNA


title: Spinal cord, 50 days, transgenic, rep1

description: Library name: G93A_3521


title: OFC astrocytes, KD_ZC3

description:
KD_ZBT_CON.peaks.annotated.txt
KD_ZC3_A_S18_L001


title: Liver, endothelial pulldown, biol rep 1


title: OFC astrocytes, KD_ZS4

description:
KD_ZBT_STRESS.peaks.annotated.txt
KD_ZS4_A_S28_L001


title: MB91_10xRNA


title: Spinal cord, 50 days, transgenic, rep7

description: Library name: G93A_3603


title: R3

city: Hangzhou

first: wang

last: my

address: Cangqian Street, Cangxing Street

institute: BoYu Intelligent Health Innovation Laboratory, Hangzhou, 311100, P. R. China.

data_processing:
The sequences were aligned to the mouse mm10 genome using Bowtie2 and GENCODE database, and gene expression was quantified using HTSeq.
Assembly: mm10
Supplementary files format and content: xlsx file include TMM values for all samples

source_name: xenograft tumors

extract_protocol:
Total RNA isolation was performed using EASYspin reagent Kit (Aidlab Biotech, Beijing, China) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: xenograft tumors

value: treat with RGLS


title: OFC astrocytes, KD_ZC2

description:
KD_ZBT_CON.peaks.annotated.txt
KD_ZC2_A_S16_L001

value: ZBT

value: OFC astrocytes


title: MB2033_10xRNA


title: MB297_10xRNA


title: Brain, tissue input, biol rep 3


title: OFC astrocytes, KD_ZC1

description:
KD_ZBT_CON.peaks.annotated.txt
KD_ZC1_A_S14_L001


title: R1


title: Brain, tissue input, biol rep 2


title: OFC astrocytes, KD_GS5

description:
KD_GFP_STRESS.peaks.annotated.txt
KD_GS5_A_S31_L001


title: MB38_10xRNA


title: M3

value: model


title: OFC astrocytes, KD_GS4

description:
KD_GFP_STRESS.peaks.annotated.txt
KD_GS4_A_S27_L001


title: Brain, tissue input, biol rep 1


title: MB183_10xRNA


title: MB177_10xRNA


title: OFC astrocytes, KD_GS3

description:
KD_GFP_STRESS.peaks.annotated.txt
KD_GS3_A_S25_L001


title: M2


title: Heart, tissue input, biol rep 3


title: M1


title: OFC astrocytes, KD_GS2

description:
KD_GFP_STRESS.peaks.annotated.txt
KD_GS2_A_S23_L001


title: MB294_10xRNA


title: Heart, tissue input, biol rep 2


title: MB165_10xRNA


title: Skin, endothelial pulldown, biol rep 2

value: skin


title: Agilent_reference_RNA, Sample50

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: Gr13_ref_S50

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 R package v1.38.0
Assembly: GRCh38 (hg38) (Homo_sapiens_assembly38)
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the RNA-Seq data alignments.

source_name: mixed

growth_protocol: human mesenchymal stromal cells from four male donors were expanded to an average population doubling level of 13.4, pooled, then seeded for long term culture and passaged whenever approaching confluence.

extract_protocol:
RNA was isolated using Rneasy mini kit (Qiagen). 1 ug of total RNA was used to construct sequencing libraries.
Library preparation for RNA sequencing was performed using the TruSeq® Stranded mRNA kit with the CD Index plate

treatment_protocol: Seeded cells were cultured for 24 hours to allow recovery, then treated with 0.12, 0.6, and 3.0 µM sodium arsenite and a vehicle control (water)

value: mixed

value: Mixed-10 human cell lines

value: pooled male and female

tag: chemical

tag: chemical longname


title: Heart, tissue input, biol rep 1

state: MD

tag: tissue


title: OFC astrocytes, KD_GS1

description:
KD_GFP_STRESS.peaks.annotated.txt
KD_GS1_A_S21_L001

value: GFP


title: Agilent_reference_RNA, Sample49

description: Library name: Gr13_ref_S49

tag: genotype


title: MB134_10xRNA

value: Cerebellar tumor


title: MB86_10xRNA


title: Liver, tissue input, biol rep 3


title: OFC astrocytes, KD_GC5

description:
KD_GFP_CON.peaks.annotated.txt
KD_GC5_A_S29_L001

value: KD