title: Early-passage HUVECs, Rep F

description:
Library name: Celula-F
3’ mRNA amplification

value: HUVECs

value: Endothelial cells


title: Bone Marrow Derived Macrophages, LL2 WT Conditioned Media, Vehicle Treatment, Replicate 1

status: Public on Dec 01 2025

type: SRA

city: Indianapolis

first: Ana

middle: S

last: Leal

state: IN

address: 980 W Walnut St

department: Department of Medicine

country: USA

institute: Indiana University

description: Library name: WT_V_1

library_source: transcriptomic

data_processing:
Reads were filtered for adapter-related content, containing undetermined bases >10%, and Qscores <=5
Filtered reads were mapped to Mus musculus GRCm39 using Kallisto for pseudo alignment.
Tximport v1.30.0 R package was used to calculate length-scaled transcripts per mission and convert to count-level data (gene counts per million).
Assembly: Mus musculus GRCm39
Supplementary files format and content: .csv file containing length-scaled TPM data of gene-level counts

molecule: polyA RNA

organism: Mus musculus

source_name: Bone Marrow Derived Macrophage

growth_protocol: Lewis lung carcinoma (LL2) cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (Complete-DMEM) in a humified incubator with 5% atmospheric CO2 at 37°C. Bone marrow-derived macrophage (BMDM) were isolated from C57BL/6 mice. Femurs and tibias were harvested under sterile conditions and bone marrow flushed out using Complete-DMEM with 20 ng/mL recombinant M-CSF. The suspension of progenitor cells was split evenly and approximately 500K cells/well plated into 6-well plates in 2mL media. Cells were incubated at 5% CO2 at 37°C for 5 days, washed 3x in PBS, and fresh 2mL Complete-DMEM with 20 ng/mL M-CSF added. After 48 hours, macrophages were ready for use.

extract_protocol:
Total RNA was extracted from macrophages using RNeasy mini kit (Qiagen).
Library construction was completed by Novogene as follows: 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

treatment_protocol: LL2 lung cancer cells (WT, KEAP1 KO, and NRF2 KO) were split 1:4 into fresh Complete-DMEM. An additional plate of Complete-DMEM without cancer cells was included as a control. After 48 hours, conditioned media (CM) was harvested and cleared through centrifugation at 500 x g for 5 minutes. Cleared cancer CM was added to naïve macrophages totaling 75% CM, 25% Complete-DMEM. 100nM CDDO-Me or vehicle control was added to macrophages and incubated for 24 hours. RNA was harvested for 3 independent samples in each treatment group.

tag: cell line

value: Bone Marrow Derived Macrophage

tag: cell type

value: Macrophage

tag: treatment

value: LL2 WT Conditioned Media, Vehicle


title: 000-475

type: RNA

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

description: Expression value derived from nCounter Digital Analyzer

hyb_protocol: Purified total RNA was processed using the Nanostring nCounter v3.0a array.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Nanostring)

data_processing: Nanostring nCounter v3.0a arrays were normalized using the top 100 genes without background subtraction using the geometric mean in the nSolver Analysis Software.v3 (Nanostring). The log2 count normalized matrices of microRNAs in the Nanostring arrays were batch-adjusted using theComBat function in the sva package (version 3.46.0) and used for all subsequent analyses.

molecule: total RNA

organism: Homo sapiens

source_name: Asthma Female

extract_protocol:
Whole blood was collected in PaxGene RNA tubes
Total RNA from whole blood samples was isolated using a column-based system (total-RNA kit; Norgen)

tag: tissue

value: Whole blood

tag: disease

value: Asthma

tag: Sex

value: Female

tag: endotype

value: low


title: Bone Marrow Derived Macrophages, Control Media, Vehicle Treatment, Replicate 3

description: Library name: V_4

value: Control Media, Vehicle


title: Early-passage HUVECs, Rep E

city: Madrid

first: Fátima

middle: Milhano

last: Santos

address: Av. de los Reyes Católicos, 2 4 planta izquierda, Moncloa - Aravaca

country: Spain

institute: IIS-FJD

description:
Library name: Celula-E
3’ mRNA amplification

data_processing:
Raw FASTQ files were quality-filtered and trimmed to remove low-quality bases, sequencing adapters, and poly-A tails. Read quality was assessed with FastQC v0.11.9, ensuring high %Q20 scores, absence of Ns, and removal of adapters and poly-A sequences.
Trimmed sequence reads were mapped to the GRCh38 reference genome using STAR v2.7.10. After alignment, duplicate reads were removed using UMI-tools, based on unique molecular identifiers (UMIs) associated with each original fragment.
Gene-level counts were computed with HTSeq-count v2.0.2, using the corresponding NCBI GTF annotation.
Assembly: GRCh38
Supplementary files format and content: individual tab-delimited text files include raw counts.

source_name: HUVECs

growth_protocol: First-passage cryopreserved HUVECs were cultured and serially passaged until reaching senescence, following the replicative senescence protocol. Cells studied within 2–8 passages (early passage; PD < 20) were regarded as early passage ECs, whereas those passaged 28–38 times (PD > 96) were regarded as senescent ECs.

extract_protocol:
Total RNA was extracted from the cell pellets using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer's instructions for ECs. EVs were processed using the Total Exosome RNA and Protein Isolation Kit (Invitrogen), following the manufacturer's recommendations.
Dual-indexed mRNA libraries were prepared using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Lexogen GmbH, Vienna, Austria), according to the user guide. According to the manufacturer's recommendations, 250 ng of starting material was used for cellular RNA analysis, while a low-input protocol (<10ng total) was used for EVs. Library quality was evaluated using the QiaXcel Advanced System (Qiagen), while the quantity was measured using a Quantus Fluorometer (Promega Corporation).

tag: genotype

value: WT


title: Early-passage EVs, Rep D

description:
Library name: Vesicula-D
3’ mRNA amplification

source_name: HUVECs derived Evs

value: HUVECs derived Evs

value: Endothelial cells derived Evs


title: Early-passage HUVECs, Rep D

description:
Library name: Celula-D
3’ mRNA amplification


title: Bone Marrow Derived Macrophages, Control Media, Vehicle Treatment, Replicate 2

description: Library name: V_3_E


title: 000-468

value: high


title: Senescent HUVECs, Rep C

description:
Library name: Celula-C
3’ mRNA amplification


title: Normoxia INPUT rep1

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

description: Library name: Sample 7

data_processing:
Trimmed sequence reads were mapped to hg38 using STAR software.
Assembly: hg38
Supplementary files format and content: bed and bigwig files

source_name: prostate

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

value: prostate

value: prostate cancer cells


title: 000-331


title: Heterozygous Rbm20-R636Q KI - Hesperadin (5 ug/mg)  treated - 3

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

country: Germany

institute: Institute of Experimental Cardiology

description: Library name: HET_Hesp5_3

data_processing:
RNA-seq reads were aligned to mouse genome reference (mm10 GRCm38) using the Rsubread R package. Quality control of the reads was performed using Fastqcr and Rqc packages, while adapter trimming was conducted with Trimmomatic using standard parameters. For data processing and analysis, we employed a R-based pipeline utilizing BiocManager for package management, ShortRead for sequence manipulation and reading.
Assembly: mm10
Supplementary files format and content: gene_counts_Hesp - Gene counts of analysis of WT_DMSO, HET_DMSO, HET_Hesp2.5, and HET_Hesp5
Supplementary files format and content: gene_counts_DKO.tsv - Gene counts of analysis of WT, Rbm20KO, Camk2dKO and DKO

source_name: heart tissue (LV)

extract_protocol:
RNA was isolated using TRIzol following manufacturers instructions.
Sequence libraries were prepared using SMART-Seq Total RNA pico input (Takara Bio) following manufacturers instructions.

value: heart tissue (LV)


title: 000-464

source_name: Asthma Male

value: Male


title: Normoxia MeRIP rep2

description: Library name: Sample 6

data_processing:
Trimmed sequence reads were mapped to hg38 using STAR software.
Assembly: hg38
Supplementary files format and content: bed and bigwig files
Library strategy: MeRIP-seq


title: Normoxia MeRIP rep1

description: Library name: Sample 5


title: Heterozygous Rbm20-R636Q KI - Hesperadin (5 ug/mg)  treated - 2

description: Library name: HET_Hesp5_2


title: EU 40min INPUT

description: Library name: Sample 10


title: N-113

source_name: Control Female

value: Control


title: A-311


title: TCF3_IP_Parental

city: Zürich

first: Valdemar

middle: Jacob Sven-Åke

last: Priebe

address: Lengghalde 5

country: Switzerland

institute: Kindersptal Zürich/University of Zurich

description: Library name: Sample4

library_source: genomic

data_processing:
ChIPseq reads were aligned to the hg38 reference genome using Bowtie2.
Read counts were computed and normalized using “bamCoverage” from deepTools.
MACS2 was used for peak calling.
“computeMatrix” from deepTools was used to generate all heat maps and plot profiles.
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set
Supplementary files format and content: bigWig, bedGraph

molecule: genomic DNA

growth_protocol: Cell lines were grown in RPMI 1640 Media (GIBCO) supplemented with 10% fetal bovine serum (FBS), 1% glutamine (GIBCO), penicillin (100U/mL) and streptomycin (100 μg/mL) at 37°C and 5% CO2. Mycoplasma tests were routinely performed.

extract_protocol:
Crosslinked chromatin was fragmented into mono-nucleosomes through digestion with MNase. Briefly, isolated and crosslinked nuclei were MNase digested in 400μl MNase digestion buffer (0.3M Sucrose, 50mM Tris pH 7.5, 30mM KCl, 7.5mM NaCl, 4mM MgCl2, 1mM CaCl2, 0.125% NP-40, 0.25% NaDeoxycholate, supplemented with cOmplete™ Protease Inhibitor Cocktail (Roche)) with 100U MNase (Roche) at 37°C for 30 minutes. The digestion was then stopped with 5mM EDTA and the digested chromatin was solubilized in 1% SDS and eight pulses of 30 seconds sonication using a Bioruptor® Pico ultrasonic cell disruptor (Diagenode). 200μg of pre-cleared chromatin was immunopurified with incubation of 20μl of E2A antibody (CST #12258) over night. The next day, Dynabeads™ Protein A (Invitrogen, 10002D) were added and incubated for 4 hours at 4°C. The samples were subsequently washed, eluted and the DNA was purified by ethanol precipitation.
NEBNext Ultra II

treatment_protocol: HAL-01 cells stably expressing Cas9GFP, were  introduced with sgRNA targeting the wild type TCF3.

value: Leukemia cell line

value: Cas9GFP, Ctr_SCR

value: TCF3 pulldown


title: Hypoxia INPUT rep2

description: Library name: Sample 4


title: EU 40min MeRIP

description: Library name: Sample 9


title: Normoxia INPUT rep2

description: Library name: Sample 8


title: 000-327

value: Whole blood


title: TCF3_IP_Knockout

description: Library name: Sample3

value: Cas9GFP, wtTCF3 KO


title: TCF3_Input_Parental

description: Library name: Sample2

value: Input control


title: Hypoxia INPUT rep1

description: Library name: Sample 3


title: Heterozygous Rbm20-R636Q KI - Hesperadin (2.5 ug/mg)  treated - 3

description: Library name: HET_Hesp2.5_3


title: Heterozygous Rbm20-R636Q KI - Hesperadin (2.5 ug/mg)  treated - 2

description: Library name: HET_Hesp2.5_2


title: Hypoxia MeRIP rep2

description: Library name: Sample 2


title: 000-023

value: Asthma

value: Female

value: low


title: TCF3_Input_Knockout

description: Library name: Sample1


title: 000-563


title: 000-491


title: Senescent HUVECs, Rep B

description:
Library name: Celula-B
3’ mRNA amplification

value: HUVECs

value: Endothelial cells

value: WT


title: Heterozygous Rbm20-R636Q KI - Hesperadin (2.5 ug/mg)  treated - 1

description: Library name: HET_Hesp2.5_1


title: Senescent HUVECs, Rep A

description:
Library name: Celula-A
3’ mRNA amplification


title: Heterozygous Rbm20-R636Q KI - Hesperadin (5 ug/mg)  treated - 1

description: Library name: HET_Hesp5_1


title: 000-561


title: TBX5 Het, atrial, d20, ATAC, rep2

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: TBX5 Het, atrial, d20, ATAC, rep2
10X Genomics

library_source: genomic single cell

data_processing:
Raw fastq files were processed with Cellranger (v2) atac count
Assembly: Human hg38
Supplementary files format and content: The fragments.tsv.gz contains one line per unique fragment
Supplementary files format and content: The fragments.tsv.gz.tbi file is a tabix index of the fragment intervals facilitating random access to records from an arbitrary genomic interval

source_name: WTC11 iPSC parental line

growth_protocol: iPSCs were maintained in mTeSR Plus media on growth factor-reduced (GFR) matrigel

extract_protocol:
Cells on day 20 or day 23 were singularized using 0.25%Trypsin, nuclei were harvested, counted and loaded on a 10X Chromium chip according to manufacturer's instructions
Next GEM Single Cell ATAC v1.1

treatment_protocol: iPSC lines were differentiated to cardiomyocytes using the Stemdiff Atrial Cardiomyocyte or Ventricular Cardiomyocyte Differentiation Kits

tag: timepoint

value: Day 20

value: WTC11 iPSC parental line

value: Atrial cardiomyocyte

value: TBX5 Heterozygous mutant

tag: batch

value: batch 2


title: Bone Marrow Derived Macrophages, Control Media, Vehicle Treatment, Replicate 1

description: Library name: V_1

value: Bone Marrow Derived Macrophage

value: Macrophage

value: Control Media, Vehicle


title: Heterozygous Rbm20-R636Q KI - DMSO treated - 2

description: Library name: HET_DMSO_2

value: heart tissue (LV)


title: WT, atrial, d20, ATAC, rep2

description:
Library name: WT, atrial, d20, ATAC, rep2
10X Genomics

value: Wildtype


title: ileal mucosal scraping, ERBB3-dIE, mouse 4

city: Los Angeles

first: Jonathan

middle: Jay

last: Hsieh

address: 4650 Sunset Blvd

institute: Children's Hospital Los Angeles

description: Library name: KO4

data_processing:
Illumina Casava software was used for basecalling.
Reads were mapped with Salmon 1.10.0.
Mapped reads were summarized to gene level with tximport.
DGE analysis was done with DESeq2 using (~ litter + genotype) as the design formula to account for possible litter effects.
Assembly: Gencode vM32 (GRCm39)
Supplementary files format and content: .csv with DESeq2 results attached to TPM table for each sample

source_name: ileum

extract_protocol:
Mice were euthanized and ileums were dissected. Mucosa was scraped from ileal tissue then homogenized and lysed. RNA was prepared using Omega Bio-Tek EZNA RNA isolation kit.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.

value: ileum

tag: litter

value: A


title: ileal mucosal scraping, ERBB3-dIE, mouse 6

description: Library name: KO6


title: ileal mucosal scraping, ERBB3-dIE, mouse 5

description: Library name: KO5


title: Heterozygous Rbm20-R636Q KI - DMSO treated - 1

description: Library name: HET_DMSO_1


title: RPE-1 cells,Fam53c siRNA replicate 1

city: Palo Alto

first: Debadrita

last: Bhattacharya

state: California

address: Lorey Lokey Stem Cell Research Building,265 Campus Drive

department: Pediatrics

institute: Stanford University

description:
Library name: f1
fam_1

data_processing:
Raw sequencing reads were trimmed using CutAdapt (v2.10)  with the TruSeq sequencing adapter (5’-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’), and a minimum read length of at least 25. Reads were then aligned to the UCSC hg38 genome with HiSat2  using reverse strandedness and discarding unaligned reads. Counts were assigned to genes (hg38 GTF) using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited file containing raw data for each sample

growth_protocol: RPE-1 lines were grown in DMEM high glucose medium supplemented with 10% bovine growth serum (BGS) (Fisher Scientific) and 1% penicillin-streptomycin-glutamine (Gibco). All cell lines tested negative for mycoplasma.

extract_protocol:
RNA was extracted using the Allprep DNA/RNA isolation microkit (Qiagen 80284)Allprep DNA/RNA isolation microkit (Qiagen 80284)
Library preparation and sequencing were performed by Novogene using the Illumina NextSeq 500 platform to obtain ~20 million paired reads/sample

treatment_protocol: FAM53C knock-down experiments in human cell lines were performed using 5 µM of ON-TARGETplus pooled siRNAs (Horizon – DharmaconTM), and ON-TARGET Control #1 as negative controls. Cells were transfected using the Lipofectamine RNAiMAX reagent, following the manufacturer’s recommendations. For RNA-seq experiments, samples were collected 48 hour post siRNA transfection.

value: Epithelial cells

value: FAM53C KD

value: Fam53c siRNA


title: 000-558

value: Whole blood

value: Asthma

value: Female

value: high


title: Widtype - DMSO treated - 3

description: Library name: WT_DMSO_3


title: ileal mucosal scraping, Erbb3-FF, mouse 5

description: Library name: FF5


title: Hypoxia MeRIP rep1

description: Library name: Sample 1

value: prostate

value: prostate cancer cells


title: 000-557


title: 000-555


title: Widtype - DMSO treated - 2

description: Library name: WT_DMSO_2


title: 000-552

value: Male


title: Widtype - DMSO treated - 1

description: Library name: WT_DMSO_1


title: ileal mucosal scraping, Erbb3-FF, mouse 4

description: Library name: FF4


title: RPE-1 cells, on-traget control replicate 3

description:
Library name: ot_3
On_Target3

value: WT

value: On-target control siRNA


title: ileal mucosal scraping, Erbb3-FF, mouse 6

description: Library name: FF6


title: ileal mucosal scraping, Erbb3-FF, mouse 3

description: Library name: FF3


title: 000-559


title: ileal mucosal scraping, Erbb3-FF, mouse 2

description: Library name: FF2

value: B


title: RPE-1 cells, on-traget control replicate 1

description:
Library name: ot_1
On_Target1


title: TBX5 Hom, atrial, d20, ATAC, rep2

description:
Library name: TBX5 Hom, atrial, d20, ATAC, rep2
10X Genomics

value: Day 20

value: WTC11 iPSC parental line

value: Atrial cardiomyocyte

value: TBX5 Homozygous mutant

value: batch 2


title: CD8_EPICv1

type: genomic

city: Philadelphia

first: Yee Hoon

last: Foong

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma8_4
205828610139_R04C01

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Quality control preprocessing were done using Minfi package. Probes with signal lower than background in >25% of the samples were eliminated using Minfi's detectionP() function. Background and dye correction were done using Minfi's preprocessFunnorm function (funnorm + noob). Only probes that are common between EPICv1 (GPL21145) and EPICv2 are included in the downstream analyses
Minfi's getBeta() was used to extract Beta values after the quality control preprocessing steps. Only probes that are common between EPICv1 (GPL21145) and EPICv2 are included in the downstream analyses

label: Cy3 and Cy5

source_name: Sacrum/ Coccyx

label_protocol: not provided

extract_protocol: Genomic DNA was extracted using standard Phenol:Chloform extraction

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M

value: Bisulfite treated


title: 000-551

value: Whole blood

value: Asthma

value: low


title: Astrocytes Donor A73 R1 BG4

city: San Diego

first: Christopher

middle: L

last: Hartl

address: Pacific Heights Blvd

department: Cell Biology

institute: Epigenome Technologies

description: Library name: G4_20250327_Age73

data_processing:
(CUT&Tag) Reads were aligned to GRCh38 using bwa mem (0.7.18-r1243-dirty) and aligned .bam files converted to fragment files by a custom script that converts read pairs into intervals consisting of the minimum starting position and maximum ending position in the pair. Single reads (mate unaligned, aligned to a different chromosome, or insert >1KBP) were converted to individual fragments the size of the read. Fragments were positionally de-duplicated, resulting in a fragment bed file. Fragments were converted to by cut sites by opening a 50bp window centered at each side of the fragment. MACS2 was used to call, and peaks were quantified by total count of fragments, and maximum depth in peak; and normalized to a set of 10,000 randomly-chosen intervals of size 250 falling outside of called peak regions.
Assembly: GRCh38
Supplementary files format and content: peak quantifications (csv), normalized track coverage (bigwig)
Library strategy: CUT&Tag

source_name: brain

growth_protocol: Primary human astrocytes were grown on poly-D-lysine coated flasks and maintained in DMEM/F-12 supplemented with 10% FBS, 1% penicillin-streptomycin at 37 degrees in a humidified 5% CO2 incubator. Media was changed every 2-3 days. Cells were passaged with accutase  at ~80% confluence and used between passages 2-4. For RNA-seq experiments, astrocytes were plated at 2 million cells per T25 flask and transduced at ~60-70% confluence.

extract_protocol:
(CUT&Tag) Astrocyte cultures were crosslinked by adding 31.25 uL of 16% formaldehyde to 1 mL of cell suspension in PBS + 0.04% BSA to reach a final concentration of 0.5%. Samples were incubated on ice for 5 minutes and quenched with 50 uL of 2.5 M glycine. Cells were pelleted at 300 x g for 5 minutes and washed once with PBS. Cells were lysed in chilled lysis buffer [10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl_2, 0.1% Tween-20, 0.1% NP-40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, and 1x protease inhibitors] using 200 uL per large sample or 100 uL for small samples. Lysis was performed on ice for 5 minutes, followed by two washes with 1 mL wash buffer [same composition as above without NP-40 substitute]. Nuclei were resuspended in PBS + 0.04% BSA and counted. 100,000 nuclei were aliquoted per CUT&Tag reaction.
(CUT&Tag) Nuclei were resuspended in 70-90 uL of incubation buffer, antibodies, and pAG-Tn5 added. The following antibodies and enzymes were added per reaction: Primary antibody: G4 scFv (Millipore MABE917, 0.25 mg/mL), 1.03 uL; Secondary antibody: Anti-FLAG M2 (Millipore F1804, 1 mg/mL), 1.48 uL; pAG-Tn5 transposome (EpiCypher, Cat# 15-1025-FT002, 3.94 uM dimer), 2.53 uL. Samples were incubated overnight at 4 oC with gentle rotation. Tagmentation was triggered by adding 4 uL of 250 mM MgCl_2 and incubating at 37 oC for 1 hour at 550 rpm. The reaction was quenched with 20 uL of 80 mM EDTA. DNA was purified using the Zymo DNA Clean & Concentrator-5 kit and eluted in 20 uL of nuclease-free water. PCR reactions (50 uL) included 25 uL NEBNext High-Fidelity 2x Master Mix and 2.5 uL of 10 uM indexed i7/i5 primers. Thermal cycling was done at 72 oC for 5 min; 98 oC for 30 s; 15 cycles of 98 oC for 10 s, 63 oC for 30 s, 72 oC for 1 min; final extension at 72 oC for 2 min. SPRIselect beads (0.75x) were used for purification, and libraries were eluted in 10 uL of water. DNA concentration was measured by Qubit, and libraries were diluted to 1 ng/uL for TapeStation QC.

treatment_protocol: Astrocytes were transduced with lentiviral vectors expressing DDX5-mScarlet or control mScarlet lentiviruses. Viruses was added in complete medium at an MOI of 10. After 16-24 h, the medium was replaced with fresh growth medium. Cells were harvested for RNA extraction 48 hr post-transduction. Independent biological replicates (5 per condition) were processed separately.

value: brain

value: astrocyte

tag: age


title: CD6_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma6_3
205832320095_R07C01

value: F


title: Astrocytes Donor A56 R2 BG4

description: Library name: G4_20250327_Age56


title: CD50_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma50
206100100175_R06C01


title: 000-546

value: Female

value: high


title: ileal mucosal scraping, ERBB3-dIE, mouse 2

description: Library name: KO2

value: ileum

value: B


title: CD5_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma5_4
205828610107_R06C01


title: 000-543

source_name: Control Male

value: Control

value: Male


title: ileal mucosal scraping, Erbb3-FF, mouse 1

description: Library name: FF1


title: RPE-1 cells, on-traget control replicate 2

description:
Library name: ot_2
On_Target2

value: Epithelial cells

value: WT

value: On-target control siRNA


title: Astrocytes Donor A53 R2 BG4

description: Library name: G4_20250327_Age53


title: Astrocytes Donor A34 R2 BG4

description: Library name: G4_20250327_Age34


title: CD47_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma47
205857030175_R07C01

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M


title: Astrocytes Donor A32 R2 BG4

description: Library name: G4_20250327_Age32


title: 000-537

value: Whole blood

value: Asthma


title: 000-540


title: 000-550


title: 000-541


title: CD46_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma46_2
205857030009_R08C01

value: Bisulfite treated


title: CD45_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma45_3
205857030009_R07C01


title: Alpha cells, E17.5 Gcg-Timer, green dominant and green/red copositive cells

city: Sagamihara City

first: Naoya

last: Shimizu

state: Kanagawa

address: 1-15-1, Kitasato

country: Japan

institute: Kitasato University Graduate School of Medical Sciences

description:
Library name: sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Following sequencing, FASTQ files were generated from the raw sequencing data using cellranger mkfastq (10x Genomics), after which they were mapped to the build 38 of the Genome Reference Consortium mouse genome to generate single-cell gene counts using cellranger count (10x Genomics). Low quality score sequences were filtered out. Cellranger aggr (10x Genomics) was used to combine data from multiple samples and ensure that all libraries had the same sequencing depth.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pancreas

extract_protocol:
Pancreata from Gcg-Timer embryos and wild-type littermates were dissected at E17.5　and dissociated using 0.5 g/L trypsin/0.53 mmol/L-EDTA solution (Nacalai Tesque, Kyoto, Japan) at 37 °C for 5 minutes. The dissociated cells were resuspended in PBS containing 1% FBS, and newly generated and differentiated α cells were sorted using BD FACSAria™ III Cell Sorter (BD Biosciences, San Jose, CA, USA).
Single-cell cDNA libraries were prepared using the 10× Genomics Chromium™ platform (Pleasanton, CA, USA). The Single Cell 3’ Reagent Kits v2 were used to generate single-cell libraries. The libraries were pooled and sequenced using an Illumina NextSeq500 platform (San Diego, CA, USA) with a 150 cycle High Output v2 kit in paired-end format with 26 bp Read 1, 8 bp I5 Index, and 85 bp Read 2.

value: pancreas

value: male

value: Alpha cells

value: Gcg-Timer


title: Astrocytes Donor A24 DDX KO R2 BG4

description: Library name: G4_20250327_Age24_DDX_Knock_Down

value: brain

value: astrocyte

value: DDX5 Knockout


title: ileal mucosal scraping, ERBB3-dIE, mouse 1

description: Library name: KO1

value: ileum

value: B


title: ileal mucosal scraping, ERBB3-dIE, mouse 3

description: Library name: KO3


title: 000-534

description: Expression value derived from nCounter Digital Analyzer

value: Male

value: high


title: 000-533


title: Astrocytes Donor A24 R2 BG4

description: Library name: G4_20250327_Age24


title: EGV_2

city: Daegu

first: Jong-Heon

last: Kim

address: 680 Gukchaebosang Street, Jung-gu

department: Brain Science & Engineering Institute

country: South Korea

institute: Kyoungpook National University

description:
Library name: Sample 8
Raw_counts_All_Samples.txt: EGV_2

data_processing:
Raw reads were quality-checked with FastQC. Adapter sequences and low-quality bases were removed, and the cleaned reads were aligned to the reference genome with STAR. Gene-level counts were generated with HTSeq-count and normalized by the TMM + CPM method implemented in the Python package Conorm (https://gitlab.com/georgy.m/conorm). Downstream analyses and visualizations were performed in ExDEGA (Ebiogen, Korea).
Assembly: GRCm39

source_name: Spinal cord

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher Scientific, Waltham, MA, USA) or the Maxwell RSC miRNA kit (Promega, Madison, WI, USA). RNA integrity was evaluated on an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA), and concentration was measured with a Qubit fluorometer (Thermo Fisher Scientific).
cDNA libraries were built with the QuantSeq 3′ mRNA-Seq V2 FWD kit (Lexogen, Vienna, Austria) according to the manufacturer’s instructions.

value: Spinal cord

value: WT


title: Astrocytes Donor A22 R2 BG4

description: Library name: G4_20250327_Age22


title: EGV_1

description:
Library name: Sample 7
Raw_counts_All_Samples.txt: EGV_1


title: CD4_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma4_3
205689130132_R07C01

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M


title: Astrocytes Donor A72 R1 BG4

description: Library name: G4_20250325_Age72


title: EAE_3

description:
Library name: Sample 6
Raw_counts_All_Samples.txt: EAE_3

value: Vehicle


title: 000-528

value: Whole blood

value: Asthma

value: Female

value: low


title: 000-526


title: CD39_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma39
205828610139_R07C01

value: F

value: Bisulfite treated


title: CD33_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma33
205828610139_R06C01


title: EAE_2

description:
Library name: Sample 5
Raw_counts_All_Samples.txt: EAE_2


title: CD3_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma3_2
205724780115_R07C01


title: CD25_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma25_2
205724780015_R07C01


title: Astrocytes Donor A32 R1 BG4

description: Library name: G4_20250325_Age32

value: brain

value: astrocyte


title: 000-522


title: EAE_1

description:
Library name: Sample 4
Raw_counts_All_Samples.txt: EAE_1


title: Astrocytes Donor A34 R1 BG4

description: Library name: G4_20250325_Age34


title: CON_3

description:
Library name: Sample 3
Raw_counts_All_Samples.txt: CON_3

value: Naïve


title: Astrocytes Donor A53 R1 BG4

description: Library name: G4_20250325_Age53


title: 000-532


title: Astrocytes Donor A56 R1 BG4

description: Library name: G4_20250325_Age56


title: CON_1

description:
Library name: Sample 1
Raw_counts_All_Samples.txt: CON_1


title: 000-523

value: Male


title: 000-519

value: high


title: CD2_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma2_3
205724780115_R06C01


title: Astrocytes Donor A24 R1 BG4

description: Library name: G4_20250325_Age24


title: CR-Mlg088

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

data_processing:
FASTQ files were processed with cellranger v3.1 Doublets and low-quality cells were excluded from subsequent analysis (< 500 or >8000 genes and > 15% expression of the percentage from mitochondrial gene). For the remaining cells, gene expression data were normalized using NormalizeData function and were scaled with the ScaleData function in Seurat package. The batch effects were removed by RunHarmony function using Seurat package (version 4.1.1).
Assembly: hg38 or mm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample, bw

source_name: liver

extract_protocol:
Tissues were rinsed with PBS, cut into 1 mm3 pieces, and transferred to 5 ml of digestive solution (DMEM High Sugar (Sigma-Aldrich) with the addition of L-glutamine-penicillin-streptomycin (100 U/ml) (Sigma-Aldrich), 20 uL of DNase (Quiagen) (75 U/ml), 2 mL of Collagenase V (2 %) (Sigma-Aldrich) and Dispase II (2. 5 U/mL) (Gibco)) in a water bath (37 °C) for 45 min.   Translated with www.DeepL.com/Translator (free version)
For scRNA sequencing, libraries were generated and prepared for single-cell suspensions using a 10X Chromium Chip Single-Cell Library Generator (10X Chromium 3'solution (V2 kit)) according to the manufacturer's instructions, with the goal of capturing 5,000-1,000 cells/channel. Sequencing was performed using the Illumina HiSeq 4000 platform.

value: liver

value: no

value: hepatocellular carcinoma

value: protac


title: Astrocytes Donor A22 R1 BG4

description: Library name: G4_20250325_Age22


title: 000-516


title: 000-520


title: CD24_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma24_2
205724780015_R06C01

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M


title: CON_2

description:
Library name: Sample 2
Raw_counts_All_Samples.txt: CON_2

value: Spinal cord

value: WT


title: Astrocytes Donor A24 DDX KO R1 BG4

description: Library name: G4_20250325_Age24_DDX_Knock_Down

value: DDX5 Knockout


title: CR-Mlg089


title: CD16_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma16_4
205724780015_R04C01


title: Astrocytes Donor A73 R1 ATAC

description:
Library name: ATAC_20250327_Age73
20250327_Age73

data_processing:
(ATAC) Reads were aligned to GRCh38 using bwa mem (0.7.18-r1243-dirty) and aligned .bam files converted to fragment files by a custom script that converts read pairs into intervals consisting of the minimum starting position and maximum ending position in the pair. Single reads (mate unaligned, aligned to a different chromosome, or insert >1KBP) were converted to individual fragments the size of the read. Fragments were positionally de-duplicated, resulting in a fragment bed file. Fragments were converted to by cut sites by opening a 50bp window centered at each side of the fragment. MACS2 was used to call, and peaks were quantified by total count of fragments, and maximum depth in peak; and normalized to a set of 10,000 randomly-chosen intervals of size 250 falling outside of called peak regions.
Assembly: GRCh38
Supplementary files format and content: Normalized peak quantifications, csv
Supplementary files format and content: Normalized ATAC depth track, bigwig

extract_protocol:
(ATAC) Primary human astrocyte cultures were thawed at 37 oC in a water bath until a small ice crystal remained. Cells were immediately diluted in RPMI supplemented with 10% FBS and centrifuged at 300 x g for 5 minutes. Pellets were washed twice in PBS containing 0.04% BSA and passed through a 40 um cell strainer to remove debris. Cell viability and counts were assessed using a hemocytometer prior to nuclei isolation. For lysis, cells were resuspended in 100 uL of chilled lysis buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Non-idet P-40 substitute, 0.01% digitonin, 1% BSA, 1 mM DTT, and 1x protease inhibitors] and incubated on ice for 3 minutes. Nuclei were washed three times in 1 mL of wash buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1x protease inhibitors] at 500 x g for 5 minutes at 4 oC. Nuclei were resuspended in PBS + 0.04% BSA, counted, and typically yielded ~4 x 10^6 nuclei per sample.
(ATAC) Fifty thousand nuclei were resuspended in 12.5 uL of 1x nuclei buffer and incubated with pA-Tn5 transposase preloaded with sequencing adapters. Tagmentation was performed in a thermocycler at 37 oC for 30 minutes. Tagmented DNA was purified using the Zymo DNA Clean & Concentrator kit (Zymo Research) and eluted in 21 uL of nuclease-free water. Libraries were amplified in 50 uL reactions using NEB-Next High-Fidelity 2x PCR Master Mix (NEB, Cat# M0541) and 2.5 uL each of 10 uM indexed i5 and i7 primers. PCR cycling conditions were: 72 oC for 5 min, 98 oC for 30 s, followed by 12 cycles of 98 oC for 10 s, 63 oC for 30 s, and 72 oC for 1 min, with a final extension at 72 oC for 1 min. Amplified libraries were cleaned with 0.75x SPRI-select beads (0.75x) with two 80% ethanol washes and eluted in 20 uL water.


title: 000-515

description: Expression value derived from nCounter Digital Analyzer

value: Whole blood

value: Control

value: Female


title: CD14_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma14_3
205724780015_R03C01

value: F

value: Bisulfite treated


title: CD10_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma10_A
205828610139_R05C01


title: CR-Mlg086


title: CR-Mlg085


title: EGV_3

description:
Library name: Sample 9
Raw_counts_All_Samples.txt: EGV_3


title: 000-511

value: Asthma


title: CD1_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma1_3
205724780115_R05C01


title: Astrocytes Donor A53 R2 ATAC

description:
Library name: ATAC_20250327_Age53
20250327_Age53

value: brain

value: astrocyte


title: Astrocytes Donor A34 R2 ATAC

description:
Library name: ATAC_20250327_Age34
20250327_Age34


title: 000-508

value: Male

value: high


title: 000-503


title: humanDLPFC_Schizophrenia_14

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

data_processing:
SMRTLink (v8.0.0)
removed primers using Lima (v2.0.0).
clustered using IsoSeq3
aligned the reads to hg38 (version 34; GRCh38.p13) using minimap2 (v2.17)
Cupcake (28.0.0) tools to collapse the clustered reads onto hg38 loci and assign unique isoform IDs
SQANTI3 QC filtering
Assembly: GRCh38.p13
Supplementary files format and content: rows are isoforms with columns containing SQANTI classification and QC information along with sample isoform counts

source_name: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)

extract_protocol:
The DLPFC tissue blocks were cryo-sectioned, and total RNA was extracted from 200 mg of cortical tissue using the RNeasy Mini Kit (QIAGEN). For a subset of replicate samples, dry homogenization was performed using a liquid nitrogen cooled mortar and pestle before RNA extraction.
Iso-Seq Express Template Preparation for Sequel and Sequel II Systems, PN 101-763-800 Version 02 (October 2019). We used the NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module, the Iso-Seq Express Oligo Kit, ProNex beads, and the SMRTbell Express Template Prep Kit 2.0 for library preparation. We used 300 ng of cDNA as our input material and subjected the samples to 12 cycles of amplification; additional cycles were added to samples with low yield. We purified the cDNA using a standard workflow. Most of our samples contained transcripts with a central length of approximately 2 kb. We conducted quality control of the SMRT bell libraries using the Qubit dsDNA HS kit and the Agilent Bioanalyzer High Sensitivity kit. We used the Sequel II primer annealing and polymerase binding kit version 2.0 or 2.1. The samples were sequenced on either the Sequel II or Sequel IIe instrument using the Sequel II sequencing plate 2.0 and the Sequel II SMRT Cell 8M. The sequencing was performed with a movie time of 24 hours and a pre-extension time of 2 hours.

tag: disease state

value: Schizophrenia


title: 000-501


title: Astrocytes Donor A32 R2 ATAC

description:
Library name: ATAC_20250327_Age32
20250327_Age32


title: CR-Mlg084

value: liver

value: no

value: hepatocellular carcinoma


title: CR-Mlg087

value: protac


title: humanDLPFC_Schizophrenia_13

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: RPE-1 cells,Fam53c siRNA replicate 2

description:
Library name: f2
fam_3

value: Epithelial cells

value: FAM53C KD

value: Fam53c siRNA


title: VA-TFoxj1Rb

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description: translating ribosome affinity purification-coupled RNAseq

data_processing:
Raw reads processed for QC using fastqc (0.11.8) and poor quality reads filtered using trimmomatic (0.39)
Aligned to mm10 genome using STAR aligner (2.7.2b) and counts quantitated, normalized, and all pairwise comparisons done using DESeq2 (1.38.3) in R programming language (4.2.2)
Assembly: mm10
Supplementary files format and content: tab-delimited raw read counts for each paired-end sample. Tab-delimited raw read gene matrix.
Supplementary files format and content: comma-separated value DESeq2 normalized gene count matrix. CSV pairwise comparison of each driver type vs input generated through DESeq2. CSV gene matrix of log2-fold change of each driver vs input with and without FDR adjusted p-value (BH) generated by DESeq2.

growth_protocol: Mus musculus strain Rosa[L10/+] were crossed to lineage-specific Cre and CreER driver lines.

extract_protocol:
Neonatal lungs (~P5) were dissected and stripped from surrounding tissue. Translating ribosomes were isolated per previous protocol (see for instance 10.1242/dev.160788), and pulled down using one of two anti-GFP antibodies (19C8 or Rb) using affinity column. RNA isolated from affinity column bound beads using RNeasy Micro kit with Trizol reagent. Separate samples of precleared lung homogenate was kept on ice and not passed over affinity columns with RNA isolated in parallel with affinity-column samples. These were used as control input samples.
100-200 ng RNA used for RT-PCR performed using SuperScript IV (Invitrogen). cDNA libraries constructed using NEBNext Ultra RNA library kit with a final double size selection using SPRIselect reagent kit (Beckman Coulter). Bar-coded using NEBNext Illumina kit. 300 bp inserts and submitted for next-gen reads on Illumina NextSeq 500 pipeline through the MD Anderson Sequencing Core.

treatment_protocol: For CreER lines, recombination induced by IP injection of 0.5-2 mg tamoxifen. P5 mice were genotyped to identify L10-Cre mice.

value: lung

value: airway ciliated cell

value: VA-TFoxj1Rb x floxed L10-GFP

value: anti-GFP (Rb)


title: VA-TFoxj1C8

value: VA-TFoxj1C8 x floxed L10-GFP

value: anti-GFP (C8)


title: 000-500

data_processing: Nanostring nCounter v3.0a arrays were normalized using the top 100 genes without background subtraction using the geometric mean in the nSolver Analysis Software.v3 (Nanostring). The log2 count normalized matrices of microRNAs in the Nanostring arrays were batch-adjusted using theComBat function in the sva package (version 3.46.0) and used for all subsequent analyses.

value: Whole blood

value: Asthma

value: Female

value: low


title: Astrocytes Donor A24 DDX KO R2 ATAC

description:
Library name: ATAC_20250327_Age24_DDX_Knock_Down
20250327_Age24_Knock_Down

value: brain

value: astrocyte

value: DDX5 Knockout


title: CDT17_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
ChordomaT17_2
205724780015_R05C01

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M

value: Bisulfite treated


title: CD12_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma12_2
205724780015_R02C01

value: F


title: Astrocytes Donor A56 R2 ATAC

description:
Library name: ATAC_20250327_Age56
20250327_Age56


title: Astrocytes Donor A24 R2 ATAC

description:
Library name: ATAC_20250327_Age24
20250327_Age24


title: humanDLPFC_Control_15

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)

value: Control


title: VA-TCRISPRRb

value: lung

value: alveolar type 1 cell

value: VA-TCRISPRRb x floxed L10-GFP

value: anti-GFP (Rb)


title: 000-498

value: Whole blood

value: Asthma


title: Astrocytes Donor A22 R2 ATAC

description:
Library name: ATAC_20250327_Age22
20250327_Age22


title: VA-TCRISPRC8

value: VA-TCRISPRC8 x floxed L10-GFP

value: anti-GFP (C8)


title: 000-495

value: Female

value: high


title: Astrocytes Donor A72 R1 ATAC

description:
Library name: ATAC_20250325_Age72
20250325_Age72

value: brain

value: astrocyte


title: humanDLPFC_Control_13


title: VA-TAplnBRb

source_name: Apln-CreER

value: endothelial cell

value: VA-TAplnBRb x floxed L10-GFP


title: VA-TAplnBC8

value: VA-TAplnBC8 x floxed L10-GFP


title: Astrocytes Donor A56 R1 ATAC

description:
Library name: ATAC_20250325_Age56
20250325_Age56


title: 000-484

description: Expression value derived from nCounter Digital Analyzer

source_name: Asthma Female


title: humanDLPFC_Control_12

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: humanDLPFC_Control_16

value: Control


title: 000-499


title: Astrocytes Donor A53 R1 ATAC

description:
Library name: ATAC_20250325_Age53
20250325_Age53


title: VA-TAplnARb

value: lung

value: VA-TAplnARb x floxed L10-GFP


title: CD44_EPICv1

description:
Processed beta values of EPICv1 and EPICv2 common probes in Chordoma_betaValues_EPICv1-EPICv2_common_probes.csv
Chordoma44_2
205857030175_R08C01

value: Sacrum/ Coccyx

value: Sacral chordoma patient

value: M

value: Bisulfite treated


title: Astrocytes Donor A34 R1 ATAC

description:
Library name: ATAC_20250325_Age34
20250325_Age34


title: VA-TAplnAC8

value: VA-TAplnAC8 x floxed L10-GFP


title: humanDLPFC_Control_10


title: 000-481

value: Whole blood

value: Male


title: Astrocytes Donor A32 R1 ATAC

description:
Library name: ATAC_20250325_Age32
20250325_Age32


title: 000-480

value: Asthma

value: low


title: TWhL-L10TCF21Rb2

value: mesencbymal cell

value: TWhL-L10TCF21Rb2 x floxed L10-GFP

value: anti-GFP (Rb)


title: 000-479

value: Female


title: humanDLPFC_Control_9

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: Astrocytes Donor A24 DDX KO R1 ATAC

description:
Library name: ATAC_20250325_Age24_DDX_Knock_Down
20250325_Age24_Knock_Down

value: brain

value: astrocyte

value: DDX5 Knockout


title: TWhL-L10TCF21Rb1

value: lung

value: TWhL-L10TCF21Rb1 x floxed L10-GFP


title: humanDLPFC_Control_14

value: Control


title: humanDLPFC_Control_8


title: 000-477

value: high


title: Astrocytes Donor A24 R1 ATAC

description:
Library name: ATAC_20250325_Age24
20250325_Age24


title: humanDLPFC_Control_7


title: 000-483


title: 000-476


title: TWhL-L10TCF21C82

value: mesenchymal cell

value: TWhL-L10TCF21C82 x floxed L10-GFP

value: anti-GFP (C8)


title: humanDLPFC_Control_11


title: humanDLPFC_Control_6


title: TWhL-L10TCF21C81

value: TWhL-L10TCF21C81 x floxed L10-GFP


title: Astrocytes Donor A22 R1 ATAC

description:
Library name: ATAC_20250325_Age22
20250325_Age22


title: humanDLPFC_Schizophrenia_12

value: Schizophrenia


title: 000-473

value: Whole blood


title: E. coli, RNA004 chemistry

city: Aurora

first: Laura

last: White

state: CO

address: 12801 E 17th Avenue RC1S

department: Biochemistry & Molecular Genetics

institute: University of Colorado

description: tRNA sequencing (RNA004)

library_source: other

data_processing:
All libraries were rebasecalled with Dorado 0.7.0 using multiple basecalling models as described in the accompanying manuscript; fastqs have been provided from the highest accuracy basecalling model for each library along with the original POD5 file.
Alignments to tRNA references were performed using BWA-MEM version 0.7.16 with the parameters bwa mem -C -W 13 -k 6 -T 20 -x ont2d.
Further description of alignment, modification analysis, custom scripts and tRNA reference files can be found at  github.com/rnabioco/tRNA004
Assembly: custom tRNA references available at github.com/rnabioco/tRNA004
Supplementary files format and content: bedgraphs of full length filtered reads aligned to tRNA references

molecule: other

organism: Escherichia coli

extract_protocol:
Total RNA extraction protocols for each sample type are detailed in the accompanying manuscript; library inputs were size selected for RNA 17-200 nt in length.
complete protocol for tRNA sequencing available at github.com/rnabioco/tRNA004


title: TWhL-L10ProxRb2

description: translating ribosome affinity purification-coupled RNAseq

value: lymphatic endothelial cell

value: TWhL-L10ProxRb2 x floxed L10-GFP


title: 000-470

extract_protocol:
Whole blood was collected in PaxGene RNA tubes
Total RNA from whole blood samples was isolated using a column-based system (total-RNA kit; Norgen)

value: Female


title: Germline specific over-expression of constituitively active Tkv

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

description:
Library name: TKV
10x Genomics

data_processing:
Cellranger 7.2.0 (10x Genomics)
Assembly: BDGP6_46
Supplementary files format and content: Tab-separated value files and matrix files

organism: Drosophila melanogaster

source_name: adult ovary

extract_protocol:
100 ovaries were dissected in Grace’s insect medium, disassociated in a solution containing 0.5% type 1 collagenase and 1% trypsin in PBS for 15 minutes, which was stopped by adding Grace’s insect medium with 10% FBS. Suspended cells were passed through a Flowmi 40-micron filter and  then centrifuged at 5 rpm for 3 minutes. Single cells were resuspended and washed with 0.04% BSA in PBS, centrifuged again for collection of single cells.
Single Cell 3’ v2 protocol (10x Genomics)

value: adult ovary


title: humanDLPFC_Schizophrenia_11

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: TWhL-L10ProxRb1

value: TWhL-L10ProxRb1 x floxed L10-GFP

value: anti-GFP (Rb)


title: TWhL-L10LyveRb2

value: lung

value: endothelial cell

value: TWhL-L10LyveRb2 x floxed L10-GFP


title: Germline specific over-expression of EcR-B1

description:
Library name: ECRB1
10x Genomics


title: 000-469

city: New Haven

first: Jose

last: Gomez

address: 300 Cedar Street

institute: Yale University

value: Asthma

value: low


title: Control patient 4, subcutaneous white adipose tissue from upper neck (dorsocervical region)

city: Ann Arbor

first: Ormond

middle: A.

last: MacDougald

state: MI

address: 2800 Plymouth Rd

department: Molecular & Integrative Physiology

institute: University of Michigan

description:
Library name: C04up
DESeq2: combined developing and developed groups compared to controls

data_processing:
FastQC (v.0.12.1) was used to check the quality of the raw read data. Alignment was conducted using STAR (version 2.7.11a), using UCSC hg38 as the reference genome sequence. A second quality control was performed post-alignment using FastQC to ensure that only high-quality data were used for gene expression quantitation and differential expression analyses. Differential expression analysis was conducted using DESeq2 and RUV (Remove unwanted variation)-seq, using RNA integrity number and fasted insulin as known covariates.
Assembly: UCSC hg38
Supplementary files format and content: DESeq2_raw_counts_postfilter_with_symbols.csv has raw counts from DESeq2 and RUV-seq analysis

source_name: Subcutaneous white adipose tissue

growth_protocol: Human patient samples

extract_protocol:
Powdered frozen adipose tissue and used Rneasy Lipid Tissue Mini Kit (Qiagen) for RNA isolation
Libraries were constructed using DNBSEQ Eukaryotic Strand-specific mRNA library kit via manufacturer instructions, performed by Beijing Genomic Institute (BGI)

treatment_protocol: Samples were taken via excision biopsy, in the same location across all patients

value: Subcutaneous white adipose tissue

value: Biopsy

value: White adipose tissue

value: Control


title: humanDLPFC_Schizophrenia_10

value: Schizophrenia


title: 000-466

value: Whole blood

value: Male

value: high


title: TWhL-L10LyveRb1

value: TWhL-L10LyveRb1 x floxed L10-GFP


title: 000-459


title: Control patient 3, subcutaneous white adipose tissue from upper neck (dorsocervical region)

description:
Library name: C03up
DESeq2: combined developing and developed groups compared to controls


title: humanDLPFC_Schizophrenia_9

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)


title: TWhL-L10LyveC82

value: TWhL-L10LyveC82 x floxed L10-GFP

value: anti-GFP (C8)


title: humanDLPFC_Schizophrenia_8


title: Control patient 4, subcutaneous white adipose tissue from abdomen

description:
Library name: C04ab
DESeq2: combined developing and developed groups compared to controls


title: 000-458

value: Female


title: TWhL-L10LyveC81

value: lung

value: endothelial cell

value: TWhL-L10LyveC81 x floxed L10-GFP


title: Control patient 3, subcutaneous white adipose tissue from abdomen

description:
Library name: C03ab
DESeq2: combined developing and developed groups compared to controls


title: 000-455

value: Asthma

value: low


title: 000-453


title: humanDLPFC_Schizophrenia_7


title: Patient 3 with developed FPLD2, subcutaneous white adipose tissue from upper neck (dorsocervical region)

description:
Library name: B03up
DESeq2: combined developing and developed groups compared to controls

value: Subcutaneous white adipose tissue

value: Biopsy

value: Developed FPLD2


title: TRAP-pWnt3aRbA

value: alveolar type 1 cell

value: TRAP-pWnt3aRbA x floxed L10-GFP

value: anti-GFP (Rb)


title: Heterozygous Rbm20-R636Q KI - DMSO treated - 3

description: Library name: HET_DMSO_3

data_processing:
RNA-seq reads were aligned to mouse genome reference (mm10 GRCm38) using the Rsubread R package. Quality control of the reads was performed using Fastqcr and Rqc packages, while adapter trimming was conducted with Trimmomatic using standard parameters. For data processing and analysis, we employed a R-based pipeline utilizing BiocManager for package management, ShortRead for sequence manipulation and reading.
Assembly: mm10
Supplementary files format and content: gene_counts_Hesp - Gene counts of analysis of WT_DMSO, HET_DMSO, HET_Hesp2.5, and HET_Hesp5
Supplementary files format and content: gene_counts_DKO.tsv - Gene counts of analysis of WT, Rbm20KO, Camk2dKO and DKO

extract_protocol:
RNA was isolated using TRIzol following manufacturers instructions.
Sequence libraries were prepared using SMART-Seq Total RNA pico input (Takara Bio) following manufacturers instructions.

value: heart tissue (LV)


title: TRAP-pWnt3aC8B

value: TRAP-pWnt3aC8B x floxed L10-GFP


title: dss_trx2

city: Heraklion

first: Zoe

last: Veneti

address: Nikolaou Plastira 100

country: Greece

institute: Institute of Molecular Biology & Biotechnology Foundation for Research & Technology - Hellas

description:
Library name: Sample 9
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

data_processing:
Firstly, fastq files were quality  trimmed with Trim Galore(https://github.com/FelixKrueger/TrimGalore) with the option “--max_n 5” to remove reads containing more than 5 ambiguous bases. Trimmed reads were aligned to the dm6 build with bowtie2 (Ben Langmead & Steven L Salzberg, 2012) using the “--local --very-sensitive-local” parameters. Duplicates were discarded with Picard (http://broadinstitute.github.io/picard.).
Peak calling was performed with MACS3 (Zhang et. al., Genome Biology 2008) using the parameters “--nomodel --shift -100 --extsize 200”.
Differential accessibility analysis was conducted using the bioconductor package DiffBind (Ross-Ines et. al., Nature, 2012). Briefly, peaks overlapping blacklist regions were removed, and only peaks present in at least two samples with more than 10 counts were retained.  Read extension and summit re-centering were disabled. Differentially accessible regions were identified using  DESEQ2 (Love et al., Genome Biology, 2014) with an absolute fold change greater than 0.5 and FDR < 0.05.
Assembly: dm6
Supplementary files format and content: bigWig files containing normalized density for each sample.

source_name: Intestine

growth_protocol: 3-4 days old mated females from F1 progeny were shifted to 29 °C for 7 days

extract_protocol:
Illumina Tagment DNA enzyme and buffer kit (REF 20034210
ATAC-seq libraries were manufactured according to the original protocol (Buenrostro JB, et.al 2015). Briefly, 50-75K GFP positive sorted cells were collected in ATAC lysis buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630). Cells were pelleted 10’ x 500g, 4oC, supernatant discarded and subsequently gently suspended in 700ul ice-cold ATAC lysis buffer. After an additional 10’ x 500g, 4oC spin, lysis buffer was removed with a 1000p pipette leaving 22.5ul covering the nuclei. We added 2.5ul Tagmentation enzyme and 25ul 2xTagmentation Buffer (Illumina Tagment DNA enzyme and buffer kit (REF 20034210). Fragmentation reactions were performed using a bioSan TS-100 Thermo-Shaker at 37oC for 40’ shaking at 800RPM. Initial 5 cycle PCR was performed with Phusion High-Fidelity PCR Master Mix (NEB M0532S) using the Illumina Set C plate (REF 20026934) in total volume of 50ul. 5ul were used to estimate product cycle saturation with SYBR green in Biorad qPCR. Final libraries were produced after 13-14 total cycles of amplification and analyzed on a Bioanalyzer DNA chip.

treatment_protocol: flies were fed with 5% sucr or 3%  DSS the last 48h of total incubation time at 29°C

value: Intestine

value: Adult  progenitors

value: esgtsGFP (x) UAS-trxRNAi (BDSC#33703)

value: 7d 29°C, the last 48h in 3% DSS


title: 000-445

value: Whole blood

value: Female

value: high


title: dss_trx1

description:
Library name: Sample 8
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter


title: Patient 5 with developed FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: B05ab
DESeq2: combined developing and developed groups compared to controls

value: White adipose tissue


title: Patient 2 with developed FPLD2, subcutaneous white adipose tissue from upper neck (dorsocervical region)

description:
Library name: B02up
DESeq2: combined developing and developed groups compared to controls


title: TRAP-pWnt3aC8A

value: lung

value: TRAP-pWnt3aC8A x floxed L10-GFP

value: anti-GFP (C8)


title: 000-444

description: Expression value derived from nCounter Digital Analyzer

value: Control

value: Male


title: suc_trx2

description:
Library name: Sample 7
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: 7d 29°C, the last 48h in sucr


title: Patient 3 with developed FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: B03ab
DESeq2: combined developing and developed groups compared to controls

value: Subcutaneous white adipose tissue

value: Biopsy

value: Developed FPLD2


title: TRAP-pFoxj1sup

source_name: no driver, supernatant input

value: input

value: TRAP-pFoxj1sup x floxed L10-GFP

value: supernatant (unfiltered input)


title: suc_trx1

description:
Library name: Sample 6
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: Adult  progenitors

value: esgtsGFP (x) UAS-trxRNAi (BDSC#33703)


title: Patient 2 with developed FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: B02ab
DESeq2: combined developing and developed groups compared to controls


title: 000-432

value: Whole blood


title: humanDLPFC_Schizophrenia_6

value: dorsolateral prefrontal cortex (DLPFC) (BA 8/9)

value: Schizophrenia


title: TRAP-pFoxj1Rb

value: lung

value: airway ciliated cell

value: TRAP-pFoxj1Rb x floxed L10-GFP

value: anti-GFP (Rb)


title: dss_ctrl3

description:
Library name: Sample 5
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: esgtsGFP (x) w1118

value: 7d 29°C, the last 48h in 3% DSS


title: TRAP-pWnt3aRbB

value: alveolar type 1 cell

value: TRAP-pWnt3aRbB x floxed L10-GFP


title: Patient 4 with developing FPLD2, subcutaneous white adipose tissue from upper neck (dorsocervical region)

description:
Library name: A04up
DESeq2: combined developing and developed groups compared to controls

value: Subcutaneous white adipose tissue

value: Biopsy

value: White adipose tissue

value: Developing FPLD2


title: TRAP-pFoxj1C8

description: translating ribosome affinity purification-coupled RNAseq

value: TRAP-pFoxj1C8 x floxed L10-GFP

value: anti-GFP (C8)


title: 000-405

value: Whole blood

value: Control

value: Female


title: dss_ctrl2

description:
Library name: Sample 4
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: Adult  progenitors


title: Patient 1 with developing FPLD2, subcutaneous white adipose tissue from upper neck (dorsocervical region)

description:
Library name: A01up
DESeq2: combined developing and developed groups compared to controls


title: 000-403

value: Male


title: Sox9L10-Sox2Sup

value: lung

value: input

value: Sox9L10-Sox2Sup x floxed L10-GFP

value: supernatant (unfiltered input)


title: dss_ctrl1

description:
Library name: Sample 3
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: esgtsGFP (x) w1118

value: 7d 29°C, the last 48h in 3% DSS


title: Patient 5 with developing FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: A05ab
DESeq2: combined developing and developed groups compared to controls

value: Subcutaneous white adipose tissue

value: Biopsy


title: Sox9L10-Sox2Rb

value: airway epithelium

value: Sox9L10-Sox2Rb x floxed L10-GFP

value: anti-GFP (Rb)


title: suc_ctrl2

description:
Library name: Sample 2
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: 7d 29°C, the last 48h in sucr


title: Sox9L10-Sox2C8

value: Sox9L10-Sox2C8 x floxed L10-GFP

value: anti-GFP (C8)


title: Patient 2 with developing FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: A02ab
DESeq2: combined developing and developed groups compared to controls

value: White adipose tissue

value: Developing FPLD2


title: 000-398

value: Whole blood

value: Asthma

value: Female

value: high


title: Patient 1 with developing FPLD2, subcutaneous white adipose tissue from abdomen

description:
Library name: A01ab
DESeq2: combined developing and developed groups compared to controls


title: suc_ctrl1

description:
Library name: Sample 1
Progenitor cells were sorted as GFP+ cells in a FACSAria III cell sorter

value: Intestine

value: Adult  progenitors


title: 000-423


title: Sox9L10-SmmhcSup

value: lung

value: input

value: Sox9L10-SmmhcSup x floxed L10-GFP

value: supernatant (unfiltered input)


title: Sox9L10-SmmhcRb

value: smooth muscle and pericytes

value: Sox9L10-SmmhcRb x floxed L10-GFP


title: MQ_B

city: Hangzhou

first: Haojie

last: Tong

state: Zhejiang

address: No.258, Xueyuan St.

department: School of life Sciences

institute: China Jiliang University

data_processing:
Illumina HiSeq 2000 sequencing platform was used to sequence
Trinity software package was used to de novo assambly and get RPKM values use Rsem
BLAST program was used to gene annotation and GO classification with E-value cut-off of 1E-5, Queries were performed against the Swiss-Prot,NR,KEGG,COG,Pfam databases
Best Reciprocal Hit BLAST method to identify putative orthologs between two populations with tblastx of BLAST-2.2.26+ and a bit-score threshold of 300
The KaKs_CALCULATOR program was performed to calculate the Ka, Ks and Ka/Ks ratio of each orthologous pair, and the YN model was meanwhile used.
Genome_build: Trinity assembly

organism: Phrynocephalus vlangalii

source_name: tissues

extract_protocol:
Total RNA was extracted using the SV Total RNA Isolation System (Promega), following the manufacture's recommended protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver, lung, heart, muscle

tag: population

value: Maqu

value: adult


title: 000-420

source_name: Control Female

value: Control


title: KB Cells, 24h, R5

city: Clayton

last: Perlaza-Jimenez

state: Victoria

address: 15 Innovation Walk

country: Australia

institute: Monash University

description: Library name: X24h.5

data_processing:
Differenctial Gene Expression and Over-representation analysis (ORA) was performed using the R package gprofiler2.
Assembly: GRCh38
Supplementary files format and content: Differential Expressed Genes, FoldChange and FDR. Filename: DEGs_table.csv

source_name: KB

growth_protocol: KB cells were cultured in low glucose DMEM, supplemented with 10% foetal bovine serum and 1% penicillin/streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
After 6, 12, or 24 hours exposure to FBP, total cellular RNA was extracted using a Monarch® RNA Miniprep Kit (NEB #T2010S).
Total RNA libraries were prepared using the MGITech RNA Directional Library Prep Kit V2.0, following the manufacturer's protocols.

treatment_protocol: KB cells were seeded in a 48-well plate and incubated overnight to attach to the well plate. The culture medium was then replaced with fresh culture medium containing FBP or 1X PBS for the test or control wells, respectively. The final concentration of FBP in the test groups was equal to 50 µM.

value: KB

value: HeLa derivative

value: 50 uM FBP

tag: time


title: 000-382

value: Whole blood

value: Asthma

value: Female

value: low


title: Sox9L10-SmmhcC8

value: lung

value: Sox9L10-SmmhcC8 x floxed L10-GFP

value: anti-GFP (C8)


title: MD_A

value: Madoi


title: HU_A_22_1

city: Tianjin

first: Xinyun

last: Zhang

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

description: Library name: sample 4

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . p<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: Escherichia coli str. K-12 substr. MG1655 and Escherichia coli BL21
Supplementary files format and content: xls files include Counts  for each Sample

extract_protocol:
RNA was harvested using Trizol.800ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: bacterial cell

value: WT

value: 0.5 mM IPTG, 16h


title: 000-350

value: high


title: Sox9L10-GliRb

value: mesenchymal cell

value: Sox9L10-GliRb x floxed L10-GFP

value: anti-GFP (Rb)


title: 000-324


title: HU_WT_1

description: Library name: sample 3


title: HU_A_1

description: Library name: sample 2


title: Sox9L10-GliC8

value: Sox9L10-GliC8 x floxed L10-GFP


title: 000-322

source_name: Asthma Male

value: Male


title: L10-P5SpcRb

source_name: Sftpc-CreER

value: alveolar type 2 cell

value: L10-P5SpcRb x floxed L10-GFP


title: 000-386

value: Whole blood

value: Control

value: Female


title: KB Cells, 24h, R1

description: Library name: X24h.1

value: KB

value: HeLa derivative

value: 50 uM FBP


title: KB Cells, 24h, R4

description: Library name: X24h.4


title: KB Cells, 24h, R3

description: Library name: X24h.3


title: KB Cells, 12h, R5

description: Library name: X12h.5


title: pET_28a_1

description: Library name: sample 1

value: bacterial cell


title: KB Cells, 24h, R2

description: Library name: X24h.2


title: 000-306

value: Asthma

value: low


title: Gwl_3

city: Shihezi City

first: sheng

last: yue

state: Xinjiang

address: Dongcheng Street, Shihezi City

department: College of Chemistry and Chemical Engineering

institute: Shihezi University

description: Gwl_3,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE2 overexpressing

data_processing:
DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by Qsep100 (BiOptic Inc.)/5300 Fragment Analyzer system (Agilent). Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2μg total RNA were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Raw sequencing data was first filtered by fastp (version 0.23.0), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Assembly: GCF_ 000146045.2
Supplementary files format and content: Tab delimed text file include all raw reads counts for each sample
Supplementary files format and content: Tab delimed text file include all raw data for each sample

organism: Saccharomyces cerevisiae

source_name: eukaryotic metagenome

growth_protocol: Genome-wide expression studies using RNA-seq analysis were performed on the Pcf11-OE1, and Pcf11-OE2 strains grown under the same growth conditions.The yeasts were cultured in liquid medium at 30°C at 220 rpm with corresponding antibiotics when necessary.

extract_protocol:
For RNA extraction, library preparation, and sequencing, total RNAs were extracted from four strains using TRIzol Reagent (Invitrogen, cat. NO.15596026); RNA was extracted using DNase I for DNA digestion. RNA quality was determined by examining the A260/A280 ratio with a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA integrity was confirmed by Qsep100 (BiOptic Inc.)/5300 Fragment Analyzer system (Agilent). Qualified RNAs were quantified using a Qubit3.0 with the Qubit TM RNA Broad Range Assay kit (Life Technologies, Q10210).
Two micrograms of total RNA were used for stranded RNA sequencing library preparation using the KC-Digital TM Stranded mRNA Library Prep Kit (Catalog No. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instructions.

treatment_protocol: Three biological replicates were conducted for each strain

value: eukaryotic metagenome

value: Pcf11-OE2 overexpressing


title: L10-P5SpcC8

value: lung

value: L10-P5SpcC8 x floxed L10-GFP

value: anti-GFP (C8)


title: KB Cells, 12h, R4

description: Library name: X12h.4


title: 000-300

description: Expression value derived from nCounter Digital Analyzer

value: high


title: KB Cells, 12h, R3

description: Library name: X12h.3


title: Gwl_2

description: Gwl_2,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE2 overexpressing


title: Gwl_1

description: Gwl_1,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE2 overexpressing


title: L10-P5AqpRb

value: alveolar type 1 cell

value: L10-P5AqpRb x floxed L10-GFP

value: anti-GFP (Rb)


title: 000-330

value: Whole blood


title: 000-299

value: Female


title: L10-P5AqpC8

value: L10-P5AqpC8 x floxed L10-GFP


title: 000-297


title: KB Cells, 12h, R2

description: Library name: X12h.2

value: KB

value: HeLa derivative


title: L10N-WtRb

value: mesothelial cell

value: L10N-WtRb x floxed L10-GFP


title: Gsy_3

description: Gsy_3,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE1 overexpressing

value: Pcf11-OE1 overexpressing


title: 000-284

value: Asthma

value: Male

value: low


title: Gsy_2

description: Gsy_2,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE1 overexpressing

value: eukaryotic metagenome


title: L10N-WtC8

value: lung

value: L10N-WtC8 x floxed L10-GFP

value: anti-GFP (C8)


title: KB Cells, 6h, R5

description: Library name: X6h.5

value: 50 uM FBP

value: 6 h


title: L10N-Sox2Rb

value: airway epithelium

value: L10N-Sox2Rb x floxed L10-GFP

value: anti-GFP (Rb)


title: Gsy_1

description: Gsy_1,RNA-seq of Saccharomyces cerevisiae：Pcf11-OE1 overexpressing


title: 000-283

value: Whole blood

value: high


title: KB Cells, 6h, R3

description: Library name: X6h.3

value: KB

value: HeLa derivative


title: SC_2

description:
RNA-seq of Saccharomyces cerevisiae：WT2,replication2
SC_2

data_processing:
DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneC spectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by Qsep100 (BiOptic Inc.)/5300 Fragment Analyzer system (Agilent). Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2μg total RNA were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.
The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
Raw sequencing data was first filtered by fastp (version 0.23.0), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Supplementary files format and content: Tab delimed text file include all raw reads counts for each sample
Supplementary files format and content: Tab delimed text file include all raw data for each sample

growth_protocol: Genome-wide expression studies using RNA-seq analysis were performed on the WT, ΔPcf11, Pcf11-AARR, Pcf11-OE1, and Pcf11-OE2 strains grown under the same growth conditions.The yeasts were cultured in liquid medium at 30°C at 220 rpm with corresponding antibiotics when necessary.

value: WT


title: SC_3

description:
RNA-seq of Saccharomyces cerevisiae：WT3,replication3
SC_3


title: L10N-Sox2C8

description: translating ribosome affinity purification-coupled RNAseq

value: L10N-Sox2C8 x floxed L10-GFP


title: 000-268

value: Asthma

value: Female


title: SC_1

description:
RNA-seq of Saccharomyces cerevisiae：WT1,replication1
SC_1

value: eukaryotic metagenome


title: 000-254


title: KB Cells, 6h, R1

description: Library name: X6h.1


title: L17_3

description:
RNA-seq of Saccharomyces cerevisiae：ΔPcf11,replication3
L17_3

value: deltaPcf11 deleting


title: 000-287

value: low


title: L10N-Cdh5Rb

value: lung

value: endothelial cell

value: L10N-Cdh5Rb x floxed L10-GFP


title: KB Cells, Control, R5

description: Library name: C.5

value: No treatment


title: 000-253


title: 000-112


title: KB Cells, 12h, R1

description: Library name: X12h.1

value: 50 uM FBP


title: L17_2

description:
RNA-seq of Saccharomyces cerevisiae：ΔPcf11,replication2
L17_2


title: L10N-Cdh5C8

value: L10N-Cdh5C8 x floxed L10-GFP

value: anti-GFP (C8)


title: 000-109

value: Whole blood

value: high


title: KB Cells, Control, R4

description: Library name: C.4

value: KB

value: HeLa derivative


title: 000-030


title: L17_1

description:
RNA-seq of Saccharomyces cerevisiae：ΔPcf11,replication1
L17_1


title: L10N-CcspRb

value: Club cell

value: L10N-CcspRb x floxed L10-GFP

value: anti-GFP (Rb)


title: KB Cells, 6h, R4

description: Library name: X6h.4

value: 6 h


title: KB Cells, Control, R3

description: Library name: C.3


title: L10N-CcspC8

value: L10N-CcspC8 x floxed L10-GFP


title: AR13_3

description:
RNA-seq of Saccharomyces cerevisiae：Pcf11-AARR,replication3
AR13_3

value: eukaryotic metagenome

value: Pcf11-AARR mutating


title: KB Cells, 6h, R2

description: Library name: X6h.2


title: L10N-SmmhcRb

value: lung

value: smooth muscle and pericytes

value: L10N-SmmhcRb x floxed L10-GFP


title: KB Cells, Control, R1

description: Library name: C.1

value: No treatment


title: AR13_1

description:
RNA-seq of Saccharomyces cerevisiae：Pcf11-AARR,replication1
AR13_1


title: 000-028

value: Asthma

value: Female

value: low


title: L10N-SmmhcC8

value: L10N-SmmhcC8 x floxed L10-GFP

value: anti-GFP (C8)


title: KB Cells, Control, R2

description: Library name: C.2

value: KB

value: HeLa derivative


title: L10N-Ascl1Rb

value: pulmonary neuroendocrine

value: L10N-Ascl1Rb x floxed L10-GFP


title: 000-015

value: Whole blood

value: high


title: OsDOF3_CUTTAG

status: Public on Nov 30 2025

city: Shanghai

first: Han

last: Lu

address: No.220 Handan Road Shanghai

institute: Fudan university

description: Library name: OsDOF3_CUTTAG

data_processing:
The sequencing data were processed through an established bioinformatics pipeline. Raw reads were initially evaluated for quality using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by alignment to the MSU Rice Genome Annotation Release 7 (RGAP7) using Bowtie256 with default parameters. Potential PCR duplicates were removed using Picard Tools (https://github.com/broadinstitute/picard). Peak calling was performed using MACS2 with the corresponding input DNA as background control, applying a q-value threshold of 0.05 for significant peak identification.
Assembly: GCF_034140825.1_ASM3414082v1
Supplementary files format and content: bigWig,narrowPeak(except for Input sample)
Library strategy: CUT&Tag

organism: Oryza sativa

source_name: leaf

extract_protocol:
To characterize the potential binding targets of OsDOF3, we conducted the CUT&Tag assay in rice protoplasts. Transfected protoplasts were subjected to fluorescence-activated nuclei sorting, and a minimum of 100,000 GFP-positive nuclei were collected per biological replicate.
we conducted a CUT&Tag assay inplants. Two-week-old seedlings were harvested, and leaf sheath tissues were collected for nuclear isolation. Tissues were finely minced in 20 mL of ice-cold Lysis Buffer (15 mM Tris-HCl [pH 7.5], 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 0.2% Triton X-100, 5 mM β-mercaptoethanol, and 1× protease inhibitor cocktail) using a surgical blade. The homogenate was filtered through a 40-μm cell strainer, and nuclei were stained with 1 μg/mL DAPI (4',6-diamidino-2-phenylindole) for fluorescence-activated nuclei sorting. Flow cytometric analysis and sorting were performed using a Sony SH800 Cell Sorter equipped with a 405-nm laser. A minimum of 100,000 nuclei were collected per biological replicate. The sorted nuclei were immediately processed for chromatin enrichment and library preparation steps using the CUT&Tag Assay Kit (Vazyme, TD904-C2) according to the manufacturer's instructions.

value: leaf

value: Transformation and flow-sorting of rice protoplasts with GFP antibody


title: OsVAL2_ChIP

description: Library name: OsVAL2_ChIP

data_processing:
The sequencing data were processed through an established bioinformatics pipeline. Raw reads were initially evaluated for quality using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by alignment to the MSU Rice Genome Annotation Release 7 (RGAP7) using Bowtie256 with default parameters. Potential PCR duplicates were removed using Picard Tools (https://github.com/broadinstitute/picard). Peak calling was performed using MACS2 with the corresponding input DNA as background control, applying a q-value threshold of 0.05 for significant peak identification.
Assembly: GCF_034140825.1_ASM3414082v1
Supplementary files format and content: bigWig,narrowPeak(except for Input sample)

extract_protocol:
Chromatin immunoprecipitation (ChIP) assays were performed as previously described with modifications.55 Briefly, 4 g of 2-week-old seedlings were frozen in liquid nitrogen and ground to a fine powder, followed by cross-linking in 50 mL of nuclei isolation buffer I (0.4 M sucrose, 10 mM HEPES pH 7.5, 10 mM MgCl2, 5 mM β-mercaptoethanol, 0.1 mM PMSF, and 1× protease inhibitor cocktail) containing 1% (v/v) formaldehyde for 10 min at room temperature.
The reaction was quenched with 3.4 ml of 2 M glycine. Chromatin was extracted by filtering through two layers of Miracloth and pelleted by centrifugation. Nuclei were subsequently isolated using NIB buffer (20 mM Tris-HCl pH 7.5, 25% [v/v] glycerol, 0.25 M sucrose, 2.5 mM MgCl2, 10 mM NaCl, 0.5% [v/v] Triton X-100, 0.5 mM spermidine, 0.15 mM spermine, 10 mM β-mercaptoethanol, 1 mM PMSF, and protease inhibitors) and lysed in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% [w/v] SDS, 1 mM PMSF, and protease inhibitors) for 30 min on ice. Chromatin was sheared to fragments using a Bioruptor sonicator (Diagenode) with 18 cycles of 30 sec ON/30 sec OFF. Immunoprecipitation was performed using anti-FLAG antibody (Sigma, H7425) conjugated to a 1:1 mixture of Protein A/G magnetic beads (Sigma, 16-663) in ChIP buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and protease inhibitors). Beads were sequentially washed with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% sodium deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Immunoprecipitated DNA was eluted in 100 μL elution buffer (1% SDS, 0.1 M NaHCO3) at 65°C for 15 min, followed by proteinase K digestion (20 μg/mL) in the presence of 0.5 M EDTA and 20 mM Tris-HCl (pH 6.5). Purified DNA libraries were sequenced on an Illumina HiSeq 2100 platform (Novogene) with 150 bp paired-end reads.

value: Fourteen-day-old rice leaves were collected from plants grown hydroponically with no other treatments.


title: OsVAL2_control_ChIP

description: Library name: OsVAL2_control_ChIP


title: OsDOF3_control_CUTTAG

description: Library name: OsDOF3_control_CUTTAG

value: Transformation and flow-sorting of rice protoplasts without GFP antibody


title: AR13_2

description:
RNA-seq of Saccharomyces cerevisiae：Pcf11-AARR,replication2
AR13_2

value: eukaryotic metagenome

value: Pcf11-AARR mutating


title: 000-011

value: Control


title: Monocytes, co-culture, Normoxia, run 3

city: New York

first: Kenny

last: Yu

state: NY

address: 1275 York Ave

department: Neurosurgery

institute: Memorial Sloan Kettering Cancer Center

data_processing:
FASTQ were checked for read quality and the clean reads were aligned to the human reference genome (hg38) using the Illumina Dragen v3.10 pipeline. Gene expression count matrices were obtained through featureCounts v2.0.3. RNA-seq analysis was performed using DESeq2 (v.1.40.2)
Assembly: hg38
Supplementary files format and content: comma-separated values files

source_name: Blood

growth_protocol: Patient-derived PBMCs from non-glioma patients are sorted for CD14+ monocytes through magnetic-activated cell sorting (MACS) using CD14 MicroBeads (Miltenyi Biotech, Germany). These monocytes are then co-cultured alongside a previously established patient-derived GBM cell line, MSK-103. Cells are maintained for three days in glioma culture media, consisting of DMEM/F12 basal media (Gibco, USA) supplemented with 1x N2 supplement (Invitrogen, USA), B27 without Vitamin A (Gibco, USA), EGF (20 ng/mL; R&D Systems), FGF2 (20 ng/mL; R&D Systems, USA), 1x Penicillin-Streptomycin (Gibco, USA), and 5% FBS (Gibco, USA). Following the initial three-day co-culture, hypoxia was induced by culturing the cells under 0.5% O2 for 4 hours

extract_protocol:
Cells from monocultures and co-cultures at normoxic and hypoxic conditions are then collected, stained for CD45 (BioLegend, USA) and sorted through FACS. The CD45+ sorted cells are then lysed for RNA collection and purification using RNeasy Mini kit (Qiagen, USA) as per the manufacturer’s protocol.
RNA libraries were prepared using the SMARTer RNA-seq Library Prep Kit following manufacturer's protocol

value: Blood

value: Monocyte

value: co-culture, Normoxia


title: Monocytes, co-culture, Hypoxia, run 2

value: co-culture, Hypoxia


title: Monocytes, co-culture, Normoxia, run 2


title: Monocytes, co-culture, Hypoxia, run 1


title: Monocytes, mono-culture, Hypoxia, run 1

value: mono-culture, Hypoxia


title: Monocytes, mono-culture, Normoxia, run 1

value: mono-culture, Normoxia


title: Monocytes, co-culture, Normoxia, run 1


title: 000-029

value: Asthma

value: Female


title: Visium_GBM_PDX_GS143_Invasion

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

country: Israel

institute: Weizmann Instititue

description: 10X Visium fresh frozen

data_processing:
Utilized CellRanger for initial alignment, filtering, and quantification of single-cell RNA-seq data.
Utilized SpaceRanger for initial alignment, filtering, and quantification of ST RNA-seq data.
Assembly: scRNA-seq aligned to GRCh38;  PDX samples were aligned to a concatenated human/mouse genome: GRCh38-and-mm10-2020-A
Supplementary files format and content: tab-separated tpm and metadata files.
Library strategy: Visium

source_name: Brain

extract_protocol:
Mice were euthanized upon reaching pre-determined clinical endpoints such as such as significant body weight loss, seizures, and a persistent hunched posture with diminished activity. The collected mice brains were imaged with a fluorescent stereomicroscope with 0.63 objective magnification (Olympus MVX10, Leica M205), which covers both the entire brain and cell morphology at single-cell resolution. Under the microscope, the brains were observed from the ipsilateral hemisphere for tumor-peripheral invasion to the contralateral hemisphere for distal invasion. For distal invasion, collected brains were physically separated into the hemisphere with the primary tumor (injection side) and the other contained invading tumor cells excluding the midline border region. For local blood vessel-associated invasion, tube-structured GFP+ cell clusters were dissected under a stereomicroscope without introducing any primary bulk tumor mass. Then, each location were mechanically and enzymatically dissociated using a papain-based neural tissue dissociation kit (Miltenyi Biotec) supplemented with 0.1% Type I collagenase (Thermo Fisher Scientific)/PBS. The dissociated cells were first stained with calcein Blue AM (BD Biosciences) and Zombie NIR (BioLegend) for 25 min at 4C, and with anti-mouse CD16/32 (BD Biosciences) for 5 min. After washing cells with ice-cold 1% BSA/PBS, the cells were then stained with PerCP anti-mouse CD45 (clone 30-F11, BD Biosciences) for 30 min at 4C. Sorting was performed with Becton Dickinson Influx cytometer (Becton Dickinson). Side scatter (SSC) width versus forward scatter (FSC) area and Trigger Pulse Width versus FSC criteria were used to discriminate doublets and gate-only singleton cells. Viable single cells were identified as calcein blue AM positive and Zombine NIR negative to low cells. We sorted viable CD45 negative/GFP positive cells from blood-vessel associated invasion samples into 96-well plates containing 10uL of TCL buffer (QIAGEN) with 1% beta-mercaptoethanol (Sigma Aldrich). Plates were frozen immediately after sorting and stored at -80 degree prior to whole transcriptome amplification, library preparation, and sequencing. For multiplexed samples, CD45 negative/GFP positive cells were sorted into 15mL tumors for subsequent 10X scRNA-seq processing.
The spheroid models in vitro were processed as a pool using TotalSeq-B/Hashtag anti-bodies (BioLegend), described previously19. Each of the dissociated cells was first stained with HumanTruStain FcX (BioLegend) in Cell Staining Buffer (BioLegend) for 10 min at 4C, and then stained with barcoded TotalSeq-B anti-bodies targeting human CD298 and b2 microglobulin in a separated tube for 30 min at 4C. We generated a single cell suspension of the pool in 0.04% PBS-BSA and loaded approximately 9,900 single cells to the Chromium Controller with a targeted recovery of 6,000 cells. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR (98C for 3 min; [98C for 15 s, 63C for 20 s, 72C for 1 min] x 12; 72C for 1 min). Gene expression cDNA and TotalSeq antibody derived barcode cDNA were size-selected and separated with SPRIselect Reagent (Beckman Coulter), and then fragmented, end-repaired, ligated with index adaptors. Quality control of the resulting libraries was performed with the Bio-analyzer High Sensitivity DNA Analysis (Agilent). The constructed gene expression library and barcode library were combined at 4:1 ratio and sequenced with paired-end, 28 and 55-base reads, using a NextSeq 2000 sequencer (Illumina).

value: Brain

value: Glioblastoma


title: MSK-102, CD45+, run 2, scRNAseq

description: 10x Genomics

data_processing:
Raw sequencing reads were aligned to the GRCh38 reference genome using Cell Ranger (v7.1).
Assembly: hg38
Supplementary files format and content: comma-separated value files and matrix files

source_name: Brain Tumor (Glioma)

extract_protocol:
Tumor tissue from glioma operations was collected immediately after resection and transported in MACS storage solution (Miltenyi Biotec, Germany) within 15 min to the laboratory. Resected tissue was morselized into small pieces under sterile conditions using sterile scalpels, triturated using pipettes, then transferred to a 50 mL falcon tube (Corning, USA) for incubation with papain (37°C, 25 min) (Worthington, USA) according to manufacturer instructions. After incubation HBSS without magnesium or calcium was then added to make up to 50 ml and the sample was centrifuged (300×g, 5 min, 4°C) and supernatant aspirated before being passed through a 70um cell strainer (BD Biosciences, USA). Erythrocytes were removed by resuspending and incubating the obtained pellet in 5 ml of 1X RBC Lysis Buffer (eBioscience, USA) for 10 min, followed by centrifugation (300×g, 5 min,4°C). Residual myelin and extracellular debris were eliminated using the Debris Removal Kit (Miltenyi Biotec, Germany). Cell counts were determined using an automated cell counter (Nexcelom Bioscience, USA) after resuspending the pellet in PBS. A portion of the single-cell suspensions were then enriched for CD45+ cells by CD45-MACS enrichment (Miltenyi Biotec, Germany). The final cell suspensions were centrifuged again (350×g, 10 min, RT) and isolated unsorted, CD45+, and CD45- cells were stored in Bambanker (Wako, Japan).
Cells were loaded for GEM generation using the 10x Genomics Chromium platform. 3’ RNA gene expression libraries were prepared using the Chromium Single-cell 3′ Reagent Kit v3 (10x Genomics, USA) according to the manufacturer’s guidelines.  Final libraries were quantified using a Qubit fluorimeter (Life Technologies, USA) and the nucleosomal pattern was verified using a BioAnalyzer (Agilent Technologies, USA). scRNA libraries were sequenced on a NovaSeq6000 (Illumina, USA).

value: Brain Tumor (Glioma)

value: Leukocytes

value: IDH-wildtype


title: MSK-NB2, CD45+, scRNAseq

description: 10x Genomics

source_name: Normal Brain (Autopsy)

value: Normal Brain (Autopsy)


title: MSK-115, CD45+, run 2, scRNAseq

description: 10x Genomics

value: IDH-mutant


title: L10N-Ascl1C8

data_processing:
Raw reads processed for QC using fastqc (0.11.8) and poor quality reads filtered using trimmomatic (0.39)
Aligned to mm10 genome using STAR aligner (2.7.2b) and counts quantitated, normalized, and all pairwise comparisons done using DESeq2 (1.38.3) in R programming language (4.2.2)
Assembly: mm10
Supplementary files format and content: tab-delimited raw read counts for each paired-end sample. Tab-delimited raw read gene matrix.
Supplementary files format and content: comma-separated value DESeq2 normalized gene count matrix. CSV pairwise comparison of each driver type vs input generated through DESeq2. CSV gene matrix of log2-fold change of each driver vs input with and without FDR adjusted p-value (BH) generated by DESeq2.

value: lung

value: pulmonary neuroendocrine

value: L10N-Ascl1C8 x floxed L10-GFP

value: anti-GFP (C8)


title: MSK-108, CD45+, run 2, scRNAseq

description: 10x Genomics


title: MSK-NB1, CD45+, scRNAseq

description: 10x Genomics


title: MSK-115, CD45+, run 1, scRNAseq

description: 10x Genomics


title: MSK-114, CD45+, scRNAseq

description: 10x Genomics


title: MSK-112, CD45+, scRNAseq

description: 10x Genomics


title: MSK-111, CD45+, scRNAseq

description: 10x Genomics


title: Monocytes, co-culture, Hypoxia, run 3

value: Blood

value: Monocyte


title: MSK-113, CD45+, scRNAseq

description: 10x Genomics


title: MSK-110, CD45+, scRNAseq

description: 10x Genomics


title: Visium_GBM_PDX_GS143_Primary

description: 10X Visium fresh frozen


title: MSK-108, CD45+, run 1, scRNAseq

description: 10x Genomics


title: MSK-106, CD45+, scRNAseq

description: 10x Genomics


title: MSK-107, CD45+, scRNAseq

description: 10x Genomics


title: MSK-109, CD45+, scRNAseq

description: 10x Genomics


title: MSK-104, CD45+, scRNAseq

description: 10x Genomics


title: MSK-103, CD45+, scRNAseq

description: 10x Genomics


title: MSK-102, CD45+, run 1, scRNAseq

description: 10x Genomics


title: MSK-101, CD45+, scRNAseq

description: 10x Genomics