title: PB bulk, 162269_B


title: PB bulk, 161910_A

status: Public on Jan 15 2026

type: SRA

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

library_source: genomic

data_processing:
Data was mapped with Bowtie2 and peak called with MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles

tag: disease state

value: Acute Myeloid Leukemia

tag: tissue

value: peripheral blood

tag: cell type

value: bulk


title: PB bulk, 161960_B


title: PB bulk, 161305_A


title: PB bulk, 161498_A


title: PB bulk, 162229_A


title: PB bulk, 161406_B


title: PB bulk, 162002_A


title: PB bulk, 248267_A


title: PB bulk, 302404_B


title: PB bulk, 161172_A


title: PB bulk, 151165_A


title: PB bulk, 150783_A


title: PB bulk, 160121_A


title: PB bulk, 120706


title: PB bulk, 187112_B


title: PB bulk, 110858


title: PB bulk, 110698


title: PB bulk, 100753


title: PB bulk, 100604


title: PB bulk, 110052


title: leukemic cells, LSCpositive, 8031_TAAGGCGA

source_name: leukemic cells, LSCpositive

value: leukemic cells, LSCpositive


title: PB bulk, 0561A


title: leukemic cells, LSCpositive, 8021_TAAGGCGA


title: leukemic cells, LSCnegative, 8013_AGGCAGAA

source_name: leukemic cells, LSCnegative

value: leukemic cells, LSCnegative


title: leukemic cells, LSCnegative, 8012_CGTACT


title: PB bulk, 0733B


title: PB bulk, 162131_B


title: leukemic cells, LSCpositive, 8041_TCCTGAGC


title: leukemic cells, LSCpositive, 8001_TAAGGCGA


title: leukemic cells, LSCnegative, 8038_TCCTGAGC


title: PB bulk, 150549_B


title: leukemic cells, LSCnegative, 8023_AGGCAGAA


title: PB bulk, 161769_A


title: PB bulk, 3286


title: IMR90 Proliferating High Ox 3

city: Belmont

first: Azucena

last: Rocha

state: Massachusetts

address: 42 Alma Avenue

department: MCB

country: USA

institute: Brown University

description: Library name: IHP3

library_source: transcriptomic

data_processing:
counts tables were generated using HTSeq
Assembly: hg38
Supplementary files format and content: .txt files, counts tables

molecule: polyA RNA

source_name: Cell Culture

growth_protocol: Cells were maintained in Ham’s F-10 nutrient mixture media (Gibco) supplemented with 15% fetal bovine serum (FBS) and antibiotics for LF1 cells and in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics for all other cell lines, in humidified atmosphere with 5% CO2 at 37C. High Ox cells were maintained at ~20% O2, Low Ox cells were maintained at ~3% O2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries. For LF1 samples, Total RNA was extracted from early passage, SW-induced quiescent, early and late senescent cells. Cells were washed with PBS and harvested using Trizol reagent (Invitrogen), after which Total RNA was harvested using the Qiagen Rneasy kit.
Libraries were constructed by Azenta. For LF1 samples, NEBNext ultra II directional RNA library prep kit for Illumina along with the NEBNext Poly(A) mRNA magnetic bead isolation module was used to make isolated mRNA and cDNA libraries. Strand specific cDNA libraries were sent to Azenta for paired-end sequencing

treatment_protocol: Contact inhibition was induced by allowing cells to reach 100%confluency for 3 days. Serum withdrawal was induced with DMEM media supplimented with 0.01% FBS for 3 days and for LF1 cells, with Ham’s F-10 nutrient mixture media (Gibco) supplemented with 0.01% fetal bovine serum (FBS; Corning), and antibiotics for 5 days for LF1 cells. Replicatively senescent LF1 cells were attained by serial passaging until cell division ceased.  1 month after cells entered senescence, LF1 cells were harvested for the early replicative senescent cell state timepoint, and late replicative senescent cells were harvested 4 months after entry into senescence.

value: Cell Culture

tag: cell line

value: Fibroblasts

tag: treatment

value: Proliferating

tag: batch


title: leukemic cells, LSCnegative, 8033_AGGCAGAA


title: leukemic cells, LSCnegative, 8047_CGTACTAG


title: leukemic cells, LSCnegative, 8042_TAAGGCGA


title: leukemic cells, LSCnegative, 8046_TAAGGCGA


title: leukemic cells, LSCpositive, 8011_TAAGGC


title: leukemic cells, LSCpositive, 8051_TCCTGAGC


title: leukemic cells, LSCnegative, 8052_TAAGGCGA


title: leukemic cells, LSCnegative, 8048_TCCTGAGC


title: leukemic cells, LSCpositive, 8032_CGTACTAG


title: leukemic cells, LSCnegative, 8054_TCCTGAGC


title: leukemic cells, LSCpositive, 8056_TAAGGCGA


title: leukemic cells, LSCpositive, 8057_CGTACTAG


title: leukemic cells, LSCnegative, 8044_TCCTGAGC


title: leukemic cells, LSCnegative, 8053_CGTACTAG


title: leukemic cells, LSCnegative, 8058_TCCTGAGC


title: leukemic cells, LSCnegative, 8063_TCCTGAGC


title: leukemic cells, LSCnegative, 8074_TAAGGCGA


title: leukemic cells, LSCnegative, 8059_TCCTGAGC


title: leukemic cells, LSCpositive, 8076_TCCTGAGC


title: leukemic cells, LSCnegative, 8073_TCCTGAGC


title: TCF4, unstimulated, contains cell line CW20107 and KOLF2.2J

city: Evanston

first: Christina

last: Thapa

state: Illinois

address: 1001 University Place

department: Center for Psychiatric Genetics (CPG)

institute: Endeavor Health

description:
Library name: 25074-02-10-01-01_S142
10X Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger v7.2.0 was used for alignment. Data were processed using Seurat (v5.3.1). Cells were initally filtered to remove low-quality cells (nCount_RNA 300–20,000, nFeature_RNA 1,000–7,500, percent.mt < 20). Filtered counts were log-normalized (LogNormalize), highly variable features were identified, and PCA was performed. Batch effects were corrected using Harmony. Cells were demultiplexed to assign them to individual libraries/cell lines. Doublets were detected and removed using DoubletFinder (v.2.0.6), retaining singlets from target cell lines. Filtered cells were merged, scaled, and used for clustering and UMAP visualization. Cell types were annotated based on canonical marker genes. Final processed counts, barcodes, features, and metadata (including library, cell line, cell type, time point, and QC metrics) are provided.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values and matrix files
Supplementary files format and content: comma-separated values

molecule: total RNA

source_name: cultured glutamatergic and GABAergic neurons derived from iPS cells

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rat glial cells. For excitatory neuronal differentiation, we used the method for deriving Ngn2-induced glutamatergic neurons with minor modifications. For generating excitatory neurons, we used the method for deriving Ascl1/Dlx2-GABAergic neurons with minor modifications. To co-culture the excitatory and inhibitory neurons, on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons, and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using Accutase at room temperature for 15-20 min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2 ug/ml doxycycline, 10 ng/ml BDNF, 10 ng/ml GDNF, 10 ng/ml NT-3, and 1% FBS. For each co-culture, we pooled cells from 2 donor lines (KOLF2.2J and CW20107) with equal proportion. On DIV8, we refilled cells with more media. From DIV9 to DIV33, media was refreshed every three days with half volume changes. Doxycycline was withdrawn at DIV14 and 1 µM AraC was added in the media from DIV8 to DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
Co-cultured neurons were briefly washed with 1x PBS and dissociated in Accutase at 37C for 40 min with gentle shaking. After Accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40 um tip filter (Sigma# BAH136800040-50EA) to obtain single cells. For each library, around 15,000 freshly isolated cells were loaded for GEM capture targeting 10,000 cell recovery.
freshly dissciated cells were captured in-house and libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following vendor's instructions

treatment_protocol: 24hr before stimulation, old media was aspirated and DIV33 neuronal-ast co-culture cells were silenced in neural culture media supplemented with 1uM TTX and 100uM DL-AP5. The next day, we added 0.45 culture media volume of warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) into silenced wells to initiate high K+ condition. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr)

value: Neuron

tag: genotype

value: untreated


title: TCF4, 1 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-11-01-01_S143
10X Genomics

value: cultured glutamatergic and GABAergic neurons derived from iPS cells

value: KCl


title: RORB, 1 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-08-01-01_S140
10X Genomics

value: RORB-/RORB-


title: TCF4,  6 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-12-01-01_S144
10X Genomics


title: MEF2C, unstimulated, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-04-01-01_S136
10X Genomics


title: MEF2C,  6 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-06-01-01_S138
10X Genomics


title: leukemic cells, LSCnegative, 8113_TAAGGCGA


title: RORB, 6 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-09-01-01_S141
10X Genomics


title: leukemic cells, LSCnegative, 8118_TCCTGAGC


title: WT, 6 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-03-01-01_S135
10X Genomics

value: WT


title: leukemic cells, LSCnegative, 8119_TAAGGCGA


title: leukemic cells, LSCnegative, 8078_CGTACTAG


title: WT, 1 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-02-01-01_S134
10X Genomics


title: leukemic cells, LSCpositive, 8077_TAAGGCGA


title: leukemic cells, LSCnegative, 8132_TCCTGAGC


title: RORB, unstimulated, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-07-01-01_S139
10X Genomics


title: MEF2C, 1 hr post stimulation, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-05-01-01_S137
10X Genomics


title: C1_Am_7dpa

city: Baton Rouge

first: Igor

last: Schneider

state: Louisiana (LA)

address: 386 Life Sciences Building, LSU

department: Biological Sciences

institute: Louisiana State University

description: Library name: C1_Am_7dpa

data_processing:
Generated libraries were sequenced on an Illumina  Novaseq 6000 or NovaSeq X Plus platform (paired-end, 150bp), with the sequencing depth of 50,000 reads per tissue covered spot. Sequence reads were mapped to Ambystoma mexicanum Genome Assembly UKY_AmexF1_1. Raw sequence data (FASTQ) and histology images were processed using Space Ranger 3.0.1
Assembly: UKY_AmexF1_1
Supplementary files format and content: *barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: *features.tsv.gv: list of gene IDs
Supplementary files format and content: *matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: *.tif: high resolution image
Library strategy: Spatial Transcriptomics

organism: Ambystoma mexicanum

source_name: forelimb

extract_protocol:
Fresh tissues were embedded in Tissue-Tek O.C.T. compound (Sakura) and flash-frozen using isopentane (2-methylbutane) chilled with liquid nitrogen.
Cryosections were placed onto 10X Genomics Visium Spatial Gene Expression Slides.  Visium slide samples were processed using the 10X Genomics Spatial Gene Expression kit (#1000188) according to the instructions in the Visium Spatial Gene Expression Use Guide, to generate the sequencing libraries.

value: forelimb

value: multiple


title: WT, unstimulated, contains cell line CW20107 and KOLF2.2J

description:
Library name: 25074-02-01-01-01_S133
10X Genomics


title: D1_Am_14dpa

description: Library name: D1_Am_14dpa


title: leukemic cells, LSCnegative, 8130_TAAGGCGA


title: HGC-27 cells, shUSP16-2

city: Lanzhou

first: Siying

last: Ren

address: Peili Street, Anning District

department: College of Life Sciences

country: China

institute: Northwest Normal University

description:
Library name: HGC27_shUSP16_2
Column name in HGC27_shUSP16_2

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

source_name: Stomach

growth_protocol: HGC-27 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidifed atmosphere with 5% CO2 at 37C

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in thepresence of 10% FBS until day 2. Cells were then fed with 1640 supplemented with 10% FBS and 10ug'ml insulin for 2 days, after which they were fed every other day with 1640 containing 10% FBS
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction ofsequencing libraries

value: Stomach

value: gastric cancer cells


title: HGC-27 cells, shControl

description:
Library name: HGC27_Scramble
Column name in HGC27_Scramble


title: Chip_6, Tetramer

city: Philadelphia

first: Ning

last: Jiang

state: PA

address: 210 S 33rd St

department: Bioengineering

institute: University of Pennsylvania

description:
BD Rhapsody
metadata_totalvi.csv

library_source: other

data_processing:
Cell barcode demultiplexing was done with BD Rhapsody Targeted Analysis Pipeline (Revision 15) available on Seven Bridges Genomics. A custom pipeline was used to quantify tetramer barcode umi counts and assign putative specificities to cells (available on github: https://github.com/JiangLabSysImmune/TetTCR-SeqHD_V2)
Assembly: peptide_3.csv
Supplementary files format and content: Combined comma-separated matrix where cells are rows and meta data is columns. Contains donor meta data, experiment information, TCR data, pMHC tetramer barcode counts, putative specificity data, phenotype/clustering data, cell phenotype assignment, and more.

molecule: other

source_name: Blood

extract_protocol:
CD8+ T cells were negatively enriched from cryopreserved PBMC samples and treated with 2.5uM Dasatinib for approximately 30 minutes. Cells were then stained on ice for 1 hour with multiplexed tetramers, then sorted on a BD AriaFusion. Single cells were then isolated and processed using the BD Rhapsody system following manufacturer's instructions.
Libraries were constructed according to manufacturer's instructions (BD Rhapsody Targeted mRNA and TCR/BCR Amplification kit) with the addition of pMHC tetramer barcode specific reverse primers during PCR1. PCR2 for pMHC tetramer barcodes were then amplified separately using the same primer sequence with a nextera partial adapter. Index PCR was then carried out using P5 and nextera N7 primers.

value: Blood

value: CD8+ T cells

tag: library type

value: Tetramer

tag: condition

value: ex vivo


title: HGC-27 cells, shUSP16-1

description:
Library name: HGC27_shUSP16_1
Column name in HGC27_shUSP16_1


title: Chip_6, mRNA+Abseq+ST

description:
BD Rhapsody
metadata_totalvi.csv
mrna_counts.csv
latent.csv
Protein_totalvi.csv
RNA_totalvi.csv

data_processing:
Cell barcode demultiplexing and gene expression quantification were done with BD Rhapsody Targeted Analysis Pipeline (Revision 15) available on Seven Bridges Genomics. Counts for mRNA and AbSeq were batch-corrected, integrated, background-corrected, and normalized with totalvi (scvi version 0.17.1: https://docs.scvi-tools.org/en/stable/)
Assembly: UTA_CustomPanel_516_genes.fasta
Supplementary files format and content: Combined comma-separated matrix where cells are rows and meta data is columns. Contains donor meta data, experiment information, TCR data, pMHC tetramer barcode counts, putative specificity data, phenotype/clustering data, cell phenotype assignment, and more.
Supplementary files format and content: Combined comma-separated file with raw umi mRNA counts in a cell x gene matrix.
Supplementary files format and content: Combined comma-separated latent representation of each cell in model generated by totalvi. Used to generate neighborhood graph with Seurat.
Supplementary files format and content: Combined comma-separated, background-corrected, and normalized totalvi normalized AbSeq (protein) counts represented in a cell x feature matrix.
Supplementary files format and content: Combined comma-separated, mormalized totalvi mRNA counts represented in a cell x feature matrix.

extract_protocol:
CD8+ T cells were negatively enriched from cryopreserved PBMC samples and treated with 2.5uM Dasatinib for approximately 30 minutes. Cells were then stained on ice for 1 hour with multiplexed tetramers, then sorted on a BD AriaFusion. Single cells were then isolated and processed using the BD Rhapsody system following manufacturer's instructions.
Libraries were constructed according to manufacturer's instructions (BD Rhapsody Targeted mRNA and TCR/BCR Amplification kit).

value: mRNA, Abseq, sampletag


title: RQ1_IR_5

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: HO

hyb_protocol: Once the hybridization reactions have been removed from the thermal cycler, proceed immediately to an nCounter Prep Station. This step can process up to 12 samples per run in approximately 2.5 to 3 hours.

scan_protocol: Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: RCC format files containing the raw data were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform. Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: NanoString barcodes

organism: Mus

source_name: prefrontal cortex

label_protocol: Label a 12-tube PCR hybridization strip. The purified RNA is diluted in nuclease-free water to 20 ng/uL. Recommended total RNA samples are 20 ng to 100 ng for hybridization assay. The prepared samples are used as input into nCounter hybridization reactions containing NanoString Reporter and Capture probes. First, remove Reporter CodeSet and Capture ProbeSet tubes from the freezer and thaw at room temperature. Second, after it has thawed, inspect the tube of Reporter CodeSet to make sure no colored precipitate is present. Third, If you see a colored precipitate, heat the entire tube to 75°C for 10 minutes and cool at room temperature before using .The purified RNA was hybridized at thermal cycler at 65°C for 16 to 24 hours into nCounter 15 µL of hybridization buffer containing NanoString Reporter and Capture probes. Add 8 μL of Master Mix to each well of a strip tube. Add 5 µL of sample to each tube containing Master Mix. Add 2 µL of Capture ProbeSet to each tube. Maximum hybridization time should not exceed 48 hours.

extract_protocol: Prefrontal cortexl tissue (10 mg) from the mice were prepared for the extraction of total RNA using a Nucleospin RNA isolation kit (Macherey-Nagel, #740955.250) as per the manufacturer’s protocol.

treatment_protocol: WT (C57BL6/J), RecQ1, WRN, RecQ4 deficient mice were exposed the whole body with γ-irradiation (IR, 6 Gy).

value: γ-irradiation

tag: Sex

value: F

tag: age

tag: strain

value: RECQL KO B6

value: prefrontal cortex


title: RQ1_IR_4

description: HO


title: RQ1_IR_3

description: HO

value: M


title: Chip_4, Tetramer

description:
BD Rhapsody
metadata_totalvi.csv


title: RQ1_IR_2

description: HO


title: Chip_5, Tetramer

description:
BD Rhapsody
metadata_totalvi.csv


title: RQ1_Veh_4

description: HO

value: Vehicle


title: RQ1_IR_1

description: HO


title: Chip_3, Tetramer

description:
BD Rhapsody
metadata_totalvi.csv

data_processing:
Cell barcode demultiplexing was done with BD Rhapsody Targeted Analysis Pipeline (Revision 15) available on Seven Bridges Genomics. A custom pipeline was used to quantify tetramer barcode umi counts and assign putative specificities to cells (available on github: https://github.com/JiangLabSysImmune/TetTCR-SeqHD_V2)
Assembly: peptide_2.csv
Supplementary files format and content: Combined comma-separated matrix where cells are rows and meta data is columns. Contains donor meta data, experiment information, TCR data, pMHC tetramer barcode counts, putative specificity data, phenotype/clustering data, cell phenotype assignment, and more.


title: Chip_4, mRNA+Abseq+ST


title: Chip_5, mRNA+Abseq+ST


title: RQ1_Veh_3

description: HO


title: B1_Am_intact

description: Library name: B1_Am_intact


title: Chip_2, mRNA+Abseq+ST


title: Chip_3, mRNA+Abseq+ST


title: RQ1_Veh_2

description: HO


title: RQ4_IR_5

description: HO

value: RECQL4 KO


title: RQ1_Veh_1

description: HO


title: Chip_2, Tetramer

description:
BD Rhapsody
metadata_totalvi.csv

data_processing:
Cell barcode demultiplexing was done with BD Rhapsody Targeted Analysis Pipeline (Revision 15) available on Seven Bridges Genomics. A custom pipeline was used to quantify tetramer barcode umi counts and assign putative specificities to cells (available on github: https://github.com/JiangLabSysImmune/TetTCR-SeqHD_V2)
Assembly: peptide_1.csv
Supplementary files format and content: Combined comma-separated matrix where cells are rows and meta data is columns. Contains donor meta data, experiment information, TCR data, pMHC tetramer barcode counts, putative specificity data, phenotype/clustering data, cell phenotype assignment, and more.


title: Chip_1, Tetramer

description:
BD Rhapsody
metadata_totalvi.csv


title: RQ4_Veh_4

description: HO


title: Chip_1, mRNA+Abseq+ST


title: RQ4_IR_4

description: HO


title: RQ4_Veh_1

description: HO


title: kdrl:mCherry prdx1-MO 48hpf rep2 scRNAseq

city: Boston

first: Mohamad Ali

last: Najia

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: 10x genomics

data_processing:
A custom Danio rerio reference genome containing an mCherry transcript was generated using Ensembl Release 101 (ftp://ftp.ensembl.org/pub/release-101/gtf/danio_rerio/) with the mkref command from cellranger v2.1 (10X Genomics)
The raw sequencing files were aligned to the custom reference processed with the Cellranger count pipeline.
Cellranger count matrices for each library were read into R v4.3.0 and analyzed with Seurat v4.3.0.1. High-quality cells were retained for subsequent analyses based on technical metrics: <7.5% mitochondrial reads, >500UMI counts, and >700 genes detected. A Seurat object of all unfiltered cells across all libraries is provided as a supplementary file.
Assembly: GRCz11-101
Supplementary files format and content: Cells by genes count matrices produced from the cellranger pipeline

organism: Danio rerio

source_name: FACS sorted kdrl:mCherry+ cells

extract_protocol:
Pools of fluorescent zebrafish embryos/larvae were dissociated using Liberase (Sigma) incubated at 34C and resuspended in 1X PBS/1mM EDTA. kdrl:GFP+ cells were FACS sorted on a FACSAria II (BD) at the BCH Flow Cytometry Core into 1X PBS containing 2% fetal bovine serum.
Single-cell RNA-seq was performed on the 10X Genomics Chromium platform using the single cell expression 3’ v3.1 profiling chemistry. kdrl:mCherry+ FACS, cells from each condition were loaded across two lanes in a 10X Genomics Single Cell 3’ Chip as independent technical replicates and libraries were constructed according to the manufacturer’s protocol. Cells were loaded into 10X lanes at cell concentrations to maintain an estimated doublet rate below 5%. The final libraries were assayed via an Agilent High Sensitivity dsDNA Bioanalyzer, normalized, pooled and  sequenced (Illumina NovaSeq).

value: FACS sorted kdrl:mCherry+ cells

value: endothelial/hematopoietic

tag: developmental stage


title: kdrl:mCherry prdx1-MO 48hpf rep1 scRNAseq

description: 10x genomics


title: RQ4_Veh_2

description: HO


title: RQ4_Veh_3

description: HO


title: cell-free DNA from healthy control sample 81.1 at T2

type: other

city: Renton

first: Dantong

last: Zhu

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: PBMC DNA from healthy control mice

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MouseMethylation array using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan and standard recommend Illumina scanner setting

data_processing: SeSame package in R environment (v. 4.4.2)

label: Cy3 and Cy5

organism: Mus musculus

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Red blood cells were removed with RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.3), and then the remaining cells were digested overnight at 65°C with proteinase K (20 mg/mL) in TESR buffer (10 mM Tris-HCl, 25 mM EDTA, 0.5% SDS, 20 µg/mL RNase). DNA was washed and isolated using SPRI beads and eluted in 10 mM Tris-HCl pH8.

value: PBMC

value: control


title: cell-free DNA from healthy control sample 81.1 at BL

description: PBMC DNA from healthy control mice


title: WRN_IR_3

description: HO

value: WRN

value: WRN/TERC


title: cell-free DNA from healthy control sample 80.4 at BL

description: PBMC DNA from healthy control mice


title: WRN_Veh_3

description: HO


title: WRN_IR_2

description: HO


title: cell-free DNA from healthy control sample 80.4 at T3

description: PBMC DNA from healthy control mice


title: WRN_IR_1

description: HO


title: WRN_Veh_2

description: HO


title: cell-free DNA from healthy control sample 80.3 at T2

description: PBMC DNA from healthy control mice


title: WT_IR_4

description: WT

value: WT


title: PB bulk, 161282_A

value: Acute Myeloid Leukemia

value: peripheral blood

value: bulk


title: cell-free DNA from healthy control sample 80.4 at T2

description: PBMC DNA from healthy control mice


title: WT_IR_5

description: WT

value: γ-irradiation


title: WT_IR_1

description: WT

value: F


title: kdrl:mCherry control 48hpf rep1 scRNAseq

description: 10x genomics


title: WT_IR_3

description: WT


title: WRN_Veh_1

description: HO


title: kdrl:mCherry control 48hpf rep2 scRNAseq

description: 10x genomics


title: cell-free DNA from healthy control sample 80.1 at T4

description: PBMC DNA from healthy control mice


title: WT_IR_2

description: WT


title: cell-free DNA from healthy control sample 80.4 at T4

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 80.2 at T2

description: PBMC DNA from healthy control mice


title: WT_Veh_4

description: WT


title: cell-free DNA from healthy control sample 80.1 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 80.1 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 80.2 at T3

description: PBMC DNA from healthy control mice


title: WT_Veh_2

description: WT


title: WT_Veh_3

description: WT


title: NOMO1_NTC_3

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

description: Sample 12

data_processing:
Quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using GRCh38.p14_genomic.gtf as the reference. Feature Counts were created by using Rsubread.
Assembly: GRCh38.p14
Supplementary files format and content: Excel file and txt file include raw counts for each Sample

extract_protocol:
Total RNA from cell lines was isolated using RNAeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.


title: cell-free DNA from healthy control sample 80.3 at BL

description: PBMC DNA from healthy control mice


title: WT_Veh_1

description: WT


title: cell-free DNA from healthy control sample 80.1 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 76.3 at T4

description: PBMC DNA from healthy control mice


title: RQ4_IR_1

description: HO


title: RQ4_IR_2

description: HO


title: cell-free DNA from healthy control sample 76.4 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 76.3 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 76.3 at T3

description: PBMC DNA from healthy control mice


title: MEK1,day15

city: Peking

first: George

last: Song

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: Sample8

data_processing:
Sequencing data from different time points of the directed evolution campaign were first subjected to quality control using Trimmomatic, applying a four-base sliding window with a quality threshold of 30. The filtered paired-end reads were then aligned to the corresponding reference sequence using BWA (paired-end mode) with 36 threads. For successfully aligned reads, an in-house Python script was used to quantify the occurrences of each mutation type at the nucleotide level, which were subsequently translated to amino-acid–level mutations for downstream analysis.
Assembly: The original KRAS and MEK1 sequence were used as reference. The reference sequence for KRAS S17N is 'ATGACTGAATATAAACTTGTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAGTGCCTTGACGATACAGCTAATTCAGAATCATTTTGTGGACGAATATGATCCAACAATAGAGGATTCCTACAGGAAGCAAGTAGTAATTGATGGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAGAGGAGTACAGTGCAATGAGGGACCAGTACATGAGGACTGGGGAGGGCTTTCTTTGTGTATTTGCCATAAATAATACTAAATCATTTGAAGATATTCACCATTATAGAGAACAAATTAAAAGAGTTAAGGACTCTGAAGATGTACCTATGGTCCTAGTAGGAAATAAATGTGATTTGCCTTCTAGAACAGTAGACACAAAACAGGCTCAGGACTTAGCAAGAAGTTATGGAATTCCTTTTATTGAAACATCAGCAAAGACAAGACAGAGAGTGGAGGATGCTTTTTATACATTGGTGAGAGAGATCCGACAATACAGATTGAAAAAAATCAGCAAAGAAGAAAAGACTCCTGGCTGTGTGAAAATTAAAAAATGCATTATAATG'; the reference sequence for MEK1 is 'ATGCCCAAGAAGAAGCCGACGCCCATCCAGCTGAACCCGGCCCCCGACGGCTCTGCAGTTAACGGGACCAGCTCTGCGGAGACCAACTTGGAGGCCTTGCAGAAGAAGCTGGAGGAGCTAGAGCTTGATGAGCAGCAGCGAAAGCGCCTTGAGGCCTTTCTTACCCAGAAGCAGAAGGTGGGAGAACTGAAGGATGACGACTTTGAGAAGATCAGTGAGCTGGGGGCTGGCAATGGCGGTGTGGTGTTCAAGGTCTCCCACAAGCCTTCTGGCCTGGTCATGGCCAGAAAGCTAATTCATCTGGAGATCAAACCCGCAATCCGGAACCAGATCATAAGGGAGCTGCAGGTTCTGCATGAGTGCAACTCTCCGTACATCGTGGGCTTCTATGGTGCGTTCTACAGCGATGGCGAGATCAGTATCTGCATGGAGCACATGGATGGAGGTTCTCTGGATCAAGTCCTGAAGAAAGCTGGAAGAATTCCTGAACAAATTTTAGGAAAAGTTAGCATTGCTGTAATAAAAGGCCTGACATATCTGAGGGAGAAGCACAAGATCATGCACAGAGATGTCAAGCCCTCCAACATCCTAGTCAACTCCCGTGGGGAGATCAAGCTCTGTGACTTTGGGGTCAGCGGGCAGCTCATCGACTCCATGGCCAACTCCTTCGTGGGCACAAGGTCCTACATGTCGCCAGAAAGACTCCAGGGGACTCATTACTCTGTGCAGTCAGACATCTGGAGCATGGGACTGTCTCTGGTAGAGATGGCGGTTGGGAGGTATCCCATCCCTCCTCCAGATGCCAAGGAGCTGGAGCTGATGTTTGGGTGCCAGGTGGAAGGAGATGCGGCTGAGACCCCACCCAGGCCAAGGACCCCCGGGAGGCCCCTTAGCTCATACGGAATGGACAGCCGACCTCCCATGGCAATTTTTGAGTTGTTGGATTACATAGTCAACGAGCCTCCTCCAAAACTGCCCAGTGGAGTGTTCAGTCTGGAATTTCAAGATTTTGTGAATAAATGCTTAATAAAAAACCCCGCAGAGAGAGCAGATTTGAAGCAACTCATGGTTCATGCTTTTATCAAGAGATCTGATGCTGAGGAAGTGGATTTTGCAGGTTGGCTCTGCTCCACCATCGGCCTTAACCAGCCCAGCACACCAACCCATGCTGCTGGCGTC'.
Supplementary files format and content: The .txt files list mutant variants at the amino-acid level along with their relative abundances compared to the directed evolution starting sequence at different time points. Each file name indicates the corresponding sample.

organism: Mesocricetus auratus

extract_protocol:
Total RNA was extracted and reverse-transcribed, followed by PCR amplification using primers specifically designed to selectively amplify the exogenous human MEK1 transcript. The resulting amplicons were then subjected to high-throughput sequencing.
Total RNA was extracted from cells at different time points along the directed evolution experiment using Trizol agent.
From the total RNA, PCR amplification was done using primers specifically designed to selectively amplify the exogenous human KRAS or MEK1 transcript. The resulting amplicons were then subjected to high-throughput sequencing.


title: cell-free DNA from healthy control sample 76.4 at T3

description: PBMC DNA from healthy control mice


title: RQ4_IR_3

description: HO


title: cell-free DNA from healthy control sample 76.4 at T2

description: PBMC DNA from healthy control mice


title: NOMO1_NTC_1

description: Sample 10


title: NOMO1_NTC_2

description: Sample 11


title: Sublibrary_8 from multiplexed Polypterus fin samples

description: Library name: Ps_sub8

data_processing:
Sequence reads were mapped to Polypterus senegalus Genome Assembly ASM1683550V1. SnRNA-seq FASTQ files were processed using the TrailmakerTM pipeline module (https://app.trailmaker.parsebiosciences.com/; v1.4.0, Parse Biosciences, 2024)
Assembly: ASM1683550V1
Supplementary files format and content: processed_matrix_Jan16.rds - RDS file from Trailmaker (control samples)

molecule: nuclear RNA

organism: Polypterus senegalus

source_name: pectoral fin

extract_protocol:
Nuclei were fixed and frozen using the Evercode Nuclei Fixation Kit v3 (#NF100, #NF200) from Parse Biosciences following the manufacturer’s protocol.
snRNA-seq libraries were generated using Parse Biosciences combinatorial barcoding technology.  Fixed and frozen nuclei from each sample were processed to generate barcoded libraries aiming for 7,000 nuclei per sample using the Evercode WT v3 Kit (#WT100A-D, #WT200) as per manufacturer’s instructions. Samples were multiplexed during barcoding and sequenced as multiple technical sublibraries at the depth of 20,000 reads per nuclei in an Illumina Novaseq Xplus platform (paired-end, 150bp).

treatment_protocol: Fish undergoing fin regenaration were treated either with 0.1% DMSO (control) or 2.5uM rapamicyn in 0.1% DMSO.

value: pectoral fin

value: multiple


title: MEK1,day10

description: Library name: Sample7


title: Sublibrary_7 from multiplexed Polypterus fin samples

description: Library name: Ps_sub7


title: cell-free DNA from healthy control sample 76.3 at BL

description: PBMC DNA from healthy control mice


title: Sublibrary_5 from multiplexed Polypterus fin samples

description: Library name: Ps_sub5


title: MEK1,day7

description: Library name: Sample6


title: cell-free DNA from healthy control sample 76.2 at T4

description: PBMC DNA from healthy control mice


title: Sublibrary_6 from multiplexed Polypterus fin samples

description: Library name: Ps_sub6


title: NOMO1_ACSL4_2

description: Sample 8

value: ACSL4 KD


title: cell-free DNA from healthy control sample 76.2 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 76.2 at T2

description: PBMC DNA from healthy control mice


title: Sublibrary_1 from multiplexed Polypterus fin samples

description: Library name: Ps_sub1


title: KRAS,day12

description: Library name: Sample3

extract_protocol:
Total RNA was extracted and reverse-transcribed, followed by PCR amplification using primers specifically designed to selectively amplify the exogenous human KRAS transcript. The resulting amplicons were then subjected to high-throughput sequencing.
Total RNA was extracted from cells at different time points along the directed evolution experiment using Trizol agent.
From the total RNA, PCR amplification was done using primers specifically designed to selectively amplify the exogenous human KRAS or MEK1 transcript. The resulting amplicons were then subjected to high-throughput sequencing.


title: PB bulk, 100249


title: cell-free DNA from healthy control sample 76.1 at T2

description: PBMC DNA from healthy control mice


title: PB bulk, 100391A


title: K562_NTC_2

description: Sample 5


title: NOMO1_ACSL4_1

description: Sample 7


title: KRAS,day5

description: Library name: Sample1


title: Sublibrary_3 from multiplexed Polypterus fin samples

description: Library name: Ps_sub3


title: K562_ACSL4_1

description: Sample 1


title: KRAS,day14

description: Library name: Sample4


title: K562_NTC_3

description: Sample 6


title: Sublibrary_2 from multiplexed Polypterus fin samples

description: Library name: Ps_sub2


title: MEK1,day5

description: Library name: Sample5


title: cell-free DNA from healthy control sample 76.2 at BL

description: PBMC DNA from healthy control mice


title: Sublibrary_4 from multiplexed Polypterus fin samples

description: Library name: Ps_sub4


title: A1_Ps_1dpa

description: Library name: A1_Ps_1dpa

data_processing:
Generated libraries were sequenced on an Illumina NovaSeq 6000 or NovaSeq X Plus platform (paired-end, 150bp), with the sequencing depth of 50,000 reads per tissue covered spot. Sequence reads were mapped to P. senegalus Genome Assembly ASM1683550V1. Raw sequence data (FASTQ) and histology images were processed using Space Ranger 3.0.1
Assembly: ASM1683550V1
Supplementary files format and content: *barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: *features.tsv.gv: list of gene IDs
Supplementary files format and content: *matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: *.tif: high resolution image
Library strategy: Spatial Transcriptomics


title: NOMO1_ACSL4_3

description: Sample 9


title: cell-free DNA from healthy control sample 76.1 at BL

description: PBMC DNA from healthy control mice


title: K562_NTC_1

description: Sample 4


first: Yukyeong

last: Lee

address: 185 Cambridge Street

institute: MGH

description:
Library name: sample_4
microglia containing cerebral organoid 3

data_processing:
Raw FASTQ files were quality-checked with FastQC, aligned to GRCh38 using STAR, quantified with featureCounts, and normalized to TPM/FPKM
Assembly: Reads were aligned to the human reference genome (GRCh38). Gene-level counts were generated, and processed data are provided as normalized TPM values.
Supplementary files format and content: Raw gene-level counts (rows = Ensembl gene IDs, columns = samples).
Supplementary files format and content: Normalized TPM expression values (rows = Ensembl gene IDs, columns = samples).

source_name: organoid

growth_protocol: Human iPSCs were maintained under feeder-free conditions in mTeSR medium at 37 °C with 5% CO₂. Cerebral organoids were cultured under standard conditions without additional treatments.

extract_protocol:
Total RNA was extracted from iPSCs and cerebral organoids using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA quality/integrity was assessed with the Agilent TapeStation D5000 ScreenTape system
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep Kit (polyA+ selection) following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 instrument.

value: organoid

value: iPSC female line 300

value: iPSC-derived organoid

value: untreated


title: cell-free DNA from healthy control sample 74.4 at T2

description: PBMC DNA from healthy control mice

value: PBMC


title: B1_Ps_7dpa

description: Library name: B1_Ps_7dpa


title: KRAS,day9

description: Library name: Sample2


title: Polypterus regenerating fin at 3dpa sample 3

description: Library name: Ps_187_3dpa

data_processing:
Raw reads were trimmed using NGmerge (version 0.3). The trimmed reads were aligned to the Polypterus senegalus reference genome from NCBI (ASM1683550v1) using Bowtie2 (version 2.2.5). Alignment BAM files were indexed using Samtools (version 1.18). Fragment size distribution was assessed using the ATACseqQC package (version 1.24.0) in RStudio (version 4.3.1). Trimmed reads were name-sorted using Samtools (version 1.18). Genrich (version 0.6.1) was used to call peaks using the parameters -j -y -r -v -m -e -f, to remove duplicate reads, multimapped reads, and reads mapped to mitochondrial chromosome. Downstream analysis of the ATAC-seq data was performed using DiffBind (version 3.10.1) to identify differential chromatin accessibility (peaks) between uninjured and regenerating fin tissues.
Assembly: ASM1683550v1
Supplementary files format and content: tab-delimited text file with differential chromatin accessibility peaks identified using DIffBind  (version 3.10.1).

extract_protocol:
For each sample, tissue from both left and right pectoral fins was collected and pooled to comprise one biological replica. Collected tissue was used for nuclei isolation and tagmentation following the ATAC-seq kit protocol (Active Motif, #105320) without modifications.
Each library was prepared using 50,000 nuclei and amplified within ten PCR cycles, following the instructions on TAC-seq kit protocol (Active Motif, #105320)


title: WT_SPT5_CT44

city: Dallas

first: Noheon

last: Park

state: Texas

address: 5323 Harry Hines BLVD, NA4.124

department: Neuroscience

institute: UT Southwestern Medical Center

description: Library name: Sample90

data_processing:
Illumina bcl2fastq version 2.17 for base calling and demultiplexing.
For ChIPseq, the adaptor and the reads with < 30bp were trimmed by CutAdapt v.1.18. Then, the data were mapped by BWA v0.7.16a-r1185-dirty with default options and the uniquely mapped reads were chosen by SAMtools v1.9. The PCR duplicates were removed by awk commands, and the final reads were extended to the MACS2 prediction sizes.
For mRNAseq, the adaptor, poly T sequences, and < 30bp reads of the raw data were trimmed by CutAdapt v.1.18 and mapped by STAR v2.5.3a. The uniquely mapped reads were chosen by SAMtools v1.9.
For PROseq, the adaptor sequences and < 16bp reads were removed by CutAdapt v.1.18 and the reverse complement (RC) sequences were made from FASTX-Toolkit. The RC was mapped by BWA v0.7.16a-r1185-dirty aln and the uniquely mapped reads were determined by SAMtools v1.9.
The normalized BigWig files are from BEDTools v2.27.1. The raw counts of the NGS data are retrieved from FeatureCounts v1.6.4.
Assembly: M14 from GENCODE
Supplementary files format and content: ChIP-seq BigWig files were made from Uniquely mapped duplicate-removed bed files. PRO-seq and mRNA-seq BigWig files were made from uniquely mapped STAR Bam files
Supplementary files format and content: Excel  file includes raw counts and RPKM values for the mRNA-seq results

source_name: Liver

growth_protocol: At 6 weeks old, the animals were housed in the two light chambers with a 2hr shifted light:dark (LD)=12hrs:12hrs condition and fed ad libitum.

extract_protocol:
For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions.
For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)

treatment_protocol: After 4 weeks of the entrainment(10 weeks old), a light/dark chamber was released to constant darkness (DD) condition 24hrs earlier than the other. The liver samples (N=3) were collected after 36 hours of DD condition beginning with the first point (CT00) and subsequent every 4hrs collections for each light chamber till CT44.

value: Liver

tag: collectiontime

tag: chip antibody

value: anti DSIF(SPT5) (BD Bioscience Cat# 611106)


title: K562_ACSL4_2

description: Sample 2


title: WT_SPT5_CT40

description: Library name: Sample89


title: WT_SPT5_INPUT

description: Library name: Sample91

value: input mix(00-44)


description:
Library name: sample_2
microglia containing cerebral organoid 1

value: control


title: cerebral organoid

description:
Library name: sample_1
cerebral organoid


description:
Library name: sample_3
microglia containing cerebral organoid 2


title: cell-free DNA from healthy control sample 74.4 at BL

description: PBMC DNA from healthy control mice


title: D1_Ps_Intact

description: Library name: D1_Ps_Intact


title: K562_ACSL4_3

description: Sample 3


title: WT_SPT5_CT32

description: Library name: Sample87

value: WT


title: non differentiated stage

description:
Library name: iPSC_1
iPSC

source_name: cell

value: cell

value: induced pluripotent stem cell


title: cell-free DNA from healthy control sample 74.3 at T3

description: PBMC DNA from healthy control mice


title: Polypterus regenerating fin at 3dpa sample 2

description: Library name: Ps_186_3dpa


title: D1_Am_3dpa

description: Library name: D1_Am_3dpa

value: forelimb


title: cell-free DNA from healthy control sample 74.2 at T4

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 74.4 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 74.3 at T4

description: PBMC DNA from healthy control mice


title: Polypterus uninjured fin sample 3

description: Library name: Ps_194_IF


title: cell-free DNA from healthy control sample 74.2 at T3

description: PBMC DNA from healthy control mice


title: Polypterus uninjured fin sample 2

description: Library name: Ps_149_IF


title: WT_SPT5_CT28

description: Library name: Sample86


title: Polypterus uninjured fin sample 1

description: Library name: Ps_142_IF


title: WT_SPT5_CT36

description: Library name: Sample88


title: B1_Ps_3dpa_DMSO

description: Library name: B1_Ps_3dpa_DMSO

value: 0.1% DMSO


title: cell-free DNA from healthy control sample 74.3 at BL

description: PBMC DNA from healthy control mice


title: Polypterus regenerating fin at 3dpa sample 1

description: Library name: Ps_185_3dpa

value: pectoral fin


title: WT_SPT5_CT24

description: Library name: Sample85


title: cell-free DNA from healthy control sample 74.2 at T2

description: PBMC DNA from healthy control mice


title: Polypterus 3dpa fin, DMSO-treated, biol rep3

description: Library name: Ps_3dpa_DM_3

data_processing:
High quality sequencing reads were mapped to Polypterus senegalus Genome Asselmby ASM1683550V1 using STAR V2.7.10b. Read count extraction was performed using featureCounts v2.0.6. Read count normalization and DGE analysis were performed using DEseq2.
Assembly: ASM1683550V1
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: pectoral fin (regenerating)

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen_ThermoFIsher) and subsequently submitted to DNAse treatment and clean-up using the RNeasy mini kit (Qiagen).
mRNA enriched libraries were preparaed and sequenced at Novogene (https://www.novogene.com/us-en). Briefly, for each sample,  mRNA was used to generated RNA sequencing librarires using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB,USA), follwing the manufacturee's recommendation.

value: pectoral fin (regenerating)


title: WT_SPT5_CT20

description: Library name: Sample84


title: cell-free DNA from healthy control sample 74.2 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 74.1 at T3

description: PBMC DNA from healthy control mice


title: Polypterus intact fin, biol rep3

description: Library name: Ps_uninjured_3

source_name: pectoral fin (intact)

value: pectoral fin (intact)


title: Polypterus 3dpa fin, DMSO-treated, biol rep2

description: Library name: Ps_3dpa_DM_2


title: WT_SPT5_CT12

description: Library name: Sample82


title: Polypterus 3dpa fin, DMSO-treated, biol rep1

description: Library name: Ps_3dpa_DM_1


title: WT_SPT5_CT16

description: Library name: Sample83


title: WT_SPT5_CT08

description: Library name: Sample81


title: WT_SPT5_CT04

description: Library name: Sample80


title: cell-free DNA from healthy control sample 74.1 at T2

description: PBMC DNA from healthy control mice


title: Polypterus intact fin, biol rep2

description: Library name: Ps_uninjured_2


title: WT_SPT5_CT00

description: Library name: Sample79


title: cell-free DNA from healthy control sample 74.1 at T4

description: PBMC DNA from healthy control mice


title: WT_NELF-E_INPUT

description: Library name: Sample78


title: Polypterus intact fin, biol rep1

description: Library name: Ps_uninjured_1


title: WT_NELF-E_CT40

description: Library name: Sample76

value: anti NELF-E (Abcam Cat# ab170104)


title: RNA-seq of Panc02 cells H2O2-treated (test0

city: St. Catharines

first: SoFong

middle: Cam

last: Ngan

state: ON

address: 1812 Sir Isaac Brock Way

department: Health Sciences

institute: Brock University

description:
Library name: Panc02_test_H2O2-treated
NA-seq of Panc02 cells treated with 0.05% H2O2 for 2 hours

data_processing:
Raw reads were generated from paired-end 150 bp sequencing using Illumina NovaSeq 6000.
Adapter trimming and quality filtering were performed to remove reads with >10% N content or >50% low-quality bases (Q<5).
Clean reads were aligned to the mouse genome (mm39) using HISAT2.
Gene-level read counts were quantified using featureCounts.
Normalization and differential expression analysis were conducted using DESeq2.
Assembly: Genome: Mus musculus (GRCm39/mm39)
Supplementary files format and content: Tab-delimited count matrix file containing gene_id, gene_name, and raw counts (columns for each sample).
Supplementary files format and content: Additional annotation columns include gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, and gene_description.

source_name: murine pancreatic cancer

growth_protocol: Murine Panc02 pancreatic cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37 °C in a humidified incubator with 5% CO₂. Cells were maintained under standard conditions and harvested at approximately 70–80% confluence.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer’s protocol. RNA quality and concentration were assessed using Qubit and Agilent Bioanalyzer.
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Poly(A) RNA was enriched using oligo(dT) beads, followed by fragmentation, cDNA synthesis, end repair, adapter ligation, and PCR enrichment. Library quality was checked with Qubit and Bioanalyzer.

treatment_protocol: Cells were divided into control and oxidative stress conditions. Treated cells were exposed to hydrogen peroxide (0.05%) for 2 hours under standard culture conditions, while control cells were left untreated or treated with PBS. Cells were immediately processed for RNA extraction following treatment.

value: murine pancreatic cancer

value: cancer cells

value: wild-type

value: 0.05% H2O2 in PBS for 2 hours


title: WT_NELF-E_CT44

description: Library name: Sample77

value: Liver


title: cell-free DNA from healthy control sample 72.3 at T2

description: PBMC DNA from healthy control mice

value: PBMC


title: cell-free DNA from healthy control sample 72.2 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 72.4 at T2

description: PBMC DNA from healthy control mice


title: RNA-seq of Panc02 cells PBS-treated (control)

description:
Library name: Panc02_control_PBS-treated
NA-seq of Panc02 cells treated with PBS for 2 hours

value: PBS for 2 hours


title: HepaRG Free Fatty Acids and Formoterol, Rep 3

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
Library name: Sample 15
HepaRG_FAF3

data_processing:
Novogene performed data analysis in the Novogene platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignments were performed with HISAT2 v2.0.5 by Novogene
Differentially expressed genes were determined with the R package DESeq2
Assembly: mm39
Supplementary files format and content: spreadsheet containing gene counts

source_name: differentiated

growth_protocol: Cells were maintained at 37°C and 5% CO2 in a humidified incubator. HepaRG growth media consisted of 1 L of Milli-Q water, 1 packet (10.9 g/L) of Williams Medium E with L-glutamine without sodium bicarbonate (HiMedia AT125-10x1L), 26.19 mL 1 M sodium bicarbonate (Thermo Fisher J62495.AP), and 2.17 uL 46 mM triamcinolone acetonide (Sigma T6501-250MG) in DMSO. Media was filter sterilized using a sterile disposable filter unit with 0.22 µm polyethersulfone filter. Following filtration,100 mL of FBS (VWR 89510-186), 10 mL of 100x PenStrep (Gibco) and 1333 L of insulin (4 mg/mL, Gibco) was added before storing at 4 degrees. Media was refreshed every other day. Cells were passaged between 5- and 7-days after seeding when they reached 90-100% confluency. For HepaRG differentiation, cells were allowed to reach confluence over two weeks in normal growth media, and then during the following two weeks differentiation was promoted by adding 1% DMSO to the HepaRG growth media for one media change, followed by 2% DMSO for two weeks. Cells were maintained in media containing 2% DMSO after differentiation until use and throughout the experiment.

extract_protocol:
Cell lysates were prepared by homogenization in Qiashredder columns and RNA was isolated using the RNeasy Qiagen kit with the optional DNaseI on-column digestion step
Briefly, mRNA was purified from total RNA 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(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. 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 was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Non-control cells were treated with 30 nM formoterol or/and 0.25 mM palmitic + 0.5mM oleic acids. Sodium palmitate (Sigma P9767-5G) and sodium oleate (Sigma 07501-1G) powder were added to prewarmed 50˚C PBS buffer and emulsified via sonication 2X for 15 seconds at an amplitude of 50, 30 seconds apart, using a Qsonica sonicator, then added to the media. Fatty acids were made fresh daily. During cell treatment, culture media was changed daily. Cells were treated for 3 days, after which media were removed and cells were washed and frozen in cell pellets for RNA isolation.

value: differentiated

value: HepaRG

value: hepatocyte and cholangiocyte-like cells

value: 30 nM formoterol and 0.5 mM oleic and 0.25 mM palmitic acid


title: control

city: 广州

first: shuo

last: zhang

address: 黄埔大道西601号

institute: 暨南大学

description: Library name: control

data_processing:
Raw reads were trimmed of adapters and low-quality bases using Fastp (v0.20.1) and processed with the SeekSoul Tools pipeline to generate a gene-expression matrix. Downstream analyses were performed in Seurat v3: nuclei or cells of high or low quality were filtered based on gene counts, UMI counts, and mitochondrial gene proportions; after normalization, PCA was applied for dimensionality reduction followed by graph-based clustering. Intestinal mucosal cell subpopulations were extracted, and differentially expressed genes (DEGs) between conditions were identified using the Wilcoxon rank-sum test (adjusted p < 0.05). Finally, GO and KEGG pathway enrichment analyses of these DEGs were conducted using ClusterProfiler to elucidate the molecular mechanisms underlying PEDV-induced changes in intestinal mucosal cells.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

source_name: brain

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Reverse transcription was carried out at 37 °C for 30 min. The barcoded cDNA on CBBs was hybridized with a random primer containing read-2 SeqPrimer sequences at the 5′ end, enabling extension to form the second strand with a 3′ cell barcode. The resulting second-strand DNA was denatured off the CBBs, purified, and amplified by PCR. The cDNA product was cleaned, ligated to adapters and sample indices, and the indexed sequencing libraries were purified with SPRI beads, quantified, and sequenced on an Illumina NovaSeq.

value: brain


title: cell-free DNA from healthy control sample 72.4 at BL

description: PBMC DNA from healthy control mice

value: control


title: HepaRG Free Fatty Acids and Formoterol, Rep 4

description:
Library name: Sample 16
HepaRG_FAF4


title: cell-free DNA from healthy control sample 72.2 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 72.3 at BL

description: PBMC DNA from healthy control mice


title: TBI-GFP

description: Library name: TBI-GFP


title: TBI-ND1

description: Library name: TBI-ND1


title: WT_NELF-E_CT32

description: Library name: Sample74

value: WT


title: WT_NELF-E_CT36

description: Library name: Sample75


title: HepaRG Free Fatty Acids and Formoterol, Rep 2

description:
Library name: Sample 14
HepaRG_FAF2


title: cell-free DNA from healthy control sample 72.2 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 74.1 at BL

description: PBMC DNA from healthy control mice


title: HepaRG Free Fatty Acids and Formoterol, Rep 1

description:
Library name: Sample 13
HepaRG_FAF1


title: HepaRG Free Fatty Acids, Rep 4

description:
Library name: Sample 12
HepaRG_FA4

value: 0.5 mM oleic and 0.25 mM palmitic acid


title: WT_NELF-E_CT16

description: Library name: Sample70


title: TyrobpKO, OC, 5

city: Hartsdale

first: michelle

last: ehrlich

state: New York

address: 88 Mercer Ave.

institute: Mount Sinai Hospital

description:
Library name: TyrobpKO_OC_5
GQ71_S42_L002

data_processing:
RNA reads were aligned to the Mus Musculus Ensembl Reference genome (GRCm38.77) using STAR aligner software (Version 2.5.2b).
Gene count filtering, normalization, and differential expression analysis were performed in R using the Limma package.
Assembly: Mus Musculus Ensembl Reference genome (GRCm38.77)
Supplementary files format and content: tab delimited .txt file with raw counts for each gene/sample

source_name: Hippocampus and cortex

extract_protocol:
Cells were lysed with Qiazol, and RNA was extracted using the miRNeasy Micro Qiagen Kit.
RNA samples were sequenced using the Illumina NovaSeq PE150 platform by Novogene. RNA quality of each sample was assessed by Novogene and cDNA libraries (150bp, paired end reads) were sequenced using an ultra-low input protocol.

treatment_protocol: Primary microglia cells from cortex and hippocampal regions of WT, Trem2 KO, and Tyrobp KO mice were isolated and plated overnight, and stimulated with control DMEM media, or LPS, or A11/OC mix, or OC-only preparation for 24h, then lysed and prepared for bulk RNA-seq.

value: Hippocampus and cortex

value: Primary microglia

value: Tyrobp KO

value: OC


title: WT_NELF-E_CT20

description: Library name: Sample71

value: anti NELF-E (Abcam Cat# ab170104)


title: cell-free DNA from healthy control sample 72.1 at T4

description: PBMC DNA from healthy control mice


title: TyrobpKO, OC, 4

description:
Library name: TyrobpKO_OC_4
GQ70_S0_L001


title: WT_NELF-E_CT24

description: Library name: Sample72


title: TyrobpKO, OC, 3

description:
Library name: TyrobpKO_OC_3
GQ69_S33_L006


title: cell-free DNA from healthy control sample 72.1 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 72.1 at BL

description: PBMC DNA from healthy control mice


title: WT_NELF-E_CT08

description: Library name: Sample68


title: TyrobpKO, OC, 1

description:
Library name: TyrobpKO_OC_1
GQ67_S41_L002


title: HepaRG Free Fatty Acids, Rep 3

description:
Library name: Sample 11
HepaRG_FA3


title: WT_NELF-E_CT12

description: Library name: Sample69


title: cell-free DNA from healthy control sample 72.1 at T2

description: PBMC DNA from healthy control mice


title: TyrobpKO, OC, 2

description:
Library name: TyrobpKO_OC_2
GQ68_S32_L006


title: HepaRG Free Fatty Acids, Rep 2

description:
Library name: Sample 10
HepaRG_FA2


title: WT_NELF-E_CT04

description: Library name: Sample67


title: HepaRG Free Fatty Acids, Rep 1

description:
Library name: Sample 9
HepaRG_FA1


title: Trem2KO, OC, 6

description:
Library name: Trem2KO_OC_6
GQ66_S2_L001

value: Trem2 KO


title: WT_NELF-E_CT00

description: Library name: Sample66

value: Liver


title: cell-free DNA from healthy control sample 71.4 at BL

description: PBMC DNA from healthy control mice

value: PBMC


title: Trem2KO, OC, 3

description:
Library name: Trem2KO_OC_3
GQ63_S40_L002


title: cell-free DNA from healthy control sample 71.3 at T3

description: PBMC DNA from healthy control mice


title: Trem2KO, OC, 4

description:
Library name: Trem2KO_OC_4
GQ64_S61_L007


title: cell-free DNA from healthy control sample 71.3 at BL

description: PBMC DNA from healthy control mice


title: WT_NELF-E_CT28

description: Library name: Sample73


title: Trem2KO, OC, 5

description:
Library name: Trem2KO_OC_5
GQ78_S43_L002


title: HepaRG Formoterol, Rep 4

description:
Library name: Sample 8
HepaRG_F4

value: 30 nM formoterol


title: WT_SER2P_CT40

description: Library name: Sample63

value: Anti phospho S2 RNAP II (Abcam Cat# ab5095)


title: WT_SER2P_INPUT

description: Library name: Sample65

value: input mix(00-44)


title: cell-free DNA from healthy control sample 71.3 at T4

description: PBMC DNA from healthy control mice


title: Trem2KO, OC, 1

description:
Library name: Trem2KO_OC_1
GQ61_S38_L002


title: Trem2KO, OC, 2

description:
Library name: Trem2KO_OC_2
GQ62_S39_L002


title: HepaRG Formoterol, Rep 3

description:
Library name: Sample 7
HepaRG_F3

value: differentiated

value: HepaRG

value: hepatocyte and cholangiocyte-like cells


title: WT_SER2P_CT36

description: Library name: Sample62


title: WT_SER2P_CT28

description: Library name: Sample60


title: WT_SER2P_CT44

description: Library name: Sample64


title: WT_SER2P_CT32

description: Library name: Sample61


title: HepaRG Control, Rep 4

description:
Library name: Sample 4
HepaRG_C4

value: vehicle (1% BSA)


title: cell-free DNA from healthy control sample 71.2 at T4

description: PBMC DNA from healthy control mice

value: control


title: HepaRG Formoterol, Rep 2

description:
Library name: Sample 6
HepaRG_F2


title: cell-free DNA from healthy control sample 71.2 at T3

description: PBMC DNA from healthy control mice


title: WT, OC, 6

description:
Library name: WT_OC_6
GQ60_S1_L001


title: HepaRG Formoterol, Rep 1

description:
Library name: Sample 5
HepaRG_F1


title: HepaRG Control, Rep 3

description:
Library name: Sample 3
HepaRG_C3


title: HepaRG Control, Rep 2

description:
Library name: Sample 2
HepaRG_C2


title: WT, OC, 5

description:
Library name: WT_OC_5
GQ59_S60_L007


title: cell-free DNA from healthy control sample 71.2 at T2

description: PBMC DNA from healthy control mice


title: WT_SER2P_CT20

description: Library name: Sample58

value: WT


title: cell-free DNA from healthy control sample 71.3 at T2

description: PBMC DNA from healthy control mice


title: HepaRG Control, Rep 1

description:
Library name: Sample 1
HepaRG_C1


title: 9 Healthy control

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description:
Library name: 47
2x150 Sequence mode to obtain at approx. 20 million read pairs

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: xlsx

source_name: Skin

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Skin


title: 8 Healthy control

description:
Library name: 46
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER2P_CT16

description: Library name: Sample57


title: cell-free DNA from healthy control sample 71.1 at T4

description: PBMC DNA from healthy control mice


title: WT, OC, 2

description:
Library name: WT_OC_2
GQ56_S59_L007

value: Hippocampus and cortex

value: Primary microglia


title: WT, OC, 3

description:
Library name: WT_OC_3
GQ57_S80_L008

value: OC


title: WT, OC, 1

description:
Library name: WT_OC_1
GQ55_S0_L001


title: WT, OC, 4

description:
Library name: WT_OC_4
GQ58_S81_L008


title: cell-free DNA from healthy control sample 71.1 at T3

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 71.1 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 71.1 at T5

description: PBMC DNA from healthy control mice


title: 10 Healthy control

description:
Library name: 48
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER2P_CT08

description: Library name: Sample55


title: TyrobpKO, A11OC, 6

description:
Library name: TyrobpKO_A11OC_6
GQ54_S0_L001

value: Tyrobp KO


title: 6 Healthy control

description:
Library name: 45
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: 5 Healthy control

description:
Library name: 44
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TyrobpKO, A11OC, 4

description:
Library name: TyrobpKO_A11OC_4
GQ52_S37_L002


title: WT_SER2P_CT12

description: Library name: Sample56


title: WT_SER7P_INPUT

description: Library name: Sample52


title: 4 Healthy control

description:
Library name: 43
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER2P_CT04

description: Library name: Sample54


title: WT_SER2P_CT00

description: Library name: Sample53


title: WT_SER7P_CT44

description: Library name: Sample51

value: Anti phospho S7 RNAP II (Millipore Cat# 04-1570)


title: cell-free DNA from healthy control sample 68.1 at T3

description: PBMC DNA from healthy control mice


title: TyrobpKO, A11OC, 5

description:
Library name: TyrobpKO_A11OC_5
GQ53_S29_L006


title: 3 Healthy control

description:
Library name: 42
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT40

description: Library name: Sample50

value: Liver


title: cell-free DNA from healthy control sample 66.4 at T3

description: PBMC DNA from healthy control mice

value: PBMC


title: TyrobpKO, A11OC, 3

description:
Library name: TyrobpKO_A11OC_3
GQ51_S58_L007


title: WT_SER2P_CT24

description: Library name: Sample59


title: cell-free DNA from healthy control sample 68.1 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 68.1 at BL

description: PBMC DNA from healthy control mice


title: TyrobpKO, A11OC, 1

description:
Library name: TyrobpKO_A11OC_1
GQ77_S63_L007


title: TyrobpKO, A11OC, 2

description:
Library name: TyrobpKO_A11OC_2
GQ50_S57_L007


title: Pt 81 drainning tunnel

description:
Library name: 40
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 66.4 at T2

description: PBMC DNA from healthy control mice


title: Pt 80 non-drainning tunnel

description:
Library name: 37
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 81 non-drainning tunnel

description:
Library name: 39
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Trem2KO, A11OC, 6

description:
Library name: Trem2KO_A11OC_6
GQ48_S79_L008

value: Trem2 KO


title: cell-free DNA from healthy control sample 66.3 at T4

description: PBMC DNA from healthy control mice


title: Pt 80 drainning tunnel

description:
Library name: 38
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT24

description: Library name: Sample46


title: Trem2KO, A11OC, 3

description:
Library name: Trem2KO_A11OC_3
GQ45_S36_L002


title: cell-free DNA from healthy control sample 66.3 at T3

description: PBMC DNA from healthy control mice


title: WT_SER7P_CT28

description: Library name: Sample47


title: Trem2KO, A11OC, 5

description:
Library name: Trem2KO_A11OC_5
GQ47_S56_L007


title: Pt 78 non-drainning tunnel

description:
Library name: 35
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT36

description: Library name: Sample49


title: cell-free DNA from healthy control sample 66.3 at T5

description: PBMC DNA from healthy control mice


title: 1 Healthy control

description:
Library name: 41
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT20

description: Library name: Sample45


title: Trem2KO, A11OC, 4

description:
Library name: Trem2KO_A11OC_4
GQ46_S78_L008


title: Pt 78 drainning tunnel

description:
Library name: 36
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Trem2KO, A11OC, 2

description:
Library name: Trem2KO_A11OC_2
GQ44_S28_L006


title: Pt 74 drainning tunnel

description:
Library name: 34
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT16

description: Library name: Sample44


title: Trem2KO, A11OC, 1

description:
Library name: Trem2KO_A11OC_1
GQ43_S55_L007


title: cell-free DNA from healthy control sample 66.4 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 66.3 at T2

description: PBMC DNA from healthy control mice


title: WT_SER7P_CT12

description: Library name: Sample43


title: WT_SER7P_CT32

description: Library name: Sample48


title: WT, A11OC, 4

description:
Library name: WT_A11OC_4
GQ40_S54_L007


title: WT_SER7P_CT08

description: Library name: Sample42


title: WT_SER7P_CT00

description: Library name: Sample40


title: Pt 72 non-drainning tunnel

description:
Library name: 31
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 74 non-drainning tunnel

description:
Library name: 33
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER5P_INPUT

description: Library name: Sample39


title: WT, A11OC, 5

description:
Library name: WT_A11OC_5
GQ41_S76_L008


title: WT_SER5P_CT44

description: Library name: Sample38

value: Anti phospho S5 RNAP II (Abcam Cat# ab5131)


title: Pt 72 drainning tunnel

description:
Library name: 32
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER7P_CT04

description: Library name: Sample41


title: cell-free DNA from healthy control sample 66.3 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 66.2 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 66.2 at T3

description: PBMC DNA from healthy control mice


title: WT, A11OC, 6

description:
Library name: WT_A11OC_6
GQ42_S77_L008


title: Pt 71 non-drainning tunnel

description:
Library name: 29
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 70 non-drainning tunnel

description:
Library name: 27
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 66.2 at T4

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 66.1 at T4

description: PBMC DNA from healthy control mice


title: Pt 71 drainning tunnel

description:
Library name: 30
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 66.2 at T2

description: PBMC DNA from healthy control mice


title: WT, A11OC, 1

description:
Library name: WT_A11OC_1
GQ37_S27_L006


title: TyrobpKO, LPS, 6

description:
Library name: TyrobpKO_LPS_6
GQ36_S0_L001

value: LPS


title: Pt 50 drainning tunnel

description:
Library name: 26
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER5P_CT36

description: Library name: Sample36


title: WT_SER5P_CT40

description: Library name: Sample37


title: cell-free DNA from healthy control sample 66.1 at T2

description: PBMC DNA from healthy control mice


title: WT, A11OC, 3

description:
Library name: WT_A11OC_3
GQ39_S35_L002


title: cell-free DNA from healthy control sample 66.1 at BL

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 66.1 at T5

description: PBMC DNA from healthy control mice


title: Pt 49 drainning tunnel

description:
Library name: 24
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER5P_CT24

description: Library name: Sample33


title: Pt 70 drainning tunnel

description:
Library name: 28
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_SER5P_CT20

description: Library name: Sample32


title: Pt 47 drainning tunnel

description:
Library name: 22
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT, A11OC, 2

description:
Library name: WT_A11OC_2
GQ38_S34_L002


title: TyrobpKO, LPS, 1

description:
Library name: TyrobpKO_LPS_1
GQ31_S75_L008


title: cell-free DNA from healthy control sample 64.4 at T4

description: PBMC DNA from healthy control mice


title: WT_SER5P_CT32

description: Library name: Sample35


title: WT_SER5P_CT16

description: Library name: Sample31


title: WT_SER5P_CT28

description: Library name: Sample34


title: Pt 50 non-drainning tunnel

description:
Library name: 25
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 64.4 at BL

description: PBMC DNA from healthy control mice


title: TyrobpKO, LPS, 2

description:
Library name: TyrobpKO_LPS_2
GQ32_S32_L002


title: WT_SER5P_CT12

description: Library name: Sample30


title: Pt 46 drainning tunnel

description:
Library name: 20
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TyrobpKO, LPS, 4

description:
Library name: TyrobpKO_LPS_4
GQ34_S33_L002


title: Trem2KO, LPS, 5

description:
Library name: Trem2KO_LPS_5
GQ29_S31_L002


title: cell-free DNA from healthy control sample 64.3 at T5

description: PBMC DNA from healthy control mice


title: TyrobpKO, LPS, 3

description:
Library name: TyrobpKO_LPS_3
GQ33_S53_L007


title: Pt 49 non-drainning tunnel

description:
Library name: 23
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 64.4 at T5

description: PBMC DNA from healthy control mice


title: WT_SER5P_CT04

description: Library name: Sample28


title: TyrobpKO, LPS, 5

description:
Library name: TyrobpKO_LPS_5
GQ35_S25_L006


title: WT_SER5P_CT08

description: Library name: Sample29


title: cell-free DNA from healthy control sample 64.3 at T4

description: PBMC DNA from healthy control mice


title: Pt 45 drainning tunnel

description:
Library name: 18
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 64.4 at T3

description: PBMC DNA from healthy control mice


title: Trem2KO, LPS, 3

description:
Library name: Trem2KO_LPS_3
GQ27_S73_L008


title: cell-free DNA from healthy control sample 64.3 at T3

description: PBMC DNA from healthy control mice


title: Pt 47 non-drainning tunnel

description:
Library name: 21
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 68.3 at T3

description: PBMC DNA from healthy control mice


title: Pt 41 drainning tunnel

description:
Library name: 16
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 46 non-drainning tunnel

description:
Library name: 19
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Trem2KO, LPS, 6

description:
Library name: Trem2KO_LPS_6
GQ30_S74_L008


title: cell-free DNA from healthy control sample 66.1 at T3

description: PBMC DNA from healthy control mice


title: Trem2KO, LPS, 2

description:
Library name: Trem2KO_LPS_2
GQ26_S52_L007


title: TyrobpKO, OC, 6

description:
Library name: TyrobpKO_OC_6
GQ72_S62_L007


title: Trem2KO, LPS, 1

description:
Library name: Trem2KO_LPS_1
GQ25_S51_L007


title: cell-free DNA from healthy control sample 71.1 at BL

description: PBMC DNA from healthy control mice


title: WT_SER5P_CT00

description: Library name: Sample27


title: Pt 45 non-drainning tunnel

description:
Library name: 17
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT, LPS, 6

description:
Library name: WT_LPS_6
GQ24_S29_L002


title: WT_8WG16_INPUT

description: Library name: Sample26

value: input mix(00-44)


title: cell-free DNA from healthy control sample 64.3 at T2

description: PBMC DNA from healthy control mice


title: cell-free DNA from healthy control sample 64.2 at T5

description: PBMC DNA from healthy control mice


title: WT_8WG16_CT40

description: Library name: Sample24

value: 8WG16 (Covance, Cat#MMS-126R)


title: cell-free DNA from healthy control sample 64.3 at BL

description: PBMC DNA from healthy control mice


title: Pt 16 drainning tunnel

description:
Library name: 14
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 41 non-drainning tunnel

description:
Library name: 15
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT44

description: Library name: Sample25


title: cell-free DNA from healthy control sample 64.2 at T3

description: PBMC DNA from healthy control mice


title: WT, LPS, 5

description:
Library name: WT_LPS_5
GQ23_S24_L006


title: WT, LPS, 4

description:
Library name: WT_LPS_4
GQ22_S28_L002


title: cell-free DNA from healthy control sample 64.2 at T4

description: PBMC DNA from healthy control mice


title: Pt 16 non-drainning tunnel

description:
Library name: 13
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 64.2 at T2

description: PBMC DNA from healthy control mice


title: WT_8WG16_CT32

description: Library name: Sample22


title: Pt 8 non-drainning tunnel

description:
Library name: 11
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Trem2KO, LPS, 4

description:
Library name: Trem2KO_LPS_4
GQ28_S30_L002


title: WT_8WG16_CT24

description: Library name: Sample20


title: Pt 7 drainning tunnel

description:
Library name: 10
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT20

description: Library name: Sample19


title: cell-free DNA from healthy control sample 64.2 at BL

description: PBMC DNA from healthy control mice


title: Pt 7 non-drainning tunnel

description:
Library name: 9
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Pt 8 drainning tunnel

description:
Library name: 12
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: cell-free DNA from healthy control sample 64.1 at T4

description: PBMC DNA from healthy control mice


title: TyrobpKO, Control, 6

description:
Library name: TyrobpKO_Control_6
GQ18_S21_L006

value: Baseline


title: cell-free DNA from healthy control sample 64.1 at T3

description: PBMC DNA from healthy control mice


title: Pt 6 drainning tunnel

description:
Library name: 8
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TyrobpKO, Control, 5

description:
Library name: TyrobpKO_Control_5
GQ17_S50_L007


title: WT, LPS, 1

description:
Library name: WT_LPS_1
GQ19_S72_L008


title: WT, LPS, 3

description:
Library name: WT_LPS_3
GQ21_S23_L006


title: cell-free DNA from healthy control sample 64.1 at T2

description: PBMC DNA from healthy control mice


title: WT_8WG16_CT08

description: Library name: Sample16


title: Pt 6 non-drainning tunnel

description:
Library name: 7
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT12

description: Library name: Sample17


title: cell-free DNA from healthy control sample 64.1 at BL

description: PBMC DNA from healthy control mice


title: Pt 5 drainning tunnel

description:
Library name: 6
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT36

description: Library name: Sample23


title: TyrobpKO, Control, 3

description:
Library name: TyrobpKO_Control_3
GQ15_S54_L002


title: Pt 4 drainning tunnel

description:
Library name: 4
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: TyrobpKO, Control, 4

description:
Library name: TyrobpKO_Control_4
GQ16_S71_L008


title: cell-free DNA from healthy control sample 61.3 at T4

description: PBMC DNA from healthy control mice


title: Pt 5 non-drainning tunnel

description:
Library name: 5
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT16

description: Library name: Sample18


title: TyrobpKO, Control, 2

description:
Library name: TyrobpKO_Control_2
GQ14_S49_L007


title: cell-free DNA from healthy control sample 61.3 at T3

description: PBMC DNA from healthy control mice


title: WT_RNAP_II_INPUT

description: Library name: Sample13


title: WT, LPS, 2

description:
Library name: WT_LPS_2
GQ20_S22_L006


title: Pt 4 non-drainning tunnel

description:
Library name: 3
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_8WG16_CT00

description: Library name: Sample14


title: Trem2KO, Control, 6

description:
Library name: Trem2KO_Control_6
GQ12_S27_L002


title: cell-free DNA from healthy control sample 61.3 at T2

description: PBMC DNA from healthy control mice


title: WT_8WG16_CT28

description: Library name: Sample21


title: TyrobpKO, Control, 1

description:
Library name: TyrobpKO_Control_1
GQ13_S20_L006


title: WT_8WG16_CT04

description: Library name: Sample15


title: WT_RNAP_II_CT44

description: Library name: Sample12

value: anti Pan Pol II (SantaCruz, Cat#SC899)


title: Pt 1 drainning tunnel

description:
Library name: 2
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: Trem2KO, Control, 5

description:
Library name: Trem2KO_Control_5
GQ11_S26_L002


title: Pt 1 non-drainning tunnel

description:
Library name: 1
2x150 Sequence mode to obtain at approx. 20 million read pairs


title: WT_RNAP_II_CT40

description: Library name: Sample11


title: cell-free DNA from healthy control sample 61.1 at T3

description: PBMC DNA from healthy control mice

value: control


title: cell-free DNA from healthy control sample 61.1 at T2

description: PBMC DNA from healthy control mice


title: Trem2KO, Control, 4

description:
Library name: Trem2KO_Control_4
GQ10_S25_L002


title: cell-free DNA from healthy control sample 61.1 at BL

description: PBMC DNA from healthy control mice


title: WT_RNAP_II_CT36

description: Library name: Sample10

value: WT


title: Trem2KO, Control, 3

description:
Library name: Trem2KO_Control_3
GQ09_S70_L008


title: 10x5_PBMC_09252020

city: Houston

first: Dawei

last: Zou

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

description: Library name: 10x5_PBMC_09252020

data_processing:
The Cell Ranger™ Single Cell Software Suite v.4.0.0 was used to perform bioinformatics analysis. The reads were aligned to the human transcriptome reference (GRCh38, ENSEMBL 98) with STAR. Raw read count tables were analyzed using the Seurat (v3.1.1) pipeline on R platform (3.5.2).
Assembly: Human transcriptome reference (GRCh38, ENSEMBL 98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD45+ cells from the PBMC

extract_protocol:
CD45+ immune cells were isolated from the kidney biopsy tissue and the matched PBMC sample by flow sorting.
Sorted CD45+ cells were processed using the Chromium Next GEM Single Cell 5’ Kit (10x Genomics). A single-cell suspension, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded to a Chromium controller (10x Genomics) to generate Gel Beads-In-Emulsions (GEMs). Within each GEM, the encapsulated cell underwent lysis and reverse transcription, producing full-length cDNA uniquely barcoded to its cell of origin. Next, the GEMs were broken, and cDNA from each cell was pooled. The cDNA underwent purification using Dynabeads MyOne Silane Beads and was then PCR-amplified. The amplified product was optimally fragmented, followed by end-repair, A-tailing, and adaptor ligation. Final libraries were generated by PCR amplification. Library concentrations were quantified using the KAPA Library Quantification Kit (Roche) and sequenced individually on an Illumina NovaSeq 6000 platform.

value: CD45+ cells from the PBMC


title: WT_RNAP_II_CT32

description: Library name: Sample9


title: Trem2KO, Control, 2

description:
Library name: Trem2KO_Control_2
GQ08_S69_L008

value: Hippocampus and cortex


title: 10x5_Graft_09252020

description: Library name: 10x5_Graft_09252020

source_name: CD45+ cells from the kidney biopsy

value: CD45+ cells from the kidney biopsy


title: Trem2KO, Control, 1

description:
Library name: Trem2KO_Control_1
GQ07_S48_L007

value: Primary microglia


title: cell-free DNA from healthy control sample 61.3 at BL

description: PBMC DNA from healthy control mice


title: WT_RNAP_II_CT28

description: Library name: Sample8


title: WT_RNAP_II_CT24

description: Library name: Sample7


title: WT, Control, 6

description:
Library name: WT_Control_6
GQ06_S19_L006


title: cell-free DNA from healthy control sample 60.4 at T3

description: PBMC DNA from healthy control mice


title: WT_RNAP_II_CT20

description: Library name: Sample6


title: 8-Rel_2_CD34_negative_CD38_negative

city: Toronto

first: Mathieu

last: Lupien

address: 101 College Street

institute: University Health Network

description: Library name: 8-Rel_2_CD34_negative_CD38_negative

data_processing:
The data is processed using bowtie2 and called peaks using MACS2.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Acute Myeloid Leukemia

extract_protocol:
Nuclei were isolated using digitnnin-containing buffer from viable frozen peripheral blood cells from AML patients and then incubated with Illumina Transposase for 30min at 37 C.
Libraries were amplified using per-sample determined PCR cycles

value: Acute Myeloid Leukemia


title: WT, Control, 5

description:
Library name: WT_Control_5
GQ05_S18_L006


title: hMS-WTMg-6

city: West Lafayette

first: Harish

last: Kothandaraman

state: IN

address: 201S South State St

department: Purdue Institute for Cancer Research

institute: Purdue University

description:
Library name: 76906
Single-cell RNA sequencing of human brain organoids with WT iPSC-derived microglia (midbrain region).

data_processing:
Data was aligned to the reference with PIPseeker v3.3.0
Assembly: pipseeker-gex-reference-GRCh38-2022.04
Supplementary files format and content: Matrix format files, features and associated barcode files

source_name: midbrain organoids

growth_protocol: Human iPSCs (KOLF2.1J, B07 WT, B11 WT and derived SCN2A C959X and GABBR1 KO lines) were maintained on Matrigel-coated plates in StemFlex or mTeSR-based medium and routinely passaged. Embryoid bodies were generated and differentiated into cortical (hCO), striatal (hStrO), and midbrain (hMO) organoids using published region-specific patterning protocols with dual-SMAD inhibition and appropriate morphogens. Organoids were matured long term in Neurobasal-A–based medium with B27 supplements and neurotrophic factors. Human microglia were generated from the same hiPSC lines via hematopoietic progenitors using a STEMdiff Hematopoietic Kit followed by differentiation in IL-34, TGF-β1, and M-CSF–containing microglia medium.

extract_protocol:
For each condition, 4–5 organoids derived from three independent hiPSC lines were pooled. Organoids were dissociated into single-cell suspensions using an enzymatic solution containing papain (30 U/mL) and DNase I (0.4%) at 37°C for 45 min, followed by gentle trituration. Cells were washed in inhibitor-containing medium, filtered through a 70 μm strainer, counted, and resuspended in Cell Suspension Buffer for downstream single-cell RNA-seq library preparation.
Single-cell RNA-seq libraries were generated using the PIPseq-T20 3' Single Cell RNA Kit v3.0 (Fluent BioSciences) according to the manufacturer’s protocol. Briefly, ~40,000 cells per reaction were loaded into PIPseq Pre-templated Instant Partitions (PIPs) with partitioning reagents to encapsulate single cells with barcoded beads. Following cell lysis and mRNA capture in PIPs, cDNA was synthesized using a template-switch oligonucleotide, whole-transcriptome amplification was performed, and cDNA was purified by SPRI bead cleanup. Libraries were prepared by fragmentation, end repair, A-tailing, adapter ligation, and PCR amplification with dual indices, followed by size selection and QC on Qubit and Bioanalyzer/TapeStation. Libraries were sequenced on an Illumina NovaSeq S4 platform with 2×150 bp paired-end reads.

treatment_protocol: For microglia-containing samples, day ≥80 cortical, striatal, or midbrain organoids were co-cultured with iPSC-derived microglial progenitors. Approximately 4×10^5 microglial cells were seeded onto each organoid in a 1:1 mixture of organoid and microglia differentiation media and allowed to integrate for 7 days, followed by an additional 7 days of maturation in standard organoid medium. No additional pharmacological treatments were applied before single-cell RNA-seq sample collection.

value: midbrain organoids

value: hiPSC line KOLF2.1J, B11WT, and B07 WT

value: midbrain organoid + microglia


title: WT, Control, 4

description:
Library name: WT_Control_4
GQ04_S17_L006


title: cell-free DNA from healthy control sample 60.3 at T3

description: PBMC DNA from healthy control mice

data_processing: SeSame package in R environment (v. 4.4.2)

extract_protocol: Red blood cells were removed with RBC lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 7.3), and then the remaining cells were digested overnight at 65°C with proteinase K (20 mg/mL) in TESR buffer (10 mM Tris-HCl, 25 mM EDTA, 0.5% SDS, 20 µg/mL RNase). DNA was washed and isolated using SPRI beads and eluted in 10 mM Tris-HCl pH8.

value: PBMC


title: cell-free DNA from healthy control sample 60.4 at BL

description: PBMC DNA from healthy control mice


title: hStrS-WTMg-8

description:
Library name: 76903
Single-cell RNA sequencing of human brain organoids with WT iPSC-derived microglia (striatum region).

source_name: striatal organoids

value: striatal organoids

value: striatum organoid + microglia


title: WT_RNAP_II_CT16

description: Library name: Sample5

value: Liver


title: hCS-WTMg-6

description:
Library name: 76905
Single-cell RNA sequencing of human brain organoids with WT iPSC-derived microglia (cortex region).

source_name: cortical organoids

value: cortical organoids

value: cortical organoid + microglia


title: cell-free DNA from healthy control sample 60.4 at T2

description: PBMC DNA from healthy control mice

source_name: PBMC


title: 7-Rel_2_CD34_negative_CD38_positive

description: Library name: 7-Rel_2_CD34_negative_CD38_positive


title: WT_RNAP_II_CT12

description: Library name: Sample4

value: anti Pan Pol II (SantaCruz, Cat#SC899)


title: cell-free DNA from healthy control sample 60.3 at T2

description: PBMC DNA from healthy control mice

value: control


title: WT_RNAP_II_CT08

description: Library name: Sample3

value: WT


title: WT, Control, 2

description:
Library name: WT_Control_2
GQ02_S68_L008

value: Baseline


title: cell-free DNA from healthy control sample 60.4 at T4

description: PBMC DNA from healthy control mice


title: 5-Rel_2_CD34_posittive_CD38_negative

description: Library name: 5-Rel_2_CD34_posittive_CD38_negative


title: WT_RNAP_II_CT04

description: Library name: Sample2


title: cell-free DNA from healthy control sample 60.2 at T4

description: PBMC DNA from healthy control mice