title: 4-week PFC WT, Bulk RNA-seq Sample 142

description: Library name: akap11_4w_PFC_WT_142


title: 4-week SSC Akap11 -/-, Bulk RNA-seq Sample 51

status: Public on Sep 04 2025

type: SRA

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

country: USA

institute: Broad Institute

description: Library name: akap11_4w_SSC_KO_51

library_source: transcriptomic

data_processing:
Reads were aligned to mm10 and gene and isoform level expression leves were estimated using Salmon
Assembly: mm10
Supplementary files format and content: CSV file contains Salmon's counts estimation for all genes and all samples

molecule: total RNA

organism: Mus musculus

source_name: Somatosensory Cortex

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Akap11 mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.

tag: tissue

value: Somatosensory Cortex

tag: genotype

tag: age


title: 4-week HP WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_HP_WT_92

source_name: Hippocampus

value: Hippocampus

value: WT


title: 4-week PFC Akap11 -/-, Bulk RNA-seq Sample 51

description: Library name: akap11_4w_PFC_KO_51

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: 4-week PFC WT, Bulk RNA-seq Sample 92

description: Library name: akap11_4w_PFC_WT_92


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 941

description: Library name: akap11_4w_SSC_HT_941


title: 4-week STR WT, Bulk RNA-seq Sample 42

description: Library name: akap11_4w_STR_WT_42

source_name: Striatum

value: Striatum


title: 4-week SSC WT, Bulk RNA-seq Sample 23

description: Library name: akap11_4w_SSC_WT_23


title: 4-week HP Akap11 -/-, Bulk RNA-seq Sample 51

description: Library name: akap11_4w_HP_KO_51


title: 4-week HP Akap11 +/-, Bulk RNA-seq Sample 22

description: Library name: akap11_4w_HP_HT_22


title: 4-week TH Akap11 +/-, Bulk RNA-seq Sample 22

description: Library name: akap11_4w_TH_HT_22

source_name: Thalamus

value: Thalamus


title: 4-week HP WT, Bulk RNA-seq Sample 23

description: Library name: akap11_4w_HP_WT_23


title: 4-week PFC Akap11 -/-, Bulk RNA-seq Sample 44

description: Library name: akap11_4w_PFC_KO_44


title: 4-week SSC Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_SSC_KO_161


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 941

description: Library name: akap11_4w_PFC_HT_941


title: 4-week PFC Akap11 -/-, Bulk RNA-seq Sample 161

description: Library name: akap11_4w_PFC_KO_161


title: 4-week PFC WT, Bulk RNA-seq Sample 23

description: Library name: akap11_4w_PFC_WT_23


title: 4-week SSC Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_SSC_KO_932


title: 4-week HP Akap11 +/-, Bulk RNA-seq Sample 941

description: Library name: akap11_4w_HP_HT_941


title: 4-week HP Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_HP_KO_932


title: 4-week TH Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_TH_KO_932


title: 4-week TH Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_TH_HT_931


title: 4-week TH WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_TH_WT_914


title: 4-week HP WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_HP_WT_914


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_PFC_HT_931


title: 4-week PFC Akap11 -/-, Bulk RNA-seq Sample 932

description: Library name: akap11_4w_PFC_KO_932


title: 4-week PFC WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_PFC_WT_914


title: 4-week HP Akap11 -/-, Bulk RNA-seq Sample 12

description: Library name: akap11_4w_HP_KO_12


title: 4-week SSC WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_SSC_WT_913


title: 4-week HP Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_HP_HT_931


title: 4-week SSC Akap11 -/-, Bulk RNA-seq Sample 12

description: Library name: akap11_4w_SSC_KO_12


title: 4-week HP WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_HP_WT_913


title: 4-week TH WT, Bulk RNA-seq Sample 23

description: Library name: akap11_4w_TH_WT_23


title: 4-week TH Akap11 -/-, Bulk RNA-seq Sample 51

description: Library name: akap11_4w_TH_KO_51


title: 4-week TH Akap11 +/-, Bulk RNA-seq Sample 11

description: Library name: akap11_4w_TH_HT_11


title: 4-week PFC Akap11 -/-, Bulk RNA-seq Sample 12

description: Library name: akap11_4w_PFC_KO_12


title: 4-week TH WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_TH_WT_913


title: 4-week PFC WT, Bulk RNA-seq Sample 913

description: Library name: akap11_4w_PFC_WT_913


title: 4-week PFC Akap11 +/-, Bulk RNA-seq Sample 11

description: Library name: akap11_4w_PFC_HT_11


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 931

description: Library name: akap11_4w_SSC_HT_931


title: 4-week SSC WT, Bulk RNA-seq Sample 914

description: Library name: akap11_4w_SSC_WT_914


title: I/R cardiomyocytes replicate 1

city: Xiamen

first: Hongwen

last: Xiao

state: Fujian

address: No. 1999, Guankou Middle Road, Jimei District

department: Department of Basic Medicine

country: China

institute: Xiamen Medical College

description:
Library name: nh1
Cells treated with 100 µM H₂O₂ for 24h, then cultured in full medium 24h

data_processing:
Raw reads were quality checked using FastQC.
Adapter trimming and low-quality read removal were performed using fastp.
Clean reads were aligned to the mouse reference genome (GRCm39) using STAR aligner.
Gene-level quantification was performed using featureCounts.
Differential expression analysis was conducted using DESeq2.
Assembly: GRCm39 (Genome Reference Consortium Mouse Build 39)
Supplementary files format and content: Text files including read counts (counts_AllSample.xls) and normalized expression values (FPKM_AllSample.xls).

source_name: Heart tissue

growth_protocol: Primary neonatal cardiomyocytes were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions.
RNA-seq libraries were prepared using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme, China), according to the manufacturer's instructions.

treatment_protocol: For ischemia-reperfusion (I/R) injury simulation, cells were treated with 100 µM H₂O₂ in serum-free medium for 24 hours, followed by 24 hours in full medium.

value: Heart tissue

tag: cell type

value: Primary neonatal mouse cardiomyocytes

tag: treatment

tag: batch


title: I/R cardiomyocytes replicate 4

description:
Library name: nh4
Cells treated with 100 µM H₂O₂ for 24h, then cultured in full medium 24h


title: I/R cardiomyocytes replicate 3

description:
Library name: nh3
Cells treated with 100 µM H₂O₂ for 24h, then cultured in full medium 24h


title: I/R cardiomyocytes replicate 2

description:
Library name: nh2
Cells treated with 100 µM H₂O₂ for 24h, then cultured in full medium 24h


title: 4-week SSC Akap11 +/-, Bulk RNA-seq Sample 11

description: Library name: akap11_4w_SSC_HT_11


title: Control cardiomyocytes replicate 3

description:
Library name: C3
Primary neonatal cardiomyocytes without any oxidative stress treatment

value: No treatment


title: Control cardiomyocytes replicate 1

description:
Library name: C1
Primary neonatal cardiomyocytes without any oxidative stress treatment


title: OxLDL-treated BMDMs from GpnmbR150X mice replicate 3

city: Beijing

first: Huan

last: Wang

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

data_processing:
All samples passed quality control based on the results of FastQC.
Reads were aligned to the mouse genome assembly mm10.GRCm38 using HISAT2.
The aligned reads were counted using FeatureCounts.
Differentially expressed genes were determined with DESeq2 program
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA was isolated with RNeasy plus Mini Kit (Qiagen) according the manufacturer's protocol.
Library preparation was performed with Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit according the manufacturer's protocol.

value: Bone marrow

tag: strain

value: DBA/2 crossed with C57BL/6 (backcrossed with C57BL/6)

value: BMDMs

value: OxLDL


title: OxLDL-treated BMDMs from GpnmbR150X mice replicate 2


title: OxLDL-treated BMDMs from control mice replicate 2


title: OxLDL-treated BMDMs from control mice replicate 3


title: Control cardiomyocytes replicate 2

description:
Library name: C2
Primary neonatal cardiomyocytes without any oxidative stress treatment


title: BMDMs from GpnmbR150X mice replicate 2

value: Non


title: OxLDL-treated BMDMs from control mice replicate 1


title: BMDMs from GpnmbR150X mice replicate 3


title: BMDMs from control mice replicate 3


title: BMDMs from control mice replicate 1


title: 4-week TH Akap11 -/-, Bulk RNA-seq Sample 12

description: Library name: akap11_4w_TH_KO_12


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, IFNγ, Replicate 2

first: Robert

middle: T

last: Manguso

address: 75 Ames Street, Rm 7053

institute: Broad Institute of MIT & Harvard

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.20.0)
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Transcript counts were quantified by pseudoalignment of trimmed reads to mm10 using Kallisto (v0.46.0)
Gene counts were aggregated from transcript counts using the tximport (v1.24.0) R package
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample

molecule: polyA RNA

source_name: pancreatic ductal adenocarcinoma

growth_protocol: KPC cells were cultured in DMEM (Gibco) + 10% FBS + 1% Penicllin-streptomycin (Penstrep)

extract_protocol:
The cells were trypsinized, and the cell pellets collected and RNA extracted using Qiagen RNAeasy Mini kit according to the manufacturer’s instructions.
Eukaryotic mRNA library (poly A enrichment) was prepared by Novogene.

treatment_protocol: Tumor cells were treated with PBS or 100ng/ml of murine IFNg (Peprotech) for 36hrs.

value: pancreatic ductal adenocarcinoma

tag: cell line

value: KPC

value: tumor cells

value: IFNgamma


title: BMDMs from GpnmbR150X mice replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, PBS, Replicate 3

value: PBS


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, PBS, Replicate 2


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, IFNγ, Replicate 3


title: RNA-seq, KPC in vitro, sgFitm2, sgIrgm1, PBS, Replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, IFNγ, Replicate 3


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, IFNγ, Replicate 2


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, PBS, Replicate 2


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, IFNγ, Replicate 3


title: OxLDL-treated BMDMs from GpnmbR150X mice replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, PBS, Replicate 3


title: RNA-seq, KPC in vitro, sgFitm2, sgIrf1, PBS, Replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, IFNγ, Replicate 2


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, PBS, Replicate 3


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, PBS, Replicate 2


title: RNA-seq, KPC in vitro, sgCtrl, sgIrgm1, IFNγ, Replicate 3


title: RNA-seq, KPC in vitro, sgCtrl, sgIrgm1, IFNγ, Replicate 2


title: BMDMs from control mice replicate 2

value: WT


title: RNA-seq, KPC in vitro, sgCtrl, sgIrgm1, PBS, Replicate 2


title: RNA-seq, KPC in vitro, sgCtrl, sgIrgm1, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgCtrl, sgIrgm1, PBS, Replicate 1


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, IFNγ, Replicate 3


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, IFNγ, Replicate 2


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, PBS, Replicate 3


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, PBS, Replicate 2


title: RNA-seq, KPC in vitro, sgCtrl, sgIrf1, PBS, Replicate 1


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, IFNγ, Replicate 3


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, IFNγ, Replicate 2


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, IFNγ, Replicate 1


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, PBS, Replicate 3


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, PBS, Replicate 1


title: ATAC: CCR3 high bone marrow eosinophils 2

city: Cincinnati

first: Jennifer

middle: M

last: Felton

state: Ohio

address: 3333 Burnet Ave, ML7028

department: Department of Allergy and Immunology

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Quality control of raw sequencing reads was performed using the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project.
ATAC-seq reads were aligned to the mouse genome (mm10) using Bowtie2 .
Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89)
Peaks were called using the default parameters of MACS2 (q < 0.01).
Assembly: mm10
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10

molecule: genomic DNA

extract_protocol:
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Corces et al. 2017
The resulting accessible DNA sequences were isolated, and libraries were prepared from 50,000 cells from each cell line using the OMNI ATAC protocol as detailed in Corces et al 2017

value: Eosinophils

tag: ccr3 level

value: CCR3 high

value: Dox induced


title: ATAC: CCR3 low bone marrow eosinophils 2

value: CCR3 low


title: Murine esophagus merged CC10-iIL13-Tg CD2-IL5

description:
BD Rhapsody
Esoph_3_4_merged

library_source: transcriptomic single cell

data_processing:
The raw single cell RNA sequencing FASTQ files were aligned to the GRCm38 reference genome using the BD Rhapsody WTA Analysis Pipeline available on the Seven Bridges Genomics platform.
The feature-barcode matrices generated from multiple runs were merged and converted to the commonly used Market Exchange (MEX) format. All subsequent data analysis steps were conducted in SciDAP, following the guidelines from Surumbayeva et al.
Downstream analysis was conducted in R v.4.2.1 with the package Seurat v.4.3.0. Low-quality cells were removed with Single-cell RNA-Seq Filtering Analysis pipeline using the following filtering thresholds: remove doublets, include cells that have at least 100 but not more than 5,000 expressed genes, exclude cells with less than 500 unique molecular counts and with >15% of transcripts mapped to mitochondrial genes.
Clustering of dimensionally reduced data was conducted with Single-cell RNA-seq Cluster Analysis pipeline using 40 dimensions and 0.3 clustering resolution.
Gene markers for each cluster were identified using FindAllMarkers with a logfc threshold of 0.25 and min.pct cut-off of 0.1. Top-ranked genes were used to define clusters. Clusters were annotated manually based on marker gene expression. Eosinophil were subclustered by sub-setting populations which expressed Siglecf, Ccr3, Il5ra and Ikzf3.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: Esophagus

extract_protocol:
Murine esophageal tissue was digested as descritbed in methods. Briefly; murie esophagus was collected and washed in EDTA stripping buffer for 10 minutes at 37°C. Stripping buffer was replaced, and samples were incubated for 5 minutes, prior to washing with PBS. Esophagi were opened longitudinally, placed in media supplemented with 2.4 mg/mL collagenase A, minced into small pieces and incubated for 30 minutes at 37°C. Following digestion, the samples were passed through a 19G needle and then passed through 40uM filter. Cells were pooled from four to eight mice per sample. Individual mice were labelled with a unique sample tag (BD Mouse Single-Cell Multiplexing Kit) according to manufacturer’s protocol.
Libraries were prepared using BD Rhapsody Express Single-Cell Analysis System according to the manufacturer’s recommendations. Briefly, cells from up to 4 barcoded samples were pooled for a total of 60,000-80,000 cells. Single cells were isolated by gravity (25mins) in the BD Rhapsody Cartridge. cDNA libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis Amplification Kit,  following the BD Rhapsody System mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol. The final libraries were quantified using the Qubit dsDNA HS  and the TapeStation D1000 dsDNA HS Kit. Sequencing was performed using an S2 flow cell, PE-100bp on the NovaSeq6000, with NovaSeq6000 S2 Reagent Kit v1.5. Reads were calculated based on quantification table provided by BD Rhapsody with targets reads of 40,000 per cell for the WTA libraries and 10,000 per cell for the sample tag libraries. Sequencing was performed in the CCHMC DNA Sequencing and Genotyping Core, Cincinnati, Ohio.

value: Esophagus

value: CC10-iIL13-Tg and CD2-IL5


title: ATAC: CCR3 low bone marrow eosinophils 1

value: Bone marrow


title: ATAC: CCR3 high bone marrow eosinophils 1


title: RNA-seq, KPC in vitro, sgFitm2, sgCtrl, PBS, Replicate 1


title: ATAC: Esophageal eosinophils 4


title: ATAC: Esophageal eosinophils 1


title: ATAC: Esophageal eosinophils 2


title: Embryoid bodies, VPA, Stella neg, day6, rep1

city: Ithaca

first: Jingyi

last: Gao

state: NY

address: 618 Tower road

department: BMS

institute: Cornell University

data_processing:
The raw fastq reads were first processed withtrim-galore package to: Trim for low quality reads; 2 color chemistry bias (next-seq); Trim for noisy short fragments; Trim for adapter sequence; "trim_galore --nextseq 20 --gzip --length 50 --paired --fastqc". The filtered reads were then aligned to reference genome with ENSEMBL annotations using STAR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Embryoid bodies

growth_protocol: Mouse ESCs with the four transcription factors inducible system (Prdm1, Prdm14, Nanog, and Tfap2c) were cultured and maintained without feeders in N2B27 2i medium: 1μM PD0325901, 3μM CHIR99021 and 1000U/mL LIF as described in Ding et al. 2024.

extract_protocol:
Total RNA was extracted from cells using TRizol Reagent (Invitrogen; 15596018).
Purified RNAs were used for Illumina RNA-seq library preparation with NEBNext Ultra II Directional RNA Library Prep Kit (NEB; E7765)

treatment_protocol: Sodium butyrate (Sigma; B5887) and valproic acid (Sigma; P4543) were dissolved in water at stocks concentrations of 100mg/ml and 1M, respectively. EBs were treated by 0.05 mg/mL SB or 0.5 mM VPA. Day 6 cells were collected for RNA-seq.

value: Embryoid bodies

value: somatic cell-like cells

value: Valproic acid 0.5 mM


title: Embryoid bodies, VPA, Stella neg, day6, rep2


title: Embryoid bodies, VPA, Stella pos, day6, rep2

value: primordial germ cell-like cells


title: Embryoid bodies, VPA, Stella neg, day6, rep3


title: Embryoid bodies, SB, Stella neg, day6, rep3

value: Sodium butyrate 0.05 mg/mL


title: Embryoid bodies, VPA, Stella pos, day6, rep3


title: Embryoid bodies, VPA, Stella pos, day6, rep1


title: Embryoid bodies, SB, Stella neg, day6, rep1


title: Embryoid bodies, SB, Stella neg, day6, rep2


title: Embryoid bodies, SB, Stella pos, day6, rep1


title: Embryoid bodies, SB, Stella pos, day6, rep2


title: Embryoid bodies, no treatment, Stella pos, day6, rep2


title: Embryoid bodies, no treatment, Stella pos, day6, rep3


title: RNA-seq, KPC in vitro, sgCtrl, sgCtrl, PBS, Replicate 2

value: pancreatic ductal adenocarcinoma

value: KPC


title: Embryoid bodies, no treatment, Stella pos, day6, rep1


title: PGCLC, 4TF, day6, rep1

source_name: primordial germ cell-like cells

growth_protocol: Naïve ESCs were cultured in 2i+ LIF medium containing 1×N2B27, 1 μM PD0325901, 3 μM CHIR99021 and 1,000 U/ml LIF on wells coated with 0.01% poly-L-ornithine and 10 ng/ml laminin.

extract_protocol:
Total RNAs were purified from naïve ESCs, EpiLCs, and PGCLCs (Stella-eGFP+) at days 2, 4 and 6 using TRIzol® reagent.
Purified RNAs were used for Illumina RNA-seq library preparation with NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7765),

treatment_protocol: For PGCLC differentiation, EpiLCs were induced as described previously (Hayashi et. al., 2013). Briefly, 1×105 ESCs were placed per well of a 12-well plate coated with 16.7 μg/mL bovine plasma fibronectin (Sigma-Aldrich, F1141) in N2B27 medium containing 20 ng/mL Activin A (Peprotech, 120-14E), 12 ng/mL bFGF (Gibco, 13256-029), and 1% knockout serum replacement (KSR, ThermoFisher, 10828010). The medium was changed the following day. A total of 48 hours after plating, 2×103 EpiLCs per well were seeded in a U-bottom 96-well plate (ThermoFisher Scientific, 268200) in GK15 medium (GMEM with 15% KSR, 0.1mM NEAA, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, penicillin-streptomycin, and 2mM L-glutamine) with Dox (Sigma, D9891). To induce PGCLCs from formative ESCs, after removing the feeder cells, 2×103 cells per well were seeded in the U-bottom 96-well plate. Transgenes were induced by addition of 2 μg/ml Dox at day 0 of PGCLC induction. Cells were cultured at 37 °C in a 5% CO2-95% air atmosphere.

tag: transgene

value: Prdm1, Prdm14, Tfap2c and Nanog


title: PGCLC, 4TF, day6, rep2


title: PGCLC, 4TF, day6, rep3


title: PGCLC, 4TF, day4, rep3


title: ATAC: Esophageal eosinophils 3


title: PGCLC, 4TF, day4, rep1


title: PGCLC, 4TF, day2, rep1


title: PGCLC, 4TF, day2, rep3


title: PGCLC, 4TF, day4, rep2


title: EpiLC, 48h, rep2

source_name: epiblast like cells

value: epiblast like cells


title: PGCLC, 4TF, day2, rep2


title: EpiLC, 48h, rep3


title: ESC, 2i LIF, rep3

source_name: embryonic stem cells

value: embryonic stem cells


title: EpiLC, 48h, rep1


title: ESC, 2i LIF, rep1


title: Embryoid bodies, SB, Stella pos, day6, rep3


title: Normal LSK cells from  Iron-overload AML BM

city: Nanjing

first: feifei

last: yang

address: Changle Road 68

institute: Nanjing first hospital,Nanjing medical university

data_processing:
Base calling was done by Illumina NovaSeq6000
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5)
FPKM values of each gene for each sample was measured via RSEM (version v1.2.12)
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

source_name: BM

extract_protocol:
Sorted macrophages and leukemia cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103).
RNA libraries were prepared for sequencing using illumina NovaSeq6000 protocols

value: BM

value: LSK cells

value: Iron,leukemia


title: Normal LSK cells from  AML BM

description: Normal LSK cells from  AML BM

value: Normal LSK cells from  AML BM

value: PBS,leukemia


title: Mtg-5-10w-Cep

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Library strategy: 16S ribosomal RNA (rRNA) gene sequencing

source_name: Colonic epithelium

extract_protocol:
Colonic epithelium were isolated by EDTA buffer and gentamicin solution. Freezing epithelium in liquid nitrogen (LN) and store at -80°C. Extract bacterial DNA followed by QIAamp Fast DNA Stool Kit  protocol
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)

treatment_protocol: Untreated

tag: stain

value: MLCKtg

tag: time

value: ten weeks old, wild-type nursing dam

value: Untreated


title: Macrophages from Iron-overload Normal bone marrow

value: Macrophage

value: Iron


title: Mtg-4-10w-Cep


title: Mtg-1-10w-Cep


title: He-5-10w-Cep

value: Hetro (Tg/+)


title: He-1-10w-Cep


title: He-3-10w-Cep


title: Mtg-3-10w-Cep


title: He-2-10w-Cep


title: Mtg-2-10w-Cep


title: B6-5-10w-Cep


title: He-4-10w-Cep


title: B6-4-10w-Cep


title: B6-3-10w-Cep


title: Mtg-3-6w-Cep

value: six weeks old, wild-type nursing dam


title: B6-1-10w-Cep


title: B6-2-10w-Cep


title: Mtg-5-6w-Cep


title: ESC, 2i LIF, rep2


title: Macrophages from  Iron-overload AML bone marrow


title: Mtg-2-6w-Cep


title: Macrophages from  AML bone marrow

description: Macrophages from  AML bone marrow

value: Macrophages from  AML bone marrow


title: Mtg-4-6w-Cep


title: Macrophages from Normal bone marrow

description: Macrophages from Normal bone marrow

value: Macrophages from Normal bone marrow

value: PBS


title: He-4-6w-Cep


title: He-5-6w-Cep


title: He-2-6w-Cep


title: Mtg-1-6w-Cep


title: He-1-6w-Cep


title: B6-4-6w-Cep


title: He-3-6w-Cep


title: B6-3-6w-Cep


title: B6-5-6w-Cep


title: B6-2-6w-Cep


title: B6-1-6w-Cep


title: Mtg-3-3w-Cep

value: three weeks old, before weaning


title: Mtg-1-3w-Cep


title: He-5-3w-Cep


title: Mtg-4-3w-Cep


title: He-4-3w-Cep


title: He-3-3w-Cep


title: He-2-3w-Cep


title: He-1-3w-Cep


title: B6-5-3w-Cep


title: B6-2-3w-Cep


title: Patient tissue 2

city: Harbin

first: jiangtian

last: Tian

state: Heilongjiang

address: 246 Xuefu Road

institute: The  Second Affiliated Hospital of Harbin Medical University

description:
Library name: Sample 4
Psor_2

data_processing:
removing reads containing adapters
removing reads containing polyA and polyG
removing reads containing more than 5% of unknown nucleotides (N)
removing low quality reads containing more than 20% of low quality (Q-value≤20) bases
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCh38
Supplementary files format and content: counts, srpbm values for each Sample

organism: Homo sapiens

source_name: Skin

extract_protocol:
Total RNA was extracted using Trizol reagent (hermofisher, 15596018) following the manufacturer's procedure.
The average insert size for the final cDNA library was 300±50bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Skin

tag: subject status

value: psoriasis patient


title: B6-4-3w-Cep


title: Healthy control 2

description:
Library name: Sample 1
Nor_2

value: healthy control


title: B6-3-3w-Cep


title: Mtg-4-10w-Feces

source_name: Feces

extract_protocol:
Fecal pellets were collected aseptically and placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit  protocol
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)


title: Mtg-2-10w-Feces


title: B6-1-3w-Cep


title: Mtg-5-10w-Feces


title: Patient tissue 3

description:
Library name: Sample 5
Psor_3


title: Patient tissue 1

description:
Library name: Sample 3
Psor_1


title: Mtg-3-10w-Feces


title: Healthy control 3

description:
Library name: Sample 2
Nor_3


title: He-5-10w-Feces


title: ADAMTS1_2

city: beijing

first: wang

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

description:
Library name: T5
T5

data_processing:
FastQC softwae was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include p-value or q-value for each Sample.

extract_protocol:
The totla RNA was extracted  for libraries construction by the Triozol kit according the standard protocol.
Libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer


title: ADAMTS1_3

description:
Library name: T6
T6


title: He-4-10w-Feces


title: ADAMTS1_1

description:
Library name: T4
T4


title: Mtg-2-3w-Cep


title: He-3-10w-Feces


title: Vector_3

description:
Library name: T3
T3


title: Mtg-5-3w-Cep


title: Vector_2

description:
Library name: T2
T2


title: He-2-10w-Feces


title: He-1-10w-Feces


title: Vector_1

description:
Library name: T1
T1


title: B6-5-10w-Feces


title: Mtg-1-10w-Feces


title: 238-C-2

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

description: Library name: Sample3

data_processing:
CellRanger v3.0.2
Assembly: GrCh38
Supplementary files format and content: Raw counts and metadata

molecule: nuclear RNA

source_name: Jejunum

extract_protocol:
Organoids were harvested, and a portion of the graft was flash frozen in liquid nitrogen. Human duodenal surgical sample was dissected and flash frozen in liquid nitrogen. Single nucleus extractions were performed on flash frozen organoids using the Minute Detergent Free Single Nucleus Isolation Kit (Invent Biotechnologies, Inc.). The manufacturer’s instructions were followed, with a few modifications. Buffer A was supplemented with 100 Units of Protector RNAse Inhibitor (Roche), 1 μM DTT (Invitrogen), and 8x10-5 M Leptomycin B (Cell Signaling). Buffer B was supplemented with 110 Units of Protector RNAse Inhibitor and 8x10-5 M Leptomycin B. After the final spin in Buffer A, the nuclei were fixed in Riley’s Buffer (PBS supplemented with 1% BSA,146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM Mg Cl2, 20 Units of SUPERaseIn (Invitrogen), and 8x10-5 M Leptomycin B) supplemented with 0.1% PFA. After fixation, the nuclei were centrifuged at 500g for four minutes, resuspended in Riley’s Buffer without PFA, and centrifuged again at 500g for four minutes. After centrifuging the nuclei in Buffer B as directed by the manufacturer’s protocol, the nuclei were resuspended in Nuclear Storage Buffer (PBS supplemented with 1% BSA, 200 Units of Protector RNAse Inhibitor, and 8x10-5 M Leptomycin B). An aliquot of the nuclei was stained with Trypan Blue, and nuclear concentration was determined using a TC20 Automated Cell Counter. Nuclei were assessed for intactness using a Nikon Eclipse Ti prior to submission to the Single Cell Genomics Core at CCHMC for 10x sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Jejunum

value: mixed

value: WT


title: B6-4-10w-Feces

value: ten weeks old, wild-type nursing dam


title: 238-C-1

description: Library name: Sample2


title: 238-B

description: Library name: Sample1


title: A375 cell, Ozonated olive oil, 6h_3

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Hokkaido university

description: Library name: A375_OZO_6h_3

data_processing:
RNA-seq reads were preprocessed with bcl2fastq and FastQC software (v. 0.11.7) and aligned to hg38 reference genome with HISAT2 (v. 2.1.0)
StringTie algorithm (v.1.3.4d) was then used with default parameter settings to assemble RNA-Seq alignments into annotated transcripts to estimate their expression using the UCSC annotated human genome (hg38) assembly files.
Transcript expression was normalized using the transcripts per million (TPM) algorithms.  For differential expression analysis, we used featurecounts (v2.1.1+galaxy0) and limma-voom (v3.58.1+galaxy0).
For analysis and interpretation, we used SAMtools (v.1.9), BEDTools (v.2.27.1), Seqkit (version 0.13.2), RSeQC (v.3.0.1), and Ngsplot (v.2.6.3).
Assembly: hg38
Supplementary files format and content: Text files include TPM values for each Sample

growth_protocol: A375 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-aldrich) contained 10% fetal bovine serum (FBS; cosmobio) at 37℃ in humidified 5% CO2/95% air atmosphere.

extract_protocol:
Total mRNA was extracted by using Tri reagent (Trizol; Sigma-aldrich) according to manufacturer's protocol
RNA libraries for RNA-seq were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's manual. After which library quality was further assessed using the TapeStation 4200 with High sensitivity D1000 Screen Tape (Agilent Technologies).

treatment_protocol: Cells were cultured in presence of 0.01% ozonated olive oil or olive oil for 6h.

value: Melanoma

value: ozonated olive oil-treated for 6h


title: B6-2-10w-Feces

value: Untreated


title: Mtg-5-6w-Feces

value: MLCKtg


title: Mtg-4-6w-Feces

value: six weeks old, wild-type nursing dam


title: A375 cell, Olive oil, 6h_2

description: Library name: A375_OLO_6h_2

value: olive oil-treated for 6h


title: Mtg-3-6w-Feces


title: A375 cell, Ozonated olive oil, 6h_2

description: Library name: A375_OZO_6h_2


title: B6-1-10w-Feces


title: Mtg-2-6w-Feces


title: A375 cell, Ozonated olive oil, 6h_1

description: Library name: A375_OZO_6h_1


title: Mtg-1-6w-Feces


title: He-5-6w-Feces

value: Hetro (Tg/+)


title: He-4-6w-Feces


title: He-3-6w-Feces


title: Hu-P-5087

city: Foster City

first: Mengshu

last: Xu

state: California

address: 300 Lakeside Drive

institute: Gilead Sciences

description:
Library name: SAM002044
Column name in TPM_counts.txt file same as library name

data_processing:
A Nextflow pipeline was developed for quality control and gene expression profiling. Multiple quality control steps were performed using FastQC (v0.11.8), RNA-SeQC2 (v2.4.2) and MultiQC (v1.10.1) to ensure high quality sequencing data for downstream analysis.
Sequencing reads were aligned to Genecode GRCh38.v38 reference genome using STAR (2.5.3a).
Gene-wise TPM and expected read counts were generated using RSEM (v1.3.1)
Assembly: GRCh38.v38
Supplementary files format and content: Tab delimited file containing TPM values for each sample

source_name: tumor

growth_protocol: FFPE blocks of patient tumor tissues were procured from commercial sources

extract_protocol:
RNA were extracted from four 10µm sections from each FFPE block using the Qiagen AllPrep FFPE Kit (Cat no. 80234; Qiagen, Germantown, MD, USA) following the manufacturer’s protocol
For RNA-seq, RNA concentration and integrity were assessed using the Qubit fluorometer with the RNA High Sensitivity Assay Kit (Cat no. Q32852; ThermoFisher Scientific, Waltham, MA, USA) and using the Fragment Analyzer with Agilent High Sensitivity RNA Kit (Cat no. DNF-472; Agilent Technologies, Santa Clara, CA, USA). RNA was used as an input material for library construction using Illumina RNA Prep with Enrichment (L) Tagmentation Kit with the Illumina Exome Panel (Cat no. 20040537 and Cat no. 20020183; Illumina, San Diego, CA, USA) following the manufacturer’s protocol. The libraries were multiplexed and then sequenced on either the Illumina NextSeq2000 or NovaSeq6000 (Illumina, San Diego, CA, USA), generating 2x100bp-paired end reads with a mean aligned pair-read count of 28 Million reads per sample.

treatment_protocol: No treatment

value: tumor

value: Colorectal cancer


title: Hu-P-5085

description:
Library name: SAM002042
Column name in TPM_counts.txt file same as library name


title: Periodontal ligament, immature

city: Xi’an

first: Xin

last: Shao

address: 98 Xiwu Road

institute: Xi’an Jiaotong University

description:
Library name: Sample 1
10× Genomics

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (Version 6.1.2) Pipeline coupled with human reference version GRCh38-2020-A. The output filtered gene expression matrices were analyzed by R software (Version 4.3.1) with the Seurat package (Version 4.4.0). A custom R script was used to combine the expression data and metadata from all libraries corresponding to a single batch, and ceslls with fewer 200 Features were removed. The expression data matrix was loaded into a Seurat object along with the library metadata for downstream processing. The precentage of mitochondrial transcripts for each cell (percent.mito) was calculated and added as metadata to the Seurat object. Cells were further filtered before dimensionality reduction(nGene-min. 200; percent.mito-max. 10%). Expression values were then scaled to 10,000 transcripts per cells and Log-transformed. Effects of variable (percent.mito) was estimated and regressed out using a GLM(ScaleData function, model.use=”linear”), and the scaled and centred residuals were used for dimensionality reduciton and clustering.
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: periodontal ligament

extract_protocol:
Tissues were digested containing collagenaseⅠ(3mg/ml) and Dispase Ⅱ (4mg/ml) at 37℃. Counted every 10 minutes, the dissociated cells were passed through a 70μm filter, centrifuged at 400g at 4℃ for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 5 min to lyse red blood cells. After cracking red, the reaction was terminated with PBS+2%FBS. Centrifuged at 400g at 4℃ for 5 min. Then discard the supernatant and re-suspend, centrifuged at 300g at 4℃ for 5 min, discard the supernatant and re-suspend, the dissociated cells were passed through a 40μm filter element, and counted by Countstar automatic counter (Countstar Rigel S5).
We loaded around 17000 cells into the 10x Chromium Controller. We used the Single-Cell 3′ Reagent Kit v3.1 according to the manufacturer’s protocol. GEM-Reverse Transcription (GEM-RT) was performed in a thermal cycler: 53℃ for 45 min, 85℃ for 5 min, and held at 4℃(P24-P31).After reverse transcription and cell barcoding, emulsions were broken and cDNA was isolated and purified with Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific), followed by PCR amplification. The cDNA was then evaluated using the Agilent Bioanalyzer. For RNA-seq library construction, amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected (P32-P38). Libraries prepared according to the manufacturer’s user guide were purified and profiled for quality assessment. Single-cell RNA library was sequenced by an Illumina NovaSeq 6000 sequencer with 150 bp paired-end reads (P39-51).

value: periodontal ligament

value: no

value: Periodontal ligament cells

tag: developmental stage

value: Immature


title: Periodontal ligament, mature

description:
Library name: Sample 2
10× Genomics

value: Mature


title: Hu-P-5084

description:
Library name: SAM002041
Column name in TPM_counts.txt file same as library name


title: B6-3-10w-Feces


title: B6-5-6w-Feces


title: He-1-6w-Feces


title: Hu-P-5083

description:
Library name: SAM002040
Column name in TPM_counts.txt file same as library name


title: A375 cell, Olive oil, 6h_3

description: Library name: A375_OLO_6h_3

value: Skin


title: B6-4-6w-Feces


title: Hu-P-5080

description:
Library name: SAM002037
Column name in TPM_counts.txt file same as library name


title: Hu-P-5081

description:
Library name: SAM002038
Column name in TPM_counts.txt file same as library name


title: B6-3-6w-Feces


title: A375 cell, Olive oil, 6h_1

description: Library name: A375_OLO_6h_1

value: WT


title: B6-1-6w-Feces


title: Hu-P-5082

description:
Library name: SAM002039
Column name in TPM_counts.txt file same as library name


title: Hu-P-5079

description:
Library name: SAM002036
Column name in TPM_counts.txt file same as library name


title: Mtg-4-3w-Feces

value: three weeks old, before weaning


title: Hu-P-5078

description:
Library name: SAM002035
Column name in TPM_counts.txt file same as library name


title: Mtg-3-3w-Feces


title: Hu-P-5077

description:
Library name: SAM002034
Column name in TPM_counts.txt file same as library name


title: Hu-P-5076

description:
Library name: SAM002033
Column name in TPM_counts.txt file same as library name


title: Mtg-5-3w-Feces


title: Hu-P-5088

description:
Library name: SAM002045
Column name in TPM_counts.txt file same as library name


title: Hu-P-5075

description:
Library name: SAM002032
Column name in TPM_counts.txt file same as library name


title: Hu-P-5074

description:
Library name: SAM002031
Column name in TPM_counts.txt file same as library name


title: He-2-6w-Feces


title: Mtg-2-3w-Feces


title: Mtg-1-3w-Feces


title: He-4-3w-Feces


title: Hu-P-5073

description:
Library name: SAM002030
Column name in TPM_counts.txt file same as library name


title: Hu-P-5071

description:
Library name: SAM002028
Column name in TPM_counts.txt file same as library name


title: He-2-3w-Feces


title: Hu-P-5072

description:
Library name: SAM002029
Column name in TPM_counts.txt file same as library name


title: He-3-3w-Feces


title: He-1-3w-Feces


title: Hu-P-5070

description:
Library name: SAM002027
Column name in TPM_counts.txt file same as library name


title: B6-2-6w-Feces


title: Hu-P-5069

description:
Library name: SAM002026
Column name in TPM_counts.txt file same as library name


title: B6-4-3w-Feces


title: Hu-P-0719

description:
Library name: SAM002025
Column name in TPM_counts.txt file same as library name


title: Hu-P-0712

description:
Library name: SAM002022
Column name in TPM_counts.txt file same as library name


title: B6-5-3w-Feces


title: Hu-P-0713

description:
Library name: SAM002023
Column name in TPM_counts.txt file same as library name


title: Hu-P-0714

description:
Library name: SAM002024
Column name in TPM_counts.txt file same as library name


title: Hu-P-0710

description:
Library name: SAM002020
Column name in TPM_counts.txt file same as library name


title: B6-1-3w-Feces


title: Hu-P-0708

description:
Library name: SAM002018
Column name in TPM_counts.txt file same as library name


title: B6-3-3w-Feces


title: B6-2-3w-Feces


title: Hu-P-0709

description:
Library name: SAM002019
Column name in TPM_counts.txt file same as library name


title: Hu-P-0203

description:
Library name: SAM002017
Column name in TPM_counts.txt file same as library name


title: Hu-P-0202

description:
Library name: SAM002016
Column name in TPM_counts.txt file same as library name


title: He-5-3w-Feces


title: Hu-P-0809

description:
Library name: SAM002015
Column name in TPM_counts.txt file same as library name


title: Hu-P-0807

description:
Library name: SAM002013
Column name in TPM_counts.txt file same as library name


title: Hu-P-0808

description:
Library name: SAM002014
Column name in TPM_counts.txt file same as library name


title: Hu-P-0810

description:
Library name: SAM002009
Column name in TPM_counts.txt file same as library name


title: Hu-P-0237

description:
Library name: SAM002006
Column name in TPM_counts.txt file same as library name


title: Hu-P-3635

description:
Library name: SAM002000
Column name in TPM_counts.txt file same as library name


title: Hu-P-3634

description:
Library name: SAM001999
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown,  blue light treatment, IgG, rep1

city: WEST LAFAYETTE

first: Weake

middle: Marie

last: Vikki

state: IN

address: 175 S University st

department: Biochemistry

institute: Purdue University

description:
Library name: mCherryBL_IgG_rep1
PE180

data_processing:
Raw fq.gz files are acquired from Indiana University Medical Genomics Core. Trimmomatic version 0.39 is used to trim the paired-end reads with the following condition:ILLUMINACLIP:NebAdaptors.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads are aligned to Drosophila melanogaster genome dm6 by bowtie2 with the –dovetail argument. Samtools version 1.17 is used to convert sam files to bam files, and to sort, index bam files.
Assembly: dm6
Supplementary files format and content: Processed files are bigWig files generated using bamCoverage from bam files.
Library strategy: CUT&Run

organism: Drosophila melanogaster

source_name: Out photoreceptor

extract_protocol:
We affinity enriched photoreceptor nuclei for DNA isolation as previously described (Jauregui-Lozano et al., 2021, Genetics). CUT&RUN was performed on bead-bound nuclei as described in (Meers et al. 2019) using pAG-MNase fusion protein (Addgene plasmid #123461) purified using the Pierce cobalt kit (ThermoFisher, PierceTM His Protein Interaction Pull-Down Kit, Cat. #21227).
CUT&RUN libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina®.

value: Out photoreceptor

value: Nuclei

value: Blue light treatment


title: mCherry knockdown,  blue light treatment, IgG, rep2

description:
Library name: mCherryBL_IgG_rep2
PE181


title: Hu-P-3651

description:
Library name: SAM001977
Column name in TPM_counts.txt file same as library name

value: Breast cancer


title: Hu-P-3633

description:
Library name: SAM001998
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown,  blue light treatment, H3K4me3, rep3

description:
Library name: mCherryBL_H3K4me3_rep3
PE179


title: mCherry knockdown,  blue light treatment, IgG, rep3

description:
Library name: mCherryBL_IgG_rep3
PE182


title: Hu-P-3649

description:
Library name: SAM001975
Column name in TPM_counts.txt file same as library name


title: Hu-P-3650

description:
Library name: SAM001976
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown,  blue light treatment, H3K4me3, rep2

description:
Library name: mCherryBL_H3K4me3_rep2
PE178


title: mCherry knockdown,  blue light treatment, H3K4me3, rep1

description:
Library name: mCherryBL_H3K4me3_rep1
PE177


title: non-fibrotic MASLD 3

type: RNA

city: Catania

first: Grete Francesca

last: Privitera

address: Via Santa Sofia

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Catania

description: Gene expression data from intestinal organoids isolated from duodenal tissue of non-fibrotic MASLD patients

hyb_protocol: Each sample was combined with a hybridization mix with the appropriate amount of components for a 49-format array. 200 μL of the mixture were loaded into single human Clariom D arrays and placed into an Affymetrix GeneChip Hybridization Oven 645 at 45 °C and rotated at 60 rpm for 16 h.

scan_protocol: Arrays were stained using an Affymetrix GeneChip Fluidics Station 450 using the specific fluidics protocol (FS450_0001) and scanned with an Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw intensity CEL files generated by GeneChip™Command Console™ were imported into Transcriptome Analysis Suite (TAC) 4.0 (Applied Biosystems). Microarray data normalization and Differentially Expressed (DE) coding and non-coding RNA identification was performed by using Transcriptome Analysis Console (TAC) Software v.4, according to the following parameters: Analysis Type: Expression Gene; Summarization Method: Gene Level - RMA. Gene-Level P-Value < 0.05 ANOVA Method: ebayes.

label: biotin

source_name: intestinal organoids isolated from non-fibrotic MASLD patient

label_protocol: Approximately 5.5 μg of ss-cDNA were obtained and then was fragmented using uracil DNA-glycosylase (10 U/μL) and apurinic/apyrimidinic endonuclease 1 (1.000 U/μL). Samples were then labeled with biotin using terminal deoxynucleotidyl transferase (30 U/μL).

growth_protocol: Isolated intestinal organoids were incubated at 37°C, 5% CO2. The organoid growth medium was changed every three days. After 7–10 days, organoid cultures were passaged. For all experiments, organoids were used at passages 3 to 6.

extract_protocol: Total RNA was isolated from organoids through the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: no treatment


title: Hu-P-3648

description:
Library name: SAM001974
Column name in TPM_counts.txt file same as library name


title: M_CRM_4_R1

city: SAN ANTONIO

first: Sijia

last: He

state: Texas

address: 7703 Floyd Curl Dr.

institute: uthealth sa

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max machine Profiler (NanoString Technologies, USA).

hyb_protocol: Hybridization reactions were performed in a 65°C thermal cycler for at least 16 hours

scan_protocol: Scan were performed with the nCounter Max Analysis System.

data_processing: Data were analyzed using nSolver 4.0 software. Basic analysis included the default Normalization Parameters which consisted of Positive Control Normalization Parameters and CodeSet Content.  Both parameters included a geometric mean calculation that flags samples if their normalization factor is outside of the 0.3-3.0 range or 0.1-1.0 range, respectively.  All pairwise ratios were selected for the Fold Change Estimation. Advanced analysis included custom analysis including pathway scoring and probe descriptive modules.  Default settings were used except selecting genotype as the selected predictor and pathway score annotation. P-value adjustments (Benjamini Hochberg) and “use all probes” were selected under the section of differential profiling and cell type profiling.

source_name: Cerebrum

label_protocol: RNA sample were not labeled as the NanoString panel contains labeled probes.

growth_protocol: Mice were housed in groups of ≤5 mice/cage in a temperature and humidity-controlled environment under a 12-h light /12-h dark cycle.

extract_protocol: Tissues were harvested at about 17 month of age post cardiac perfusion, snap-frozen, and homogenized for total RNA extraction.

treatment_protocol: Tamoxifen was administered to induce ST deficiency at 3 month of age.

tag: species

tag: Sex

value: Male

value: Cre+/Trem2 KO


title: M_CRM_4_R3


title: MASLD-cirrhosis 2

description: Gene expression data from intestinal ogranoids isolated from duodenal tissue of MASLD-cirrotic patients

source_name: intestinal organoids isolated from MASLD-cirrhosis patient

value: intestinal organoids isolated from duodenal tissue


title: M_CRM_4_R2


title: non-fibrotic MASLD 4


title: non-fibrotic MASLD 5


title: MASLD-cirrhosis 5


title: non-fibrotic MASLD 2


title: Hu-P-3647

description:
Library name: SAM001973
Column name in TPM_counts.txt file same as library name

value: tumor


title: MASLD-cirrhosis 3


title: MASLD-cirrhosis 4


title: MASLD-cirrhosis 1


title: Hu-P-3644

description:
Library name: SAM001971
Column name in TPM_counts.txt file same as library name


title: Hu-P-3643

description:
Library name: SAM001970
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown,  blue light treatment, H3K27me3, rep2

description:
Library name: mCherryBL_H3K27me3_rep2
PE175


title: Hu-P-3642

description:
Library name: SAM001969
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown,  blue light treatment, H3K27me3, rep1

description:
Library name: mCherryBL_H3K27me3_rep1
PE174


title: mCherry knockdown, no blue light treatment, IgG, rep1

description:
Library name: mCherry_IgG_rep1
PE171

value: No treatment


title: mCherry knockdown,  blue light treatment, H3K27me3, rep3

description:
Library name: mCherryBL_H3K27me3_rep3
PE176


title: M_CRM_2_R3

value: Cre+/Trem2 WT


title: M_CRM_3_R1

value: Cre-/Trem2 KO


title: M_CRM_3_R2


title: M_CRM_2_R2


title: mCherry knockdown, no blue light treatment, IgG, rep3

description:
Library name: mCherry_IgG_rep3
PE173


title: non-fibrotic MASLD 1


title: M_CRM_1_R1

value: Cre-/Trem2 WT


title: M_CRM_3_R3


title: M_CRM_1_R3


title: mCherry knockdown, no blue light treatment, IgG, rep2

description:
Library name: mCherry_IgG_rep2
PE172


title: Hu-P-3639

description:
Library name: SAM001967
Column name in TPM_counts.txt file same as library name


title: Hu-P-3640

description:
Library name: SAM001968
Column name in TPM_counts.txt file same as library name


title: F_SC_4_R3

source_name: Spinal cord

value: Female


title: F_SC_4_R2


title: M_CRM_2_R1


title: Hu-P-3636

description:
Library name: SAM001964
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown, no blue light treatment, H3K4me3, rep1

description:
Library name: mCherry_H3K4me3_rep1
PE169


title: F_SC_3_R2


title: F_SC_4_R1

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max Profiler (NanoString Technologies, USA).


title: Hu-P-3591

description:
Library name: SAM001963
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown, no blue light treatment, H3K4me3, rep3

description:
Library name: mCherry_H3K4me3_rep3
PE170


title: Hu-P-3590

description:
Library name: SAM001962
Column name in TPM_counts.txt file same as library name


title: mCherry knockdown, no blue light treatment, H3K27me3, rep3

description:
Library name: mCherry_H3K27me3_rep3
PE168


title: F_SC_3_R3

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max machine Profiler (NanoString Technologies, USA).


title: F_SC_3_R1


title: F_SC_2_R2


title: Hu-P-3589

description:
Library name: SAM001961
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown,  blue light treatment, IgG, rep3

description:
Library name: AhcyBL_IgG_rep3
PE166


title: mCherry knockdown, no blue light treatment, H3K27me3, rep2

description:
Library name: mCherry_H3K27me3_rep2
PE167


title: F_SC_1_R3


title: F_SC_1_R2


title: Ahcy knockdown,  blue light treatment, IgG, rep2

description:
Library name: AhcyBL_IgG_rep2
PE165


title: Hu-P-3587

description:
Library name: SAM001959
Column name in TPM_counts.txt file same as library name


title: F_SC_1_R1


title: Ahcy knockdown,  blue light treatment, IgG, rep1

description:
Library name: AhcyBL_IgG_rep1
PE164


title: Hu-P-3586

description:
Library name: SAM001958
Column name in TPM_counts.txt file same as library name


title: F_CRM_4_R3


title: F_CRM_4_R1


title: F_CRM_4_R2


title: Ahcy knockdown,  blue light treatment, H3K4me3, rep3

description:
Library name: AhcyBL_H3K4me3_rep3
PE163


title: F_CRM_3_R3


title: F_CRM_3_R2


title: Hu-P-3585

description:
Library name: SAM001957
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown,  blue light treatment, H3K4me3, rep2

description:
Library name: AhcyBL_H3K4me3_rep2
PE162


title: Hu-P-1467

description:
Library name: SAM001954
Column name in TPM_counts.txt file same as library name


title: F_SC_2_R1


title: F_SC_2_R3


title: F_CRM_2_R3


title: F_CRM_3_R1


title: Ahcy knockdown,  blue light treatment, H3K4me3, rep1

description:
Library name: AhcyBL_H3K4me3_rep1
PE161


title: Hu-P-1466

description:
Library name: SAM001953
Column name in TPM_counts.txt file same as library name


title: F_CRM_2_R2


title: Ahcy knockdown,  blue light treatment, H3K27me3, rep3

description:
Library name: AhcyBL_H3K27me3_rep3
PE160


title: Hu-P-1465

description:
Library name: SAM001952
Column name in TPM_counts.txt file same as library name


title: F_CRM_1_R2


title: Ahcy knockdown,  blue light treatment, H3K27me3, rep2

description:
Library name: AhcyBL_H3K27me3_rep2
PE159


title: Liver, cell line, infected with WT HEV, control, late time point

city: Heidelberg

first: CARL

last: HERRMANN

state: Baden-Wurtemberg

address: INF 364

department: Institut für Pharmazie und Molekulare Biotechnologie

country: Germany

institute: CRomLab

description:
Library name: WTL
10x Genomics

data_processing:
Fastq files were aligned and counted using the cell ranger 7.1.0 pipeline. As human genome reference we used GRCh38-3.0.0
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: cytoplasmic RNA

source_name: Liver cell line

growth_protocol: HepG2/C3A cells were grown on collagen-coated cell culture ware at 37 °C in a 95% humidified environment and 5% CO2.

extract_protocol:
At respective time points, cells were trypsinized for 10 min, gently resuspend, and singularized by pipetting three times through a 70 µm cell strainer. Single-cell suspension were resuspended in appropriate volumes of 0.04% BSA/PBS, counted, and loaded onto the 10x Chromium controller according to manufacturer's instructions. The targeted cell recovery was 5,000.
Libraries were constructed and pooled accrording to the manufacturer's instructions of the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) Kit.

treatment_protocol: HepG2/C3A cells were infected with HEV virus particles by binding at 4 °C for 2 h and internalization at 37 °C for 8 h.

value: Liver cell line

value: Hepatocyte

value: Infected with WT HEV

tag: time point

value: Late

value: batch 2


title: Liver, cell line, infected with WT HEV, control, early time point

description:
Library name: WTE
10x Genomics

tag: tissue

value: WT

value: Early

value: batch 1


title: Ahcy knockdown,  blue light treatment, H3K27me3, rep1

description:
Library name: AhcyBL_H3K27me3_rep1
PE158

value: Out photoreceptor

value: Nuclei

value: Blue light treatment


title: F_CRM_1_R1

tag: genotype


title: Liver, cell line, infected with mutant HEV, control, early time point

description:
Library name: orf2E2
10x Genomics

value: Mutant HEV


title: Liver, cell line, untreated, control, late time point

description:
Library name: MockL
10x Genomics

value: Control


title: Ahcy knockdown, no blue light treatment, IgG, rep3

description:
Library name: Ahcy_IgG_rep3
PE157

value: No treatment


title: TOP3BKO_HT1080_S6

city: Bethesda

first: Anjali

last: Dhall

state: MD

address: 37 Convent Drive

department: DTB

institute: NCI

description:
Library name: Sample6
dual index (101x8x8x101)

data_processing:
Salmon quant (version 1.10.1) tool used for quantifying transcript expression in RNA-seq data
Assembly: hg19
Supplementary files format and content: Read count and normalized RPKM expression matrix for WT and TOP3BKO HT1080 cell line.

source_name: fibrosarcoma tumor in the connective tissue

growth_protocol: HT1080 cell lines were grown in Dulbecco’s modified Eagle’s medium (Life Technologies, Carlsbad, CA) supplemented with 10% Fetal Bovine Serum (Gemini, West Sacramento, CA, 100–106) and 1% penicillin-streptomycin (ThermoFisher Scientific, 15140122) at 37°C in humidified 5% CO2 chamber.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), followed by further purification using PureLink RNA Mini Kit (Cat No. 12183018A;Invitrogen) with DNase treatment (QIAGEN). RNA quality and quantity were analyzed with 2100 Expert (Agilent). RIN (the RNA Integrity Number) of all samples were above 8.0.
NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB #E7400) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) were used. NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB, E6440) were used with 13 cycles of PCR amplification. The final 750 pM library was sequenced paired-end with dual index (101x8x8x101) using the Illumina NextSeq2000 P2 Reagents (200cycles) on the Illumina NextSeq2000 instrument. The total number of reads was 550M (see below for individual sample).

value: HT1080 Cell line

value: Human  fibrosarcoma cell

value: TOP3B Knock out


title: Liver, cell line, untreated, control, early time point

description:
Library name: MockE
10x Genomics

value: Liver cell line


title: Hu-P-1116

description:
Library name: SAM001948
Column name in TPM_counts.txt file same as library name

value: tumor

value: Breast cancer


title: TOP3BKO_HT1080_S5

description:
Library name: Sample5
dual index (101x8x8x101)

value: fibrosarcoma tumor in the connective tissue


title: Hu-P-1117

description:
Library name: SAM001949
Column name in TPM_counts.txt file same as library name


title: F_CRM_2_R1

value: Female

value: Cre+/Trem2 WT


title: TOP3BKO_HT1080_S4

description:
Library name: Sample4
dual index (101x8x8x101)


title: WT_HT1080_3_S3

description:
Library name: Sample3
dual index (101x8x8x101)

value: Wild Type


title: Hu-P-1115

description:
Library name: SAM001947
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown, no blue light treatment, IgG, rep2

description:
Library name: Ahcy_IgG_rep2
PE156


title: Hu-P-1114

description:
Library name: SAM001946
Column name in TPM_counts.txt file same as library name


title: Hu-P-3588

description:
Library name: SAM001960
Column name in TPM_counts.txt file same as library name


title: WT_HT1080_2_S2

description:
Library name: Sample2
dual index (101x8x8x101)


title: Hu-P-1462

description:
Library name: SAM001950
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown, no blue light treatment, H3K4me3, rep3

description:
Library name: Ahcy_H3K4me3_rep3
PE154


title: 08_E2_4_TOP3BKO_HCT116

description:
Library name: Sample8
dual index (60x8x8x60)

data_processing:
BAM files were generated using BWA aligner and picrad tool used to filter and remove duplicate reads.
MACS2 algorithm was used for peak calling
Assembly: hg19
Supplementary files format and content: Bed file format showing: WT and TOP3B KO peak calling files for HCT116 and HT1080 cell lines.
Supplementary files format and content: BigWig file format of DRIP-seq dataset
Library strategy: DRIP-seq

source_name: Colon

growth_protocol: HCT116 and HT1080 cell lines were grown in Dulbecco’s modified Eagle’s medium (Life Technologies, Carlsbad, CA) supplemented with 10% Fetal Bovine Serum (Gemini, West Sacramento, CA, 100–106) and 1% penicillin-streptomycin (ThermoFisher Scientific, 15140122) at 37°C in humidified 5% CO2 chamber.

extract_protocol:
Genomic DNA from cell cultures were purified after SDS and Pro-K mediated lysis, fragmented using a mix of restriction enzymes (HindIII, SspI, EcoRI, BsrGI and  XbaI), subjected to S9.6 antibody immunoprecipitation and sonication as described in Sanz et al., 2021, journal of Visualized Experiments.
The kits used for the library prep were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440) were used with 13 cycles of PCR amplification. The final 750 pM library was sequenced paired-end with dual index (60x8x8x60) using the Illumina NextSeq2000 P2 Reagents (100cycles) on the Illumina NextSeq2000 instrument.
DNA: RNA Immunoprecipitation using S9.6 antibody followed by high-throughput sequencing (DRIP-seq)

value: Colon

value: HCT116 Cell line

value: Human colon cancer cell line


title: Hu-P-1112

description:
Library name: SAM001944
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown, no blue light treatment, H3K4me3, rep1

description:
Library name: Ahcy_H3K4me3_rep1
PE153

value: Out photoreceptor

value: Nuclei


title: 07_WT_HCT116

description:
Library name: Sample7
dual index (60x8x8x60)


title: 06_E2_2_TOP3BKO_HT1080

description:
Library name: Sample6
dual index (60x8x8x60)

value: Human  fibrosarcoma cell lie


title: Hu-P-1109

description:
Library name: SAM001941
Column name in TPM_counts.txt file same as library name


title: F_CRM_1_R3

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max machine Profiler (NanoString Technologies, USA).

value: Cre-/Trem2 WT


title: 04_E2_4_TOP3BKO_HCT116

description:
Library name: Sample4
dual index (60x8x8x60)


title: Hu-P-1108

description:
Library name: SAM001940
Column name in TPM_counts.txt file same as library name


title: Ahcy knockdown, no blue light treatment, H3K27me3, rep3

description:
Library name: Ahcy_H3K27me3_rep3
PE152

value: No treatment


title: 03_WT_HCT116

description:
Library name: Sample3
dual index (60x8x8x60)


title: Ahcy knockdown, no blue light treatment, H3K27me3, rep2

description:
Library name: Ahcy_H3K27me3_rep2
PE151


title: 02_E2_2_TOP3BKO_HT1080

description:
Library name: Sample2
dual index (60x8x8x60)

value: HT1080 Cell line


title: Hu-P-1107

description:
Library name: SAM001939
Column name in TPM_counts.txt file same as library name


title: 01_WT_HT1080

description:
Library name: Sample1
dual index (60x8x8x60)


title: Ahcy knockdown, no blue light treatment, IgG, rep1

description:
Library name: Ahcy_IgG_rep1
PE155


title: Ahcy knockdown, no blue light treatment, H3K27me3, rep1

description:
Library name: Ahcy_H3K27me3_rep1
PE150


title: Retina, Foxn3KO, E19, replicate 2

city: Ann Arbor

first: David

last: Turner

state: MI

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

description:
Library name: RNAseq_Foxn3KO2
column name in All_samples_DEG.txt: Foxn3_KO_2

data_processing:
Illumina BCL Convert Conversion Software v4.0 was used to generate de-multiplexed Fastq files.
While the RNA-seq libraries used adaptors with 11nt UMIs, the UMIs were not used for the analysis. The 11nt UMIs are included as part of the sequence names in the R1/R2 fastq files, with the original index/UMI reads in the I1 fastq files.
RNA-seq reads were mapped to mm39 using star. Differential expression of genes and fpkm values based on mapped reads were determined with DEseq2.
Assembly: mm39
Supplementary files format and content: All_samples_DEG.txt: text matrix file (tab delimited) with gene expression data by gene.
Supplementary files format and content: Data columns: Gene_symbol, Gene_id, baseMean_expression, fold_change(log2), std_error, pvalue, adjusted_pvalue, FPKM(by sample), raw_read counts(by sample)

source_name: retina

extract_protocol:
Retinas from individual genotyped E19 embryos (Foxn3KO with deletion of exon 3, or wild-type) were isolated, and total RNA from each retina was purified using TRIzol (ThermoFisher).
500 ng of total RNA was used to prepare each RNA-seq library using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina and NEB Unique Dual Index UMI Adaptors (New England Biolabs), following the manufacturer’s instructions.

value: retina


title: Retina, Foxn3KO, E19, replicate 1

description:
Library name: RNAseq_Foxn3KO1
column name in All_samples_DEG.txt: Foxn3_KO_1


title: Retina, wild-type, E19, replicate 1

description:
Library name: RNAseq_control1
column name in All_samples_DEG.txt: Foxn3_WT_1

value: wild-type


title: Hu-P-1103

description:
Library name: SAM001935
Column name in TPM_counts.txt file same as library name

value: tumor


title: Hu-P-1105

description:
Library name: SAM001937
Column name in TPM_counts.txt file same as library name

value: Breast cancer


title: shRNA targets at mCherry, no treatment, rep2

description:
Library name: SCS_11
PE150

data_processing:
Raw fq.gz files are acquired from Indiana University Medical Genomics Core. Trimmomatic version 0.39 is used to trim the paired-end reads with the following condition:ILLUMINACLIP:NebAdaptors.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. Trimmed reads are aligned to Drosophila melanogaster genome dm6 by hisat2 version 2.2.1 with the following seeting --rna-strandness FR. Samtools version 1.17 is used to convert sam files to bam files, and to sort, index bam files. FeatureCounts function in Subread version 2.0.1 is used to count mapped reads using the following setting: -p -t exon ig gene_id
Assembly: dm6
Supplementary files format and content: Processed data files are txt files that contain quantification results of mapped reads for genes using featureCounts.

source_name: Outer photoreceptor

growth_protocol: To knockdown Ahcy in the Drosophila eye, we crossed longGMR-Gal4, Rh1-KASHGFP flies to UAS-RNAi flies targeting either Ahcy (y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.HMC03222}attP40/CyO, Bloomington Stock #51477) or mCherry (control) in a cnbw background. We then collected male progeny, which were raised in 12-hour light: 12-hour dark conditions at 25C until 5 days post-eclosion.

extract_protocol:
We affinity enriched photoreceptor nuclei for RNA isolation as previously described (Jauregui-Lozano et al., 2021, Genetics). Nuclear RNA was purified using ZYMO Direct-zol RNA Microprep Kits (#R2061).
RNA library were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S). rRNA was depleted with lab-designed probes using NEBNext® RNA Depletion Core Reagent Set with RNA Sample Purification Beads (E7870L).  Libraries were sequenced using NovaSeq Plus.

treatment_protocol: Flies treated with blue light were secured in a blacked-out box with strip LED lights surrounding the samples and were exposed to continuous blue light for three hours relative to untreated controls.

value: Outer photoreceptor

value: mCherry KD


title: shRNA targets at mCherry, no treatment, rep3

description:
Library name: SCS_12
PE150


title: Retina, wild-type, E19, replicate 2

description:
Library name: RNAseq_control2
column name in All_samples_DEG.txt: Foxn3_WT_2


title: WT_HT1080_1_S1

description:
Library name: Sample1
dual index (101x8x8x101)

value: fibrosarcoma tumor in the connective tissue

value: Human  fibrosarcoma cell


title: Hu-P-1102

description:
Library name: SAM001934
Column name in TPM_counts.txt file same as library name


title: Retina, CD-1, E16, Mouse IgG (control for Foxn4), replicate 2

description:
Library name: CUT_RUN ms-IgG-Foxn4-control-2
E16 embryonic retinas

data_processing:
Illumina BCL Convert Conversion Software v3.9.3 (for Foxn4 and mouse IgG samples) or v4.0 (for all other samples) was used to generate de-multiplexed Fastq files.
Sequences had adaptors trimmed using Cutadapt, then were mapped to the mm10 mouse genome and to the Saccharomyces cerevisiae genome (for yeast spike-in DNA) with bowtie2
Mapped read pairs were deduplicated based on UMIs using UMI-Tools. The 11nt UMIs are listed within the sequence names in the R1/R2 fastq files. The I1 index fastq files contain the index/UMI reads. Mapped paired-end reads were filtered for insert sizes of ≤120nt as recommended for transcription factor peak finding with CUT&RUN. Bedgraph files of read coverage for the mouse genome were generated using bedtools genomecov and normalized based on total yeast spike-in read counts for each library. Peaks of read accumulation were identified using SEACR (Meers et al. 2019, PMID: 3130002) with relaxed peak finding. Peaks were identified from two CUT&RUN libraries for each transcription factor, relative to two matched IgG control libraries. For Foxn3, peaks identified in two separate CUT&RUN experiments (each with two Foxn3 samples and two control samples) were intersected to generate a high confidence set of Foxn3 peaks that was used for subsequent Foxn3 binding region analysis. Peaks were filtered using exclude lists for CUT&RUN (Nordin et al., 2023, PMID: 37563719) and ENCODE Chip-seq (Amemiya et al., 2019, PMID: 31249361); non-chromosomal and chrM mappings also were discarded.
Assembly: mm10
Supplementary files format and content: bed files of SEACR called CUT&RUN peaks.
Supplementary files format and content: BED columns: chr, start, end, name(=peak number and transcription factor), peak_score(from SEACR), strand (always +).
Library strategy: CUT&Run

extract_protocol:
E16 retinas from CD-1 mice were isolated, pooled, and dissociated into single cells using Accutase (Gibco). Approximately 3×10⁵ cells were used for each CUT&RUN assay. Samples were processed using the CUT&RUN Assay Kit (Cell Signaling Technologies 86652S) as directed by the manufacturer for live cell preparations. The Micrococcal Nuclease digestion step was performed at 0° C for 1hr for all samples except for the Foxn4 and mouse IgG control samples, which were digested with Micrococcal Nuclease at 0° C for ~12hrs.
Genomic DNA recovered from the CUT&RUN assay was used to prepare a DNA library using the NEBNext Ultra II DNA Library Prep Kit for Illumina, adhering to the manufacturer’s protocol with the following modifications: after the addition of End Prep Buffer and Enzyme Mix, samples were incubated at 20°C for 30 minutes and subsequently at 50°C for 30 minutes. For ligation, 2.5 µl of 1:50 diluted NEB Unique Dual Index UMI Adaptors were added. Adaptor-ligated DNA was purified using 1.1X volume of NEBNext Sample Purification Beads. Following PCR enrichment, the adaptor-ligated DNA was again purified using a 1.1X volume of beads. The PCR product was separated on a 6% TBE gel (Life Technologies), and a gel slice corresponding to 200–500 bp (determined using size markers in an adjacent lane) was excised. The DNA from the gel slice was eluted, precipitated using 2-propanol, and resuspended in Tris-HCl buffer.

value: Mouse IgG


title: shRNA targets at mCherry, no treatment, rep1

description:
Library name: SCS_10
PE150


title: Retina, CD-1, E16, anti-Foxn4, replicate 2

description:
Library name: CUT_RUN Foxn4-2
E16 embryonic retinas

value: anti-Foxn4 antibody


title: Hu-P-1101

description:
Library name: SAM001933
Column name in TPM_counts.txt file same as library name


title: 05_WT_HT1080

description:
Library name: Sample5
dual index (60x8x8x60)

value: Wild Type


title: Retina, CD-1, E16, anti-Foxn4, replicate 1

description:
Library name: CUT_RUN Foxn4-1
E16 embryonic retinas


title: Retina, CD-1, E16, Rabbit IgG (control for Foxn3 experiment 2), replicate 2

description:
Library name: CUT_RUN rb-IgG-Foxn3-control-4
E16 embryonic retinas

value: Rabbit IgG


title: shRNA targets at Ahcy, no treatment, rep3

description:
Library name: SCS_9
PE150

value: Nuclei

value: Ahcy KD


title: Hu-P-1099

description:
Library name: SAM001932
Column name in TPM_counts.txt file same as library name


title: Retina, CD-1, E16, Mouse IgG (control for Foxn4), replicate 1

description:
Library name: CUT_RUN ms-IgG-Foxn4-control-1
E16 embryonic retinas


title: shRNA targets at Ahcy, no treatment, rep2

description:
Library name: SCS_8
PE150


title: Retina, CD-1, E16, anti-Foxn3(experiment 2), replicate 2

description:
Library name: CUT_RUN Foxn3-4
E16 embryonic retinas

value: anti-Foxn3 antibody


title: Retina, CD-1, E16, Rabbit IgG (control for Foxn3 experiment 2), replicate 1

description:
Library name: CUT_RUN rb-IgG-Foxn3-control-3
E16 embryonic retinas


title: Retina, CD-1, E16, anti-Foxn3(experiment 2), replicate 1

description:
Library name: CUT_RUN Foxn3-3
E16 embryonic retinas


title: M_CRM_1_R2

description: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen, Canada, Cat. #: 25700). NanoString multiplex gene expression analysis was performed using the Mouse Neuroinflammation Panel on the nCounter® Max machine Profiler (NanoString Technologies, USA).

value: Male

value: Cre-/Trem2 WT


title: shRNA targets at Ahcy, no treatment, rep1

description:
Library name: SCS_7
PE150

value: No treatment


title: Hu-P-1090

description:
Library name: SAM001930
Column name in TPM_counts.txt file same as library name


title: Retina, CD-1, E16, Rabbit IgG (control for Rfx3), replicate 1

description:
Library name: CUT_RUN rb-IgG-Rfx3-control-1
E16 embryonic retinas

value: retina


title: Retina, CD-1, E16, Rabbit IgG (control for Rfx3), replicate 2

description:
Library name: CUT_RUN rb-IgG-Rfx3-control-2
E16 embryonic retinas


title: shRNA targets at mCherry, Blue light, rep3

description:
Library name: SCS_6
PE150

value: Blue light


title: Retina, CD-1, E16, anti-Rfx3, replicate 2

description:
Library name: CUT_RUN Rfx3-2
E16 embryonic retinas

value: anti-Rfx3 antibody


title: Hu-P-2139

description:
Library name: SAM001571
Column name in TPM_counts.txt file same as library name

value: tumor

value: HNSC


title: Hu-P-2138

description:
Library name: SAM001570
Column name in TPM_counts.txt file same as library name


title: Retina, CD-1, E16, Rabbit IgG (control for Foxn3 experiment 1), replicate 1

description:
Library name: CUT_RUN rb-IgG-Foxn3-control-1
E16 embryonic retinas


title: shRNA targets at mCherry, Blue light, rep1

description:
Library name: SCS_4
PE150

value: Outer photoreceptor

value: mCherry KD


title: Retina, CD-1, E16, anti-Rfx3, replicate 1

description:
Library name: CUT_RUN Rfx3-1
E16 embryonic retinas


title: Retina, CD-1, E16, anti-Foxn3(experiment 1), replicate 2

description:
Library name: CUT_RUN Foxn3-2
E16 embryonic retinas


title: Hu-P-2136

description:
Library name: SAM001568
Column name in TPM_counts.txt file same as library name


title: shRNA targets at Ahcy, Blue light, rep3

description:
Library name: SCS_3
PE150


title: Hu-P-2137

description:
Library name: SAM001569
Column name in TPM_counts.txt file same as library name


title: shRNA targets at Ahcy, Blue light, rep2

description:
Library name: SCS_2
PE150


title: Hu-P-3842

description:
Library name: SAM001322
Column name in TPM_counts.txt file same as library name


title: shRNA targets at Ahcy, Blue light, rep1

description:
Library name: SCS_1
PE150


title: Hu-P-3841

description:
Library name: SAM001321
Column name in TPM_counts.txt file same as library name


title: Hu-P-1097

description:
Library name: SAM001931
Column name in TPM_counts.txt file same as library name

value: Breast cancer


title: DNA_2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

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: RRC 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: flourescence

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: Total RNA was purified from cells using RNeasy Mini Kit (Qiagen) as per the manufacturer’s protocol. Purified RNA was quantified on a NanoDrop ND-1000 spectrophotometer and diluted in nuclease-free water to 20 ng/uL.

treatment_protocol: For HMC3 cells UA treatment, cells were kept in growth medium containing 10 μM UA for five days and then in medium with 12.5 μM UA for 48 h prior to cGAS-STING stimulation by dsDNA (500 ng).   For gene expression analysis, we used the human neuroinflammation panel (XT-CSO-MNROI1-12).

value: immortalized embryonic microglia

tag: cell name

value: HMC3 cells

value: DNA


title: Hu-P-3840

description:
Library name: SAM001320
Column name in TPM_counts.txt file same as library name

tag: cell type


title: UA+DNA_2

tag: treatment

value: UA+DNA


title: UA+DNA_1


title: 82L, Mouse STR LEFT, female, MG-, no treatment

city: Kuopio

first: Katrina

last: Albert

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

description: Library name: 82-L

data_processing:
Reads in FASTQ format were sorted to human and mouse origin using BBsplit tool and reference genomes GRCh38 and GRCm39, respectively. Transcripts were quantified using Salmon.
Assembly: GRCh38, GRCm39
Supplementary files format and content: Excel files containing normalized counts for each gene by sample, separate files for mouse counts and human counts

organism:
Homo sapiens
Mus musculus

source_name: microglia

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Universal micro kit following the manufacturer’s instructions (Qiagen)
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB)

value: microglia

value: human M-CSF knockin


title: UA _3

source_name: UA _3

value: UA


title: Hu-P-3839

description:
Library name: SAM001319
Column name in TPM_counts.txt file same as library name


title: DNA_1


title: 83R, Mouse STR RIGHT, female, sham, PFF

description: Library name: 83-R

value: PFF


title: shRNA targets at mCherry, Blue light, rep2

description:
Library name: SCS_5
PE150

value: Nuclei


title: Retina, CD-1, E16, anti-Foxn3(experiment 1), replicate 1

description:
Library name: CUT_RUN Foxn3-1
E16 embryonic retinas

value: retina

value: anti-Foxn3 antibody


title: UA _1

source_name: UA _1


title: Retina, CD-1, E16, Rabbit IgG (control for Foxn3 experiment 1), replicate 2

description:
Library name: CUT_RUN rb-IgG-Foxn3-control-2
E16 embryonic retinas

value: Rabbit IgG


title: M39R-P21-3

city: London

first: Rosellina

last: Guarascio

address: 11-43 Bath street

country: United Kingdom

institute: UCL Institute of Ophthalmology

description:
Library name: sample 7
post natal 21

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: Mus Musculus GRCm38
Supplementary files format and content: All the files are in a format of csv containing columns with each sample name and raw read count for each transcript

source_name: Retina

growth_protocol: The RhoM39R line was generated by CRISPR-cas9 HDR technology on C57BL/6J mouse strain. A specific gRNA was used in combination with a donor template containing a change in the spCas9 PAM site (CCA>CTC) and introducing the Met to Arg (ATG>AGG) mutation. Rho+/+ C57BL/6J mice were used as controls.

extract_protocol:
Retinae from Rho+/+ and RhoM39R/M39R at 3 weeks were processed for RNA extraction using an RNeasy MicroKit (QIAGEN)
cDNA synthesis was performed using a Tetro cDNA synthesis kit (Bioline)

value: Retina

value: retinal cells

value: untreated


title: 77L, Mouse STR LEFT, male, MG-, no treatment

description: Library name: 77-L


title: M39R-P25-2

description:
Library name: sample 6
post natal 25


title: 77R, Mouse STR RIGHT, male, MG+, PFF

description: Library name: 77-R


title: Hu-P-3838

description:
Library name: SAM001318
Column name in TPM_counts.txt file same as library name

value: tumor

value: HNSC


title: UA+DNA_3

value: immortalized embryonic microglia


title: Hu-P-3837

description:
Library name: SAM001317
Column name in TPM_counts.txt file same as library name


title: UT_3

value: HMC3 cells

value: control


title: M39R-P25-1

description:
Library name: sample 5
post natal 25


title: UA _2

source_name: UA _2


title: UT_2


title: 70R, Mouse STR RIGHT, female, MG+, PFF

description: Library name: 70-R


title: Hu-P-3835

description:
Library name: SAM001315
Column name in TPM_counts.txt file same as library name

source_name: tumor


title: DNA_3

value: DNA


title: WT-P21-4

description:
Library name: sample 4
post natal 21

value: Rho+/+


title: UT_1


title: 70L, Mouse STR LEFT, female, MG-, no treatment

description: Library name: 70-L

value: microglia

value: human M-CSF knockin


title: Hu-P-3834

description:
Library name: SAM001314
Column name in TPM_counts.txt file same as library name


title: 65R, Mouse STR RIGHT, female, MG+, PFF

description: Library name: 65-R

value: PFF


title: WT-P21-3

description:
Library name: sample 3
post natal 21


title: HEL tumor, BAY 2666605 4

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

description: Library name: Bay_248

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to hg38 using STAR
Gene counting was performed using htseq-count version 0.6 1p1
Differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited file with read counts per gene

source_name: Flank tumor

extract_protocol:
For RNA-seq analysis, four tumors per group from mice bearing HEL flank tumors treated with vehicle control or BAY 2666605 were processed into a single-cell suspension for subsequent isolation of RNA with RNEasy Plus Mini Kit as described by the manufacturer (Qiagen). RNA was reconstituted in RNase-free water. RNA quality and quantity were assessed by Bioanalyzer RNA pico chip and Qubit RNA HS assay kit, respectively.
One thousand nanogram of RNA was used as input for library construction using Illumina stranded total RNA prep with Ribo-zero plus (Illumina 20040529) according to manufacturers’ protocol with the following modification: To retain the ribosomal RNA, we skipped the ribosomal RNA depletion step and started with RNA fragmentation and denaturation directly.

value: Flank tumor

value: HEL

value: Erythroid leukemia cell line

value: WT


title: HEL tumor, BAY 2666605 3

description: Library name: Bay_247


title: Hu-P-3833

description:
Library name: SAM001313
Column name in TPM_counts.txt file same as library name


title: WT-P21-2

description:
Library name: sample 2
post natal 21

value: Retina


title: HEL tumor, BAY 2666605 2

description: Library name: Bay_243


title: Hu-P-3831

description:
Library name: SAM001311
Column name in TPM_counts.txt file same as library name


title: 65L, Mouse STR LEFT, female, MG-, no treatment

description: Library name: 65-L


title: 63R, Mouse STR RIGHT, female, MG+, PFF

description: Library name: 63-R


title: Hu-P-3829

description:
Library name: SAM001309
Column name in TPM_counts.txt file same as library name


title: 63L, Mouse STR LEFT, female, MG-, PFF

description: Library name: 63-L


title: HEL tumor, BAY 2666605 1

description: Library name: Bay_241


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-deficient diet, Rep 2

city: Singapore

first: Valerie Chun Ling

last: Lin

address: 60, Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: Library name: RMB5022

data_processing:
Trim galore was used to trim the FASTQ files for all samples. FASTQC was done on these files.
STAR was used to map the reads to the mouse genome GRCm39
featureCounts were then used to generate the gene counts.
The gene counts were then used for an DESeq2 analysis
Assembly: GRCm39
Supplementary files format and content: xlsx file for raw counts and log2tpm

source_name: Brain hippocampus

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific, USA) and treated with Dnase I using the DNA-free™ DNA Removal Kit (Invitrogen, Carlsbad, CA, USA) to remove any contaminating DNA.
The total RNA was sent to Genome Institute of Singapore, Agency for Science, Technology and Research for library preparation and pair-end sequencing

value: Brain hippocampus


title: Hu-P-3827

description:
Library name: SAM001307
Column name in TPM_counts.txt file same as library name


title: HEL tumor, Vehicle Control 4

description: Library name: Control_246

value: Vehicle control (PEG-400)


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-deficient diet, Rep 1

description: Library name: RMB5021


title: Hu-P-3828

description:
Library name: SAM001308
Column name in TPM_counts.txt file same as library name

value: tumor


title: WT-P21-1

description:
Library name: sample 1
post natal 21

value: retinal cells

value: untreated


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-deficient diet, Rep 3

description: Library name: RMB5023


title: HEL tumor, Vehicle Control 3

description: Library name: Control_244


title: HEL tumor, Vehicle Control 2

description: Library name: Control_242


title: Hu-P-3826

description:
Library name: SAM001306
Column name in TPM_counts.txt file same as library name

value: HNSC


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-Supplement diet, Rep 3

description: Library name: RMB5020


title: 59L, Mouse STR LEFT, female, MG-, no treatment

description: Library name: 59-L


title: HEL tumor, Vehicle Control 1

description: Library name: Control_240


title: Hu-P-3821

description:
Library name: SAM001301
Column name in TPM_counts.txt file same as library name


title: 58R, Mouse STR RIGHT, female, MG+, SAL

description: Library name: 58-R

value: SAL


title: 58L, Mouse STR LEFT, female, MG-, SAL

description: Library name: 58-L


title: Donor5

first: Yudai

last: Miyashita

address: Simpson Querrey 5-402-C 303 E Superior Street

department: Thoracic Surgery

institute: Northwestern Univesity

description: Library name: AB-24-30

data_processing:
Raw sequencing data were processed using Cell Ranger (version 8.0.1) for demultiplexing, alignment to the GRCh38 reference genome, and generation of gene-barcode matrices.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: The processed data files include gene-barcode matrices (barcodes.tsv, features.tsv, matrix.mtx) and Seurat objects (RDS files) for downstream analysis.
Supplementary files format and content: Data are provided in TSV format for raw counts and RDS format for processed Seurat objects, including metadata, clustering information, and expression matrices.

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from human lung tissues using enzymatic digestion (collagenase and DNase) and mechanical dissociation to isolate viable single cells for downstream processing.
Single-cell RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3.1 following the manufacturer's protocols.

treatment_protocol: No specific treatments were applied for the study purpose. Patients received routine post-transplant clinical care, including immunosuppressive therapy, antibiotics, and other medications as clinically indicated.

value: Lung


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-Supplement diet, Rep 1

description: Library name: RMB5018


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Choline-Supplement diet, Rep 2

description: Library name: RMB5019


title: Donor4

description: Library name: AB-24-2


title: 57R, Mouse STR RIGHT, female, MG+, PFF

description: Library name: 57-R


title: Hu-P-3819

description:
Library name: SAM001299
Column name in TPM_counts.txt file same as library name

data_processing:
A Nextflow pipeline was developed for quality control and gene expression profiling. Multiple quality control steps were performed using FastQC (v0.11.8), RNA-SeQC2 (v2.4.2) and MultiQC (v1.10.1) to ensure high quality sequencing data for downstream analysis.
Sequencing reads were aligned to Genecode GRCh38.v38 reference genome using STAR (2.5.3a).
Gene-wise TPM and expected read counts were generated using RSEM (v1.3.1)
Assembly: GRCh38.v38
Supplementary files format and content: Tab delimited file containing TPM values for each sample

extract_protocol:
RNA were extracted from four 10µm sections from each FFPE block using the Qiagen AllPrep FFPE Kit (Cat no. 80234; Qiagen, Germantown, MD, USA) following the manufacturer’s protocol
For RNA-seq, RNA concentration and integrity were assessed using the Qubit fluorometer with the RNA High Sensitivity Assay Kit (Cat no. Q32852; ThermoFisher Scientific, Waltham, MA, USA) and using the Fragment Analyzer with Agilent High Sensitivity RNA Kit (Cat no. DNF-472; Agilent Technologies, Santa Clara, CA, USA). RNA was used as an input material for library construction using Illumina RNA Prep with Enrichment (L) Tagmentation Kit with the Illumina Exome Panel (Cat no. 20040537 and Cat no. 20020183; Illumina, San Diego, CA, USA) following the manufacturer’s protocol. The libraries were multiplexed and then sequenced on either the Illumina NextSeq2000 or NovaSeq6000 (Illumina, San Diego, CA, USA), generating 2x100bp-paired end reads with a mean aligned pair-read count of 28 Million reads per sample.


title: 59R, Mouse STR RIGHT, female, MG+, PFF

description: Library name: 59-R


title: Hu-P-3666

description:
Library name: SAM001293
Column name in TPM_counts.txt file same as library name


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Normal diet, Rep 1

description: Library name: RMB5015


title: 53R, Mouse STR RIGHT, male, MG-, PFF

description: Library name: 53-R


title: 56R, Mouse STR RIGHT, female, MG-, PFF

description: Library name: 56-R


title: Donor3

description: Library name: AB-23-23


title: Hu-P-3814

description:
Library name: SAM001294
Column name in TPM_counts.txt file same as library name


title: Hu-P-3816

description:
Library name: SAM001296
Column name in TPM_counts.txt file same as library name


title: Hu-P-3815

description:
Library name: SAM001295
Column name in TPM_counts.txt file same as library name


title: CLAD3

description: Library name: AB-23-25


title: Donor1

description: Library name: CK-23-4


title: Hu-P-3665

description:
Library name: SAM001292
Column name in TPM_counts.txt file same as library name


title: 56L, Mouse STR LEFT, female, MG+, no treatment

description: Library name: 56-L


title: Mice hippocampus tissue, Non-pregnant Mice (nulliparous), Normal diet, Rep 2

description: Library name: RMB5013


title: Hu-P-3817

description:
Library name: SAM001297
Column name in TPM_counts.txt file same as library name


title: Mice hippocampus tissue, Non-pregnant Mice (nulliparous), Normal diet, Rep 3

description: Library name: RMB5014


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Normal diet, Rep 2

description: Library name: RMB5016


title: 57L, Mouse STR LEFT, female, MG-, PFF

description: Library name: 57-L


title: 55L, Mouse STR LEFT, male, MG-, SAL

description: Library name: 55-L


title: 53L, Mouse STR LEFT, male, MG+, no treatment

description: Library name: 53-L


title: Mice hippocampus tissue, Young Mice, Normal diet, Rep 2

description: Library name: RMB5010


title: Mice hippocampus tissue, Pregnant Mice (Multiparous), Normal diet, Rep 3

description: Library name: RMB5017


title: Hu-P-3664

description:
Library name: SAM001291
Column name in TPM_counts.txt file same as library name


title: CLAD4

description: Library name: AB-24-6


title: Mice hippocampus tissue, Non-pregnant Mice (nulliparous), Normal diet, Rep 1

description: Library name: RMB5012


title: Hu-P-3820

description:
Library name: SAM001300
Column name in TPM_counts.txt file same as library name


title: CLAD5

description: Library name: AB-24-32


title: 55R, Mouse STR RIGHT, male, MG+, SAL

description: Library name: 55-R


title: 52R, Mouse STR RIGHT, male, MG+, SAL

description: Library name: 52-R


title: Hu-P-3663

description:
Library name: SAM001290
Column name in TPM_counts.txt file same as library name


title: CLAD1

description: Library name: CK-23-5


title: Mice hippocampus tissue, Young Mice, Normal diet, Rep 1

description: Library name: RMB5009