title: Mouse liver scRNA-seq, EP2 WT Young, biol rep 2

city: Stanford

first: Katrin

middle: I

last: Andreasson

state: CA

address: 1201 Welch Road

department: Neurology and Neurological Sciences

institute: Stanford University

description:
Library name: EP2 WT Young rep2
10x Genomics Chromium X; Seurat sample ID: Youngwt8; Folder: 266

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.1 for demultiplexing, barcode/UMI processing, and alignment to the mouse reference genome (GRCm39).
Filtered gene-barcode matrices were imported into Seurat v5.2.0 (R v4.3.2). Cells with <400 genes, >5500 genes, or >25% mitochondrial reads were excluded. 126,443 cells and 27,398 genes retained after filtering.
Expression values normalized using NormalizeData() and scaled using ScaleData().
Samples integrated using Reciprocal PCA (RPCA) workflow. PCA performed; top 30 PCs selected. UMAP computed with RunUMAP(dims=1:30). Clustering with FindNeighbors() and FindClusters(resolution=0.1).
Assembly: GRCm39
Supplementary files format and content: matrix.mtx.gz: merged post-QC counts matrix in Matrix Market Exchange format (126,443 cells x 27,398 genes)
Supplementary files format and content: barcodes.tsv.gz: cell barcode identifiers; features.tsv.gz: gene names; cell_metadata.csv.gz: cell-to-sample mapping with sample ID and group assignment

growth_protocol: N/A (primary tissue from C57BL/6J mice)

extract_protocol:
Livers were perfused in situ with collagenase IV (500 U/mL) in HBSS with Ca2+/Mg2+. After enzymatic digestion and mechanical dissociation, cells were filtered through 70 um strainers and red blood cells lysed. Hepatocytes were pelleted at 50g for 1 min; non-parenchymal cells were collected from the supernatant at 400g for 10 min. Cells were stained with CD45-APC (BD 559864), CD1d-PerCP/Cy5.5 (BD 562713), CD31-BV605 (BD 740356), Ter119-PE (Biolegend 116208), and viability dyes. Live CD45+, CD1d+, or CD31+ single cells were FACS-sorted in a 1:1:1 ratio.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium X platform following the Next GEM Single Cell 3' Gene Expression protocol. Individual cells were encapsulated with barcoded gel beads into nanoliter-scale GEMs for cell-specific cDNA synthesis and UMI-based transcript labeling. cDNA was amplified, enzymatically fragmented, end-repaired, ligated to adaptors, and indexed for Illumina sequencing.

treatment_protocol: Tamoxifen was administered at 4-6 months of age to both Cx3cr1CreER;EP2wt/wt (WT) and Cx3cr1CreER;EP2lox/lox (EP2 cKO) genotypes. Young mice were evaluated at 6-8 months and aged mice at 23-25 months.

value: Young (6-8 months)

value: Sorted liver cells (CD45+, CD1d+, CD31+ sorted 1:1:1)

value: Cx3cr1CreER;EP2wt/wt (WT)

value: Male


title: rheb3;head;Lpp[TS]>Rheb;rep3

status: Public on Jul 16 2026

type: SRA

city: changsha

first: Jun

last: Wang

state: HuNan

address: Lushan

department: College of Life Science

country: China

institute: Hunan Normal University

description:
Library name: rheb3
feed for 2 days

library_source: transcriptomic

data_processing:
Raw reads of FASTQ format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads that were mapped to the reference genome using HISAT2.FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: BDGP6.46
Supplementary files format and content: csv file includes raw counts for each Sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: head

growth_protocol: growth with standard food

extract_protocol:
Total RNA was extracted from heads of females for RNA-seq analysis. Fly heads were dissected in ice-cold PBS, transferred into RNAiso Plus (TaKaRa #9109), and homogenized with the Precellys Evolution Homogenizer (Bertin Technologies). 20 heads were used for each sample in biological triplicates. Total RNA extraction was performed as previously described 84. RNA concentration was measured by Nanodrop One (Thermo Fisher Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Then, the sequencing libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme) and sequenced on an Illumina Novaseq 6000 platform with 150 bp paired-end reads.

treatment_protocol: (i) Diet group: 7-days-old w1118 iso (iso31) females raised on CD followed by 2 days with either a control diet (2% sucrose) or a protein-rich diet (2% sucrose + 3.3% yeast extract) at 25ºC; (ii) Age group: 3-day-old (as Young) and 50-day-old (as Old) Oregon-R flies raised on CD at 25°C; (iii) Lsp2 and Rheb overexpression: flies with fat body specific overexpression of Lsp2 or Rheb by LppTS and respective control raised on CD for 3 days prior to a sugar-only diet (5% sucrose) for 2 days at 29°C.

tag: tissue

value: head

tag: genotype

value: lppTS>rheb

tag: treatment


title: mESC IgG - 10K cells - Replicate 3

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

country: USA

institute: Versiti Blood Research Institte

description: Library name: M10K_IgG_R3

library_source: genomic

data_processing:
For each of the mESCs and rat C6 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion ‘-a CTGTCTCTTATACACATCT -m 20 -q 20’.
Then all the raw reads were aligned to their respective genome (mm10 for mESC samples, and rn7 for rat C6 samples) using bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, replicate alignment files for each sample were merged and sorted by using $PICARD MergeSamFiles.
These merged alignment files were used for peak calling by MACS2 (2.2.9.1). We called the ‘broad’ Peak for H3K27me3, and for CTCF, ‘narrow’ peaks were called.
These merged alignment files were used to generate bigwig files (CPM normalization).
Assembly: mm10 and rn7
Supplementary files format and content: .bw file for normalized signal files for visualization
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: mESC cells were cultured in mouse ES cell media and Rat C6 were cultured in DMEM, both media supplemented with 15% and 10% FBS, respectively.

extract_protocol:
Genomic DNA of mESCs and rat C6 was extracted to perform CUT&Tag using CUT&Tag-direct with CUTAC V.3 (Steven Henikoff, Jorja Henikoff, Kami Ahmad 2021. CUT&Tag-direct with CUTAC. protocols.io https://dx.doi.org/10.17504/protocols.io.bqwvmxe6).
CUT&Tag libraries for CTCF, H3K27me3, IgG were then prepared based on the before-mentioned protocol and sent all mESCs and RatC6 samples to the Novogene (illumina Novaseq 6000) for sequencing.

treatment_protocol: Both mESC and rat C6 cells were grown up to ~80% confluency before collecting cells for CUT&Tag experiment.

tag: cell line

value: mESC

tag: cell type

value: murine Embryonic Stem Cells (mESC)

value: WT


title: Mouse liver scRNA-seq, EP2 WT Young, biol rep 1

description:
Library name: EP2 WT Young rep1
10x Genomics Chromium X; Seurat sample ID: Youngwt7; Folder: 265

library_source: transcriptomic single cell

source_name: Liver

value: Liver

tag: age

tag: Sex


title: DSP-1012550005943-G-D01

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

description:
Library name: TMA_MASH|018|CK8_18+
FFPE samples from human liver samples

data_processing:
Morphology markers: CK8/18 and Nuclear stain morphology markers Segment ROI (CK8/18+)
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Assembly: The human genome assembly GRCh38
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, Healthy/MASH Group
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Sequencing Saturation is a measure of sequencing depth for a sample [1 – % Unique reads]. Below 50% the counts become less reliable. Sensitivity for low expressing genes is depressed with lower sequencing saturation.  We use Q3 normalization as we find it consistently outperforms other methods like Negative Probe, which can over-normalize small regions and Housekeeper Normalization, which is susceptible to inconsistency in experiments investigating disparate sample types that often have different expression levels.
Using a patented DNA barcoding technology, synthetic DNA oligonucleotide barcodes are attached to antibodies for protein detection, and In Situ Probes for mRNA detection via a UV photocleavable linker. A single tissue section is labeled with a cocktail of these probes and 4 fluorescently labeled morphology markers. Regions of interest for molecular profiling are selected based on the fluorescent images, and UV light illuminates each region independent, which releases the barcodes from that region for subsequent counting. Molecular counts for each target in the panel can then be mapped back to distinct regions of interest and comparisons made within and between samples. The workflow is simple with many aspects of it automated in the system.  Staining can be done on an Autostainer, or manually on the bench.  The system first scans the fluorescence, and ROI selection is done right through the software.  Once ROIs are selected, the system goes through and picks from each region one at a time.  As barcodes are released, a microcapillary system sips up the tags, and dispenses them into a 96 well microtiter plate.  Those barcodes can then be read out on our nCounter platform, or an Illumina sequencer.

value: Healthy


title: rheb2;head;Lpp[TS]>Rheb;rep2

description:
Library name: rheb2
feed for 2 days


title: mESC IgG - 10K cells - Replicate 2

description: Library name: M10K_IgG_R2


title: Mouse liver scRNA-seq, EP2 cKO Young, biol rep 2

description:
Library name: EP2 cKO Young rep2
10x Genomics Chromium X; Seurat sample ID: Youngflox6; Folder: 255

value: Cx3cr1CreER;EP2lox/lox (EP2 cKO)


title: rheb1;head;Lpp[TS]>Rheb;rep1

description:
Library name: rheb1
feed for 2 days


title: mESC IgG - 10K cells - Replicate 1

description: Library name: M10K_IgG_R1


title: DSP-1012550005943-G-C11

description:
Library name: TMA_MASH|017|CK8_18+
FFPE samples from human liver samples


title: Mouse liver scRNA-seq, EP2 cKO Young, biol rep 1

description:
Library name: EP2 cKO Young rep1
10x Genomics Chromium X; Seurat sample ID: Youngflox5; Folder: 254


title: DSP-1012550005943-G-C09

description:
Library name: TMA_MASH|016|CK8_18+
FFPE samples from human liver samples

value: MASH


title: ctrl6;head;Lpp[TS]>w1118[CJ1];rep3

description:
Library name: ctrl6
feed for 2 days


title: mESC IgG - 1K cells - Replicate 3

description: Library name: M1K_IgG_R3


title: ctrl5;head;Lpp[TS]>w1118[CJ1];rep2

description:
Library name: ctrl5
feed for 2 days


title: Mouse liver scRNA-seq, EP2 WT Aged, biol rep 1

description:
Library name: EP2 WT Aged rep1
10x Genomics Chromium X; Seurat sample ID: Agedwt3; Folder: 249

value: Aged (23-25 months)


title: mESC IgG - 1K cells - Replicate 2

description: Library name: M1K_IgG_R2


title: DSP-1012550005943-G-C07

description:
Library name: TMA_MASH|015|CK8_18+
FFPE samples from human liver samples


title: mESC IgG - 1K cells - Replicate 1

description: Library name: M1K_IgG_R1


title: ctrl4;head;Lpp[TS]>w1118[CJ1];rep1

description:
Library name: ctrl4
feed for 2 days


title: Mouse liver scRNA-seq, EP2 cKO Aged, biol rep 2

description:
Library name: EP2 cKO Aged rep2
10x Genomics Chromium X; Seurat sample ID: Agedflox2; Folder: 237


title: DSP-1012550005943-G-C05

description:
Library name: TMA_MASH|014|CK8_18+
FFPE samples from human liver samples


title: DSP-1012550005943-G-C03

description:
Library name: TMA_MASH|013|CK8_18+
FFPE samples from human liver samples


title: SF9236 (G2)

city: San Francisco

first: Joanna

last: Phillips

address: 1450 Third Street, Room HD492B

institute: University of California San Francisco

description:
Library name: sample 2
G2

data_processing:
The demultiplexing, barcode processing,and gene counting and aggregation were made using 10X Genomics CellRanger software v3.0.2. using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value files and matrix files

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Single-nucleus capture, reverse transcription, cell lysis for snRNA-seq were performed on the 10x Genomics platform as per manufacturer’s protocol. Approximately 15,000 nuclei were loaded per capture.
snRNA-seq library prepration were performed on the 10x Genomics platform as per manufacturer’s protocol.

value: Brain


title: lsp23;head;Lpp[TS]>Lsp2;rep3

description:
Library name: lsp23
feed for 2 days


title: Mouse liver scRNA-seq, EP2 cKO Aged, biol rep 1

description:
Library name: EP2 cKO Aged rep1
10x Genomics Chromium X; Seurat sample ID: Agedflox1; Folder: 236


title: DSP-1012550005943-G-B09

description:
Library name: TMA_MASH|010|CK8_18+
FFPE samples from human liver samples


title: mESC CTCF - 100K cells - Replicate 3

description: Library name: M100K_CTCF_R3


title: lsp22;head;Lpp[TS]>Lsp2;rep2

description:
Library name: lsp22
feed for 2 days


title: mESC CTCF - 100K cells - Replicate 2

description: Library name: M100K_CTCF_R2


title: DSP-1012550005943-G-B07

description:
Library name: TMA_MASH|009|CK8_18+
FFPE samples from human liver samples


title: lsp21;head;Lpp[TS]>Lsp2;rep1

description:
Library name: lsp21
feed for 2 days


title: inv(16);Smc3 wt scRNA-seq replicate 1

description:
Library name: Smc3Wt-Rep1
10x Genomics v.3.1

data_processing:
Cell Ranger count pipeline was used to perform the alignment, filtering, and Unique Molecular Identifier (UMI) counting
Seurat in R was used to perform quality control, analysis, and exploration.
Assembly: mm10
Supplementary files format and content: Tab seperated value files and Matrix files

source_name: bone marrow

growth_protocol: mouse, in vivo

extract_protocol:
LSK sorting flow cytometry
10x genomics v3.1

treatment_protocol: PIPC

value: bone marrow

value: Lineage negative, c-Kit+, Sca1+


title: mESC CTCF - 100K cells - Replicate 1

description: Library name: M100K_CTCF_R1


title: DSP-1012550005943-G-B01

description:
Library name: TMA_MASH|006|CK8_18+
FFPE samples from human liver samples


title: inv(16);Smc3 wt scRNA-seq replicate 2

description:
Library name: Smc3Wt-Rep2
10x Genomics v.3.1


title: mESC CTCF - 50K cells - Replicate 3

description: Library name: M50K_CTCF_R3


title: ctrl3;head;Lpp[TS]>w1118;rep3

description:
Library name: ctrl3
feed for 2 days


title: DSP-1012550005943-G-F01

description:
Library name: TMA_MASH|030|CK8_18+
FFPE samples from human liver samples


title: inv(16);Smc3 het scRNA-seq replicate 2

description:
Library name: Smc3Het-Rep2
10x Genomics v.3.1


title: DSP-1012550005943-G-A11

description:
Library name: TMA_MASH|005|CK8_18+
FFPE samples from human liver samples


title: mESC CTCF - 50K cells - Replicate 2

description: Library name: M50K_CTCF_R2


title: ctrl2;head;Lpp[TS]>w1118;rep2

description:
Library name: ctrl2
feed for 2 days


title: inv(16);Smc3 het scRNA-seq replicate 1

description:
Library name: Smc3Het-Rep1
10x Genomics v.3.1


title: DSP-1012550005943-G-A05

description:
Library name: TMA_MASH|002|CK8_18+
FFPE samples from human liver samples


title: ctrl1;head;Lpp[TS]>w1118;rep1

description:
Library name: ctrl1
feed for 2 days


title: mESC CTCF - 50K cells - Replicate 1

description: Library name: M50K_CTCF_R1


title: inv(16);Smc3 wt replicate 3

description: Library name: Smc3Wt-Rep3

data_processing:
Mapping was done with Bowtie2 to mm10 using end-to-end, very-sensitive, and phred33 settings
Only mapped reads and non-mitochondrial reads were kept.
Peaks were called using MACS2 with BAMPE parameters and a q-value cutoff of 0.05
Assembly: mm10
Supplementary files format and content: Excel Spreadsheet and Called Peaks

source_name: Bone marrow

treatment_protocol: viral transduction, tamoxifen-induction of Creon

value: Bone marrow

value: HSPC


title: DSP-1012550005943-G-A03

description:
Library name: TMA_MASH|001|CK8_18+
FFPE samples from human liver samples


title: DYE30S3;head;w1118;YE group+30%S;rep3

description:
Library name: DYE30S3
feed for 2 days

value: 30%sucrose+3.3%yeast extract


title: mESC CTCF - 10K cells - Replicate 3

description: Library name: M10K_CTCF_R3


title: DYE30S2;head;w1118;YE group+30%S;rep2

description:
Library name: DYE30S2
feed for 2 days


title: DSP-1012550005943-G-A01

description:
Library name: No template control A
FFPE samples from human liver samples


title: mESC CTCF - 10K cells - Replicate 2

description: Library name: M10K_CTCF_R2


title: inv(16);Smc3 wt replicate 2

description: Library name: Smc3Wt-Rep2


title: inv(16);Smc3 wt replicate 1

description: Library name: Smc3Wt-Rep1


title: DYE30S1;head;w1118;YE group+30%S;rep1

description:
Library name: DYE30S1
feed for 2 days


title: elongating heart organoid, day 13

city: Suwon-si

first: Jinwoo

last: Lee

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

institute: Sungkyunkwan university

description:
Library name: eHO_D13
10x Genomics

data_processing:
Single cell gene expression data was analyzed using Cell Ranger v7.2.0 (10x Genomics; https://www.10xgenomics.com/support/software/cell-ranger/7.2). Briefly, raw BCL files from Illumina NovaSeq6000 were demultiplexed to generate FASTQ files using ‘cellranger mkfastq’. Then, these raw FASTQ files were analyzed using ‘cellranger count’. The ‘cellranger count’ step includes mapping to the human reference genome (GRCh38-2020-A), measuring gene expression with unique molecular identifier (UMI) and cell barcode, determining cell clusters, and conducting differential gene expression analysis.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tap-seperated values files and matrix files

extract_protocol:
eHOs were pooled into a 15 mL conical tube. Organoids were washed with PBS and incubated in pre-warmed 10x TrypLE Select Enzyme solution (Gibco) for 20 minutes at 37°C, with gentle pipetting every minute. To reduce sheer stress on the cells, pipette tips were trimmed. Dissociated cells were transferred to 5 mL of pre-warmed N2B27 medium, centrifuged 200 x g for 5 minutes, and resuspended gently in cold PBS for further processing.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol (CG000315). Briefly, the cell suspensions were diluted in nuclease free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation.

tag: model

value: heart organoid model

tag: developmental stage

value: day 13


title: mESC CTCF - 10K cells - Replicate 1

description: Library name: M10K_CTCF_R1


title: inv(16);Smc3 het replicate 3

description: Library name: Smc3Het-Rep3


title: DYE2S3;head;w1118;YE group;rep3

description:
Library name: DYE2S3
feed for 2 days

value: head

value: 2%sucrose+3.3%yeast extract


title: elongating heart organoid, day 5

description:
Library name: eHO_D5
10x Genomics

value: day 5


title: mESC CTCF - 1K cells - Replicate 3

description: Library name: M1K_CTCF_R3

value: mESC

value: murine Embryonic Stem Cells (mESC)

value: WT


title: inv(16);Smc3 het replicate 2

description: Library name: Smc3Het-Rep2


title: DYE2S2;head;w1118;YE group;rep2

description:
Library name: DYE2S2
feed for 2 days


title: sgk1_CS_rep2

city: Freiburg

first: Gang

last: Wu

state: Freiburg

address: Schänzlestraße 1, 79104 Freiburg, Institute of biology III, 5th floor

department: Bio II/III

country: Germany

institute: University of Freiburg

description: Library name: lib474575_7362_2

data_processing:
Data processing was performed on Galaxy server according to this tutorial: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
Assembly: WBcel235.51
Supplementary files format and content: tabular files mentioned in the last section, as "processed data file"

organism: Caenorhabditis elegans

source_name: all

growth_protocol: C. elegans strains were cultured and maintained at 20 °C with NGM plates seeded with Escherichia coli (E. coli), using standard protocols. The N2 Bristol strain was used as the WT strain.

extract_protocol:
Synchronized day 1 adult worms were collected and stored at -80 °C until all the conditions and replicates were ready. Three biological replicates were used to perform statistics analysis. To extract total RNA, worms were thawed and washed three times using M9 buffer. Then worms were lysed using Precellys 24 tissue homogenizer, using 6500 rpm X 3 times. Total RNA extraction was performed using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instruction. Total RNA was digested with DNAase to remove DNA contaminations. RNA concentration was quantified using a Nanodropt spectrophotometer (NanoPhotometer NP80, IMPLEN).
Library construction was performed by the BMKgene company

treatment_protocol: To avoid potential transgenerational effects of temperature shifts on post CS survival, worms were maintained on 20 °C for at least three generations before they were used for a post CS survival assay. Synchronized L4 stage larvae were transferred to new plates to avoid stage specific effects on post CS survival. 18-20 hours after L4 synchronization, worms are transferred to 2 °C for 6 hours in a Binder KB E6 incubator. During the CS and early recovery period post CS, the lid of the plate container box was removed and plates were placed in one layer without staggering. During the CS period, the door of the incubator was not opened again to avoid temperature disturbance. During the CS and early recovery period post CS, the temperature of the NGM agar was recorded using a NIST traceable TMP117 digital temperature sensor (Texas Instruments). After cold shock, worms were immediately transferred to 20 °C.

value: all

value: cold stress

tag: batch


title: inv(16);Smc3 het replicate 1

description: Library name: Smc3Het-Rep1


title: mESC CTCF - 1K cells - Replicate 2

description: Library name: M1K_CTCF_R2


title: sgk1_CS_rep1

description: Library name: lib474574_7362_2


title: mESC CTCF - 1K cells - Replicate 1

description: Library name: M1K_CTCF_R1


title: DYE2S1;head;w1118;YE group;rep1

description:
Library name: DYE2S1
feed for 2 days


title: sgk1_ctrl_rep2

description: Library name: lib474573_7362_2


title: 2D_D16_rep3

city: Lisboa

first: Alice

last: Borges

address: Av. Rovisco Pais

country: Portugal

institute: IBB

description:
Library name: sample 22
D16c3

data_processing:
Raw RNA-sequencing reads in FASTQ format were processed using the R/Bioconductor environment (version 4.4.2). Reference genome indexing and read alignment were performed using the Rsubread package (version 2.20.0)25 against the human GRCh38 primary assembly obtained from Ensembl release 115. Gene-level read quantification was generated from aligned reads using featureCounts with Ensembl GRCh38 gene annotations. Gene identifiers were converted from Ensembl IDs to HGNC gene symbols using the biomaRt package and the Ensembl hsapiens_gene_ensembl dataset. Genes without corresponding HGNC annotations were excluded from downstream analyses. For genes mapping to multiple Ensembl identifiers, read counts were collapsed by summing counts across shared HGNC symbols.
Assembly: Human (GRCh38) Lexogen QuantSeq 2.2.3 FWD (genome version GRCh38.115)
Supplementary files format and content: aligned raw counts (unprocessed)

growth_protocol: For hiPSC culture, mTeSR™1 (STEMCELL Technologies™, #85850) supple- mented 1:200 (v/v) with penicillin/ streptomycin (Gibco™, #15140122) was used as culture medium in six-well plates coated with Matrigel® Growth Factor Reduced Matrix (Corning®, #354230). Culture medium was changed daily. Cell passaging was performed every three to four days when reaching a confluency ~70% using 0.5 mM EDTA (Invitrogen™,15575020).

extract_protocol:
For sample collection at selected time points, culture medium was removed, and cells were washed with PBS. Then cells were incubated with Accutase® solution (Sigma-Aldrich®, #A6964) in the case of hiPSCs or 0.25% (v/v) trypsin-EDTA (Gibco™, #R001100) in PBS for differentiated cells, both at 37ºC for 7 min. Culture medium was added to inactivate enzymatic digestion and cells were homogenized and centrifuged at 200 xg for 3 min. The cell pellet was washed with PBS and centrifuged again at 200 xg for 3 min. After removing the PBS, cell pellet was stored at -80ºC until further analysis. Total RNA was extracted using the High Pure RNA Isolation Kit (Roche, #11828665001) following the provided instructions.
Libraries were prepared using Lexogen QuantSeq 3′mRNA-Seq Library Prep. Kit FWD for Illumina using standard protocols. Sequencing was performed using Illumina HiSeq (50 cycle’s protocol) or NextSeq (75 cycle’s protocol) platforms

treatment_protocol: Neural induction was initiated when hiPSCs reached 90–100% confluency. The basal differentiation medium, N2B27, consisted of 50% (v/v) DMEM/F12/N2 and 50% Neurobasal/B27. DMEM/F12/N2 was prepared using DMEM/F12 medium (Thermo Fisher Scientific) supplemented with 1% (v/v) N2 supplement (Thermo Fisher Scientific), 1.6 g/L glucose (Sigma), 1% (v/v) penicillin/streptomycin, and 20 μg/mL insulin (Sigma). Neurobasal/B27 was prepared using Neurobasal medium (Thermo Fisher Scientific) supplemented with 2% (v/v) B27 supplement (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), and 1% (v/v) penicillin/streptomycin. Cells were cultured for 12 days in differentiation medium supplemented with 10 μM SB431542 and 100 nM LDN193189 (StemMACS™), with daily medium change.

tag: source

value: foreskin fibroblasts

value: iPSC-derived neural rosettes

tag: mode of_growth

value: 2D monolayer

tag: time

value: 16 days


title: D2S3;head;w1118;S group;rep3

description:
Library name: D2S3
feed for 2 days


title: mESC H3K27me3 - 100K cells - Replicate 3

description: Library name: M100K_H3K27me3_R3


title: 2D_D16_rep2

description:
Library name: sample 21
D16c2


title: sgk1_ctrl_rep1

description: Library name: lib474572_7362_2


title: D2S2;head;w1118;S group;rep2

description:
Library name: D2S2
feed for 2 days


title: mESC H3K27me3 - 100K cells - Replicate 2

description: Library name: M100K_H3K27me3_R2


title: PS_CS_rep2

description: Library name: lib474571_7362_2


title: 2D_D16_rep1

description:
Library name: sample 20
D16c1


title: 2D_D12_rep3

description:
Library name: sample 19
D12c3

value: iPSC-derived neural progenitors

value: 12 days


title: mESC H3K27me3 - 100K cells - Replicate 1

description: Library name: M100K_H3K27me3_R1


title: Mouse liver scRNA-seq, EP2 WT Aged, biol rep 2

description:
Library name: EP2 WT Aged rep2
10x Genomics Chromium X; Seurat sample ID: Agedwt4; Folder: 250

value: Liver

value: Aged (23-25 months)

value: Sorted liver cells (CD45+, CD1d+, CD31+ sorted 1:1:1)

value: Cx3cr1CreER;EP2wt/wt (WT)

value: Male


title: D2S1;head;w1118;S group;rep1

description:
Library name: D2S1
feed for 2 days

value: head


title: PS_CS_rep1

description: Library name: lib474570_7362_2


title: ey-Gal4>UAS-dTet rep3

city: Beirut

first: Margret

last: Shirinian

address: Bliss street

country: Lebanon

institute: American University of Beirut

description: RNA-seq

data_processing:
Quality check for raw sequencing reads was performed using FastQC v0.12.1
RNA-seq reads were aligned to dm6 genome assembly using hisat2 v2.2.0
RNA-seq featurecounts matrix was generated using FeatureCounts v2.0.6 from SubRead package
Assembly: dm6
Supplementary files format and content: processed data files include featureCounts file

source_name: eye-antennal imaginal discs

growth_protocol: flies were maintained on standard cornmeal-agar medium at room temperature at 18˚C for maintenance and 25°C for experiments.

extract_protocol:
Total RNA from eye-antennal imaginal discs  of 3rd instar larvae were extracted  of ey-Gal4>UAS dTet and control ey-Gal4>W1118  using the TRI Reagent (Sigma-Aldrich). 6 RNA samples (three biological replicates for each) were sent in ethanol to Macrogen (Seoul, South Korea) for RNA-Seq analysis.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

value: eye-antennal imaginal discs

value: ey-Gal4;UAS-dTet 3


title: 2D_D12_rep2

description:
Library name: sample 17
D12c2


title: PS_ctrl_rep2

description: Library name: lib474569_7362_2


title: mESC H3K27me3 - 50K cells - Replicate 3

description: Library name: M50K_H3K27me3_R3

value: mESC

value: murine Embryonic Stem Cells (mESC)

value: WT


title: ey-Gal4>UAS-dTet rep2

description: RNA-seq

value: ey-Gal4;UAS-dTet 2


title: 2D_D12_rep1

description:
Library name: sample 16
D12c1

value: foreskin fibroblasts


title: mESC H3K27me3 - 50K cells - Replicate 2

description: Library name: M50K_H3K27me3_R2


title: ey-Gal4>UAS-dTet rep1

description: RNA-seq

value: ey-Gal4;UAS-dTet 1


title: mESC H3K27me3 - 50K cells - Replicate 1

description: Library name: M50K_H3K27me3_R1


title: PS_ctrl_rep1

description: Library name: lib474568_7362_2

value: all

value: cold stress


title: ey-Gal4>W1118 rep3

description: RNA-seq

value: ey-Gal4;W1118 control 3


title: 2D_D9_rep2

description:
Library name: sample 14
D9c2

value: iPSC-derived neural progenitors

value: 2D monolayer

value: 9 days


title: mESC H3K27me3 - 10K cells - Replicate 3

description: Library name: M10K_H3K27me3_R3


title: pqm1_CS_rep2

description: Library name: lib474567_7362_2


title: 2D_D9_rep3

description:
Library name: sample 15
D9c3


title: pqm1_CS_rep1

description: Library name: lib474566_7362_2


title: mESC H3K27me3 - 10K cells - Replicate 2

description: Library name: M10K_H3K27me3_R2


title: ey-Gal4>W1118 rep2

description: RNA-seq

value: ey-Gal4;W1118 control 2


title: 2D_D9_rep1

description:
Library name: sample 13
D9c1


title: pqm1_ctrl_rep2

description: Library name: lib474565_7362_2


title: mESC H3K27me3 - 10K cells - Replicate 1

description: Library name: M10K_H3K27me3_R1


title: 2D_D6_rep3

description:
Library name: sample 12
D6c3

value: 6 days


title: ey-Gal4>W1118 rep1

description: RNA-seq

value: ey-Gal4;W1118 control 1


title: pqm1_ctrl_rep1

description: Library name: lib474564_7362_2


title: Cgas-/- iBMDMs, 16hr time point, S. epidermidis, biological replicate 1_exp2

status: Public on Jul 17 2026

city: Boston

first: Stephanie

last: Ragland

state: MA

address: 1 Blackfan Circle

department: Gastroenterology

institute: Boston Children's Hospital

description: Library name: 189

data_processing:
Galaxy Server
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: iBMDMs

extract_protocol:
RNA was extraced from infected iBMDMs using 300 μL lysis buffer with 1% BME, followed by isolation with the Thermo Fisher Scientific PureLink kit (#12183025). RNA  was treated with Turbo DNase (Thermo #AM190) according to manufacturer's instructions. Illumina RNA-sequencing was performed by Azenta/Genewiz.
NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module

value: iBMDMs

value: macrophage

value: Cgas-/-

value: S. epidermidis

value: same batch for all


title: TcellCD3CD28IL2_DonorC

city: Cambridge, MA

first: Praveen Krishna

last: Veerasubramanian

address: 1 Portland Street

institute: Pfizer Inc.

description: Library name: RSA-0000113313

data_processing:
Adapters were trimmed using Cutadapt (v4.9), reads were aligned using STAR (v2.7.9a) using the GRCh38 assembly (release 111) and quantiﬁed using Salmon (v1.10.1). Downstream analysis was performed in R (v4.4.1). Genes were ﬁltered using the ﬁlterByExpr function in EdgeR (v4.4.2), and voom function in Limma (v3.62.2) was used for normalization and differential gene expression analysis with an absolute fold change of 1.5 and FDR-adjusted P-value of 0.05 being set as the threshold for determining differential expression. Gene Ontology (GO) enrichment analysis of the differentially expressed genes was conducted using clusterProﬁler (v4.14.6). Signiﬁcance was deﬁned by an FDR-adjusted p-value of less than 0.05.
Assembly: Human GRCh38 assembly (release 111)
Supplementary files format and content: Raw counts used for downstream analysis in the publication have been provided as csv files.

source_name: CD3+ T cells derived from PBMCs

extract_protocol:
Cells were dissolved in RLT buffer (Qiagen, Cat. 79216) with 1% 2-mercaptoethanol for RNA isolation. RNA was isolated using NucleoSpin RNA Plus kits (Takara, Cat. 740984.50).
Poly-A enrichment (stranded mRNA) library construction was performed, and an average of 30 million paired end reads were sequenced per sample.

value: CD3+ T cells derived from PBMCs

value: Anti-CD3/CD28/IL-2 stimulated for 4h

value: Donor C


title: 2D_D6_rep2

description:
Library name: sample 11
D6c2

value: foreskin fibroblasts


title: mESC H3K27me3 - 1K cells - Replicate 2

description: Library name: M1K_H3K27me3_R2

value: mESC

value: murine Embryonic Stem Cells (mESC)

value: WT


title: mESC H3K27me3 - 1K cells - Replicate 1

description: Library name: M1K_H3K27me3_R1


title: 2D_D6_rep1

description:
Library name: sample 10
D6c1

value: iPSC-derived neural progenitors

value: 2D monolayer


title: DSP-1012550005943-G-F11

description:
Library name: TMA_MASH|035|CK8_18+
FFPE samples from human liver samples

value: Liver

value: MASH


title: TcellUnstim_DonorC

description: Library name: RSA-0000113312

value: Unstimulated


title: N2_CS_rep2

description: Library name: lib474563_7362_2

value: all

value: wild type

value: cold stress


title: N2_CS_rep1

description: Library name: lib474562_7362_2


title: eye-brain complex, WT, Rep3, NovaSeq X Plus

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description:
Library name: w1118_eyebrainfd_R3
Column name in McNeill_ftfd_raw_gene_counts.txt: w1118_eyebrain_R3

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

source_name: Eye-brain complex

growth_protocol: Larvae from a ubi-Gal4; UAS-FtICD-3xFLAG (Ft overexpression) stock, ft^fd5-5/ft^X13 (Ft null), and w^1118 (wild-type)  were grown in standard Drosophila media at 25C and tissues dissected in ice cold PBS. Embryos were collected and aged at 25 C on grape agar plates.

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds.  cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus and NovaSeq 6000 using paired end reads extending 150 bases

value: Eye-brain complex


title: Cgas-/- iBMDMs, 16hr time point, L. innocua, biological replicate 1_exp2

description: Library name: 190

value: iBMDMs

value: macrophage

value: Cgas-/-

value: L. innocua

value: same batch for all


title: TcellCD3CD28IL2_DonorB

description: Library name: RSA-0000113306

value: CD3+ T cells derived from PBMCs

value: Anti-CD3/CD28/IL-2 stimulated for 4h

value: Donor B


title: 2D_D3_rep3

description:
Library name: sample 9
D3c3

value: foreskin fibroblasts

value: iPSC-derived neural progenitors

value: 3 days


title: N2_ctrl_rep2

description: Library name: lib474561_7362_2


title: eye-brain complex, WT, Rep2, NovaSeq X Plus

description:
Library name: w1118_eyebrainfd_R2
Column name in McNeill_ftfd_raw_gene_counts.txt: w1118_eyebrain_R2

value: WT


title: TcellUnstim_DonorB

description: Library name: RSA-0000113305

value: Unstimulated


title: 2D_D3_rep2

description:
Library name: sample 8
D3c2

value: 2D monolayer


title: N2_ctrl_rep1

description: Library name: lib474560_7362_2

value: all

value: wild type


title: TcellCD3CD28IL2_DonorA

description: Library name: RSA-0000113299

value: Donor A


title: eye-brain complex, WT, Rep1, NovaSeq X Plus

description:
Library name: w1118_eyebrainfd_R1
Column name in McNeill_ftfd_raw_gene_counts.txt: w1118_eyebrain_R1

value: Eye-brain complex


title: 2D_D3_rep1

description:
Library name: sample 7
D3c1


title: human lung, FFPE, Pulmonary Tuberculosis, 211a, 221b, 222, 223

city: Chicago

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

description:
Library name: ptb211a_ptb221b_ptb222_ptb223
Sample was part of pool C scRNA-seq run; raw sequencing data is shared among samples

data_processing:
For poolB, it was processed using CellRanger v7.2.0 with the GRCh38-2020-A reference genome. For pool C, read alignment and feature quantification were performed using CellRanger v9.0.1 (10x Genomics) against the GRCh38-2024-A reference genome.
Assembly: GRCh38-2024-A provided by 10x Genomics
Supplementary files format and content: .h5 expression matrics were provided for each sample

source_name: lung

extract_protocol:
For each FFPE sample, 15 µm scrolls were sectioned and processed using the pestle-based dissociation method described in the “Sample Preparation from FFPE Tissue Sections for Chromium Fixed RNA Profiling” protocol. Nuclei were isolated through sequential steps: deparaffinization of the tissue scrolls, pestle grinding, and digestion with Liberase.
Single-cell library preparation was performed using 10x Genomics GEM-X chemistry. Libraries were sequenced on one lane of the NovaSeq X Plus 10B platform (2×50 bp). Each sample was assigned a unique barcode ID. Following pre-hybridization cell counts, samples were hybridized, and post-hybridization cell numbers were recorded. A defined number of cells from each sample were then selected and added to the pooled library for sequencing. This balanced pooling ensured even representation of each sample in downstream analyses.

value: lung

value: poolC


title: eye-brain complex, Fd5-5, Rep3, NovaSeq X Plus

description:
Library name: ftfd_eyebrainfd_R3
Column name in McNeill_ftfd_raw_gene_counts.txt: ftfd_eyebrain_R3


title: 2D_D1_rep3

description:
Library name: sample 6
D1c3

value: 1 day


title: human lung, FFPE,Tuberculous Lymphadenitis, CIC16, CIC62; Pulmonary Tuberculosis, ptb221

description:
Library name: CIC16_CIC62_ptb221
Sample was part of pool B scRNA-seq run; raw sequencing data is shared among samples

value: poolB


title: TcellUnstim_DonorA

description: Library name: RSA-0000113298

value: CD3+ T cells derived from PBMCs


title: eye-brain complex, Fd5-5, Rep2, NovaSeq X Plus

description:
Library name: ftfd_eyebrainfd_R2
Column name in McNeill_ftfd_raw_gene_counts.txt: ftfd_eyebrain_R2


title: d8_endotome_H3K27ac

city: Hong Kong

first: Tianming

state: Hong Kong

address: LKS Int Biomed Sci Bldg

department: School of Biomedical Sciences

institute: Chinese University of Hong Kong

description:
Library name: CUTTag_Sample4
CUT&Tag
d8_endotome_H3K27ac.RPGC.bw

data_processing:
For CUT&Tag, raw single-indexed fastq reads were aligned to the human genome reference hg38 using STAR (v2.7.10a) with default settings. For scRNA-seq data generated using the Singleron platform, raw reads were processed with the SCOPE tools pipeline (https://github.com/SingleronBio/SCOPE-tools) and aligned to the GRCh38 reference genome (Ensembl v99).
Assembly: hg38
Supplementary files format and content: For CUT&Tag processed data, bigwig outputs and corresponding index files were generated for d6 somite and d8 endotome cells. For scRNA-seq processed data, the integrated objects (.qs format) for somite compartments, BAs of endotome, BAs of dermomyotome and vSMC of endotome were included. MSC-derived beige adipocyte object was not integrated with other samples.
Library strategy: CUT&Tag

source_name: Endotome cultures

extract_protocol:
For CUT&Tag, Cells from day-6 somite and day-8 endotome cultures were dissociated into single-cell suspensions using Accutase. Then the cells were counted using a hemocytometer. 100,000 live cells were processed according to manufacturer’s instruction of CUT&Tag assay kit (CST, #77552).  For scRNA-seq, monolayered cells were dissociated from TC surface using Accutase at 37 °C for 5-10 minutes. For densely packed brown (endotome-derived BA at day24, dermomyotome-derived BAs at day 36 and 46) and beige adipocyte cultures, which were rich in extracellular matrix and lipids, cells were detached using 2.5 mg/ml collagenase IV (Thermo, 17104019) and 0.25% Trypsin-EDTA (Thermo, 25200056) at 37 °C for 10-15 minutes. The resulting brown and beige adipocyte suspensions were filtered through 100 µm strainers, centrifuged at 1,000 rpm for 4 minutes, and resuspended in DPBS at a density of 1 x 105 cells/ml in DPBS for single-cell capture using Singleron platform. The resulting brown and beige adipocyte suspensions were filtered through 100 µm strainers, centrifuged at 1,000 rpm for 4 minutes, and resuspended in DPBS at a density of 1 x 105 cells/ml in DPBS for single-cell capture using Singleron platform.
CUT&Tag libraries were amplified using i5 and i7 single-end index priemrs, and purified using 1.3x Mag-Bind TotalPure NGS beads. Final CUT&Tag libraries were sequenced on a Nextseq 2000 with pair-end mode. scRNA-seq was conducted using GEXSCOPE® Single‑Cell RNA Library Kit (Singleron Biotechnologies). Libraries were sequenced on a Hiseq Ten instrument with PE150 mode.

value: Endotome cultures

value: female


title: 2D_D1_rep2

description:
Library name: sample 5
D1c2

value: foreskin fibroblasts


title: C_ZSZ47_3

city: Baoding

first: dai

last: zhang

address: No. 2596, Lekai South Street, Lianchi District

department: College of Plant Protection

institute: Hebei Agricultural University

description:
Library name: C_ZSZ47_3
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the early stage of pathogen infection.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM v6.1  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: DM v6.1
Supplementary files format and content: tab-delimited text files include gene count and TPM value for each Sample

organism: Solanum tuberosum

source_name: tuber

extract_protocol:
RNA was extracted from tuber using TRIzol reagent. Briefly, tuber were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: tuber

tag: time point


title: d6_somite_H3K27ac

description:
Library name: CUTTag_Sample3
CUT&Tag
d6_somite_H3K27ac.RPGC.bw

source_name: Somite cultures

value: Somite cultures


title: eye-brain complex, Fd5-5, Rep1, NovaSeq X Plus

description:
Library name: ftfd_eyebrainfd_R1
Column name in McNeill_ftfd_raw_gene_counts.txt: ftfd_eyebrain_R1


title: 2D_D1_rep1

description:
Library name: sample 4
D1c1

value: iPSC-derived neural progenitors


title: d8_endotome_EBF2

description:
Library name: CUTTag_Sample2
CUT&Tag
d8_endotome_EBF2.RPGC.bw


title: C_ZSZ47_2

description:
Library name: C_ZSZ47_2
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the early stage of pathogen infection.


title: 16-20 h embryo, WT, Rep4, NovaSeq X Plus

description:
Library name: w1118_embryo_R4
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_embryo_R4

source_name: 16-20 h embryo

value: 16-20 h embryo

value: WT


title: 2D_D0_rep3

description:
Library name: sample 3
D03

value: induced pluripotent stem cells

value: 2D monolayer

value: 0 days


title: C_ZSZ47_1

description:
Library name: C_ZSZ47_1
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the early stage of pathogen infection.


title: d6_somite_EBF2

description:
Library name: CUTTag_Sample1
CUT&Tag
d6_somite_EBF2.RPGC.bw


title: 16-20 h embryo, WT, Rep3, NovaSeq X Plus

description:
Library name: w1118_embryo_R3
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_embryo_R3


title: 2D_D0_rep2

description:
Library name: sample 2
D02


title: C_ZSH3_3

description:
Library name: C_ZSH3_3
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the early stage of pathogen infection.


title: Z138SOX11Resc Replicate 3

city: Barcelona

first: Virginia

middle: Amador

last: Espinosa

state: Barcelona

address: Carrer del Rosselló, 149

country: Spain

institute: FCRB - IDIBAPS

description:
Library name: ZSOX11.3
Column name in matrixlogcpm.txt: ZSOX11.3

data_processing:
Sequencing reads were quality-checked using FastQC (v0.11.9)
rRNA reads were removed using SortMeRNA (v4.3.2)
Adapter trimming and quality filtering were performed with Trimmomatic (v0.40)
Reads were pseudo-aligned to the GRCh38.p13 reference transcriptome using kallisto (v0.46.1) with Ensembl release 100. Gene-level abundances were quantified
Gene-level counts were imported into R (v4.3.2) using tximport (v1.12.3), and differential expression analysis was performed with DESeq2 (v1.24.0), using apeglm for shrinkage
GRCh38.p13
Assembly: Tab-delimited text file containing log2-transformed variance-stabilized normalized gene expression counts (VST) from DESeq2 for all samples, annotated with Ensembl gene IDs and gene symbols.
Supplementary files format and content: Tab-delimited text file containing log2-transformed variance-stabilized normalized gene expression counts (VST) from DESeq2 for all samples, annotated with Ensembl gene IDs and gene symbols.

source_name: lymphoid

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin–streptomycin at 37°C in 5% CO₂

extract_protocol:
RNA from Z138 cell lines was extracted using the RNeasy Plus kit (QIAGEN) following the manufacturer's instructions
RNA-seq libraries were generated using the TruSeq RNA Sample Prep Kit v2 or the TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina), following the manufacturer’s protocol. Libraries were amplified, pooled, and sequenced on an Illumina NextSeq2000 platform to generate 50 bp paired-end or single-end reads.

value: lymphoid

value: lymphoblast cell line


title: 16-20 h embryo, WT, Rep2, NovaSeq X Plus

description:
Library name: w1118_embryo_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_embryo_R2


title: 2D_D0_rep1

description:
Library name: sample 1
D01


title: Z138SOX11KO Replicate 3

description:
Library name: ZKO.3
Column name in matrixlogcpm.txt: ZKO.3


title: C_ZSH3_2

description:
Library name: C_ZSH3_2
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the early stage of pathogen infection.


title: 16-20 h embryo, WT, Rep1, NovaSeq X Plus

description:
Library name: w1118_embryo_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_embryo_R1


title: C_ZSH3_1

description:
Library name: C_ZSH3_1
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the early stage of pathogen infection.


title: 76 3P extract, HT-29 cells, 48 h

city: Kuala Terengganu

first: Norhaslinda

last: Ridzwan

state: Terengganu

address: No 50C, Kampung Pantai Ali

country: Malaysia

institute: Universiti Sultan Zainal Abidin

description:
Library name: P36_AA
Column name in raw_counts all.xls:P36_AA_48h

data_processing:
Hisat2 v2.0.5
Assembly: GRCh38/hg38
Supplementary files format and content: csv files incluide FPKM values for each samples

source_name: colon

growth_protocol: The HT29 cell lines were grown and kept at a temperature of 37⁰C in an incubator humidified with 5% carbon dioxide in RPMI-1640 (Gibco, Invitrogen, USA) supplemented with 10% FBS (Gibco, Invitrogen, USA), 1% of penicillin/streptomycin (Gibco, Invitrogen, USA) and at 95% relative humidity.

extract_protocol:
The RNA extraction of treated cells was performed in accordance with the manufacturer’s guidelines, Prime Way Total RNA Extraction Kit (First Base, KIT-9021, Singapore).
Library preparation and high-throughput sequencing were performed on an Illumina platform. Raw reads were quality-filtered and mapped to the human reference genome using HISAT2.

treatment_protocol: IC50 value of MRQ 74 and MRQ 76 rice extracts were treated in HT-29 cells at 24 hours and 48 hours time-dependent study.

value: colon

value: enterocyte

value: 76 3P extract

value: plant extract


title: Z138 Replicate 3

description:
Library name: ZWT.3
Column name in matrixlogcpm.txt: ZWT.3


title: 16-20 h embryo, Ubi>FtC, Rep4, NovaSeq X Plus

description:
Library name: ubiFtICD_embryo_R4
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_embryo_R4

value: Ubi>FtICD


title: C_BF017_3

description:
Library name: C_BF017_3
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the early stage of pathogen infection.


title: 76 3P extract, HT-29 cells, 24 h

description:
Library name: P36_A
Column name in raw_counts all.xls:P36_A_24h


title: Z138SOX11Resc Replicate 2

description:
Library name: ZSOX11.2
Column name in matrixlogcpm.txt: ZSOX11.2


title: C_BF017_2

description:
Library name: C_BF017_2
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the early stage of pathogen infection.


title: 16-20 h embryo, Ubi>FtC, Rep3, NovaSeq X Plus

description:
Library name: ubiFtICD_embryo_R3
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_embryo_R3


title: 74 3NP extract, HT-29 cells, 48 h

description:
Library name: NP34_AA
Column name in raw_counts all.xls:NP34_AA_48h

value: 74 3NP extract


title: Z138SOX11KO Replicate 2

description:
Library name: ZKO.2
Column name in matrixlogcpm.txt: ZKO.2


title: 74 3NP extract, HT-29 cells, 24 h

description:
Library name: NP34_A
Column name in raw_counts all.xls:NP34_A_24h


title: 16-20 h embryo, Ubi>FtC, Rep2, NovaSeq X Plus

description:
Library name: ubiFtICD_embryo_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_embryo_R2


title: C_BF017_1

description:
Library name: C_BF017_1
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the early stage of pathogen infection.


title: 16-20 h embryo, Ubi>FtC, Rep1, NovaSeq X Plus

description:
Library name: ubiFtICD_embryo_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_embryo_R1


title: 5-FU drug, HT-29 cells, 48 h

description:
Library name: FLU_AA
Column name in raw_counts all.xls:5-FU_AA_48h

value: 5-FU drug


title: Z138 Replicate 2

description:
Library name: ZWT.2
Column name in matrixlogcpm.txt: ZWT.2


title: C_Hx226_3

description:
Library name: C_Hx226_3
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the early stage of pathogen infection.

value: tuber


title: Z138SOX11Resc Replicate 1

description:
Library name: ZSOX11.1
Column name in matrixlogcpm.txt: ZSOX11.1


title: 5-FU drug, HT-29 cells, 24 h

description:
Library name: FLU_A
Column name in raw_counts all.xls:5-FU_A_24h


title: MERFISH of Human lung cancer (NSCLC_7)

type: RNA

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

scan_protocol: Samples were initially imaged at low-resolution using 10x magnification to select regions of interest which were imaged at high-resolution using 60x magnification.

data_processing: Images were visualized using MERSCOPE Vizualizer (v2.1.2593.1) and single-cell analysis was conducted using the the scanpy (v1.9.1) Python package as previously described. Briefly, cells with <10 and >750 counts or with <10 unique genes expressed were removed. Furthermore, cells with a high fraction of blank counts (top 5th percentile) or with high or low spot density or polyT signaling staining intensity (top and bottom 0.0005 percentile) were filtered to remove debris, apoptotic cells, and suspected doublets.

source_name: Lung

extract_protocol: FFPE or fresh frozen samples from HCC and NSCLC patients were processed as previously described and tissue sections were incubated with a custom designed MERSCOPE Gene Panel Mix for 36-48 hours at 37°C. Samples were gel embedded and underwent tissue clearing as previously described. Tissue slides were prepared for imaging as previously described and loaded onto the MERSCOPE system (Vizgen 10000001).

value: Human lung cancer (NSCLC)


title: Z138SOX11KO Replicate 1

description:
Library name: ZKO.1
Column name in matrixlogcpm.txt: ZKO.1


title: C_Hx226_2

description:
Library name: C_Hx226_2
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the early stage of pathogen infection.


title: MERFISH of Human lung cancer (NSCLC_6)


title: control, HT-29 cells, 48 h

description:
Library name: CON_AA
Column name in raw_counts all.xls:Control_AA_48h

value: control


title: C_Hx226_1

description:
Library name: C_Hx226_1
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the early stage of pathogen infection.


title: Z138 Replicate 1

description:
Library name: ZWT.1
Column name in matrixlogcpm.txt: ZWT.1


title: MERFISH of Human lung cancer (NSCLC_5)


title: control, HT-29 cells, 24 h

description:
Library name: CON_A
Column name in raw_counts all.xls:Control_A_24h


title: G_ZSZ47_3

description:
Library name: G_ZSZ47_3
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the peak stage of pathogen infection.

value: at the peak stage of pathogen infection


title: Z138_24h_DMSO Replicate 3

description:
Library name: CT24_3
Column name in matrixlogcpm.txt: CT24_3

data_processing:
rRNA reads were removed using SortMeRNA (v4.3.2)
Adapter trimming and quality filtering were performed with Trimmomatic (v0.40)
Reads were pseudo-aligned to the GRCh38.p13 reference transcriptome using kallisto (v0.46.1) with Ensembl release 100. Gene-level abundances were quantified
Gene-level counts were imported into R (v4.3.2) using tximport (v1.12.3), and differential expression analysis was performed with DESeq2 (v1.24.0), using apeglm for shrinkage
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file containing log2-transformed variance-stabilized normalized gene expression counts (VST) from DESeq2 for all samples, annotated with Ensembl gene IDs and gene symbols.

extract_protocol:
RNA from Z138 cell lines was extracted using the RNeasy Plus kit (QIAGEN) following the manufacturer's instructions
RNA-seq libraries were generated using the TruSeq RNA Sample Prep Kit v2 or the TruSeq Stranded Total RNA kit with Ribo-Zero Gold (Illumina), following the manufacturer’s protocol. Libraries were amplified, pooled, and sequenced on an Illumina NextSeq2000 platform to generate 50 bp paired-end or single-end reads.
Sequencing reads were quality-checked using FastQC (v0.11.9)

treatment_protocol: Cells were treated with DMSO or the PROTAC degrader AU-15330 (0.5 μM) for 8 or 24 hours prior to harvest

value: WT

value: DMSO


title: G_ZSZ47_2

description:
Library name: G_ZSZ47_2
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the peak stage of pathogen infection.


title: MERFISH of Human lung cancer (NSCLC_4)


title: Z138_24h_DMSO Replicate 2

description:
Library name: CT24_2
Column name in matrixlogcpm.txt: CT24_2


title: MERFISH of Human lung cancer (NSCLC_3)


title: Z138_24h_DMSO Replicate 1

description:
Library name: CT24_1
Column name in matrixlogcpm.txt: CT24_1


title: MERFISH of Human lung cancer (NSCLC_2)


title: G_ZSZ47_1

description:
Library name: G_ZSZ47_1
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuzao 47" at the peak stage of pathogen infection.


title: G_ZSH3_3

description:
Library name: G_ZSH3_3
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the peak stage of pathogen infection.


title: Z138_8h_DMSO Replicate 3

description:
Library name: CT8_3
Column name in matrixlogcpm.txt: CT8_2


title: MERFISH of Human lung cancer (NSCLC_1)


title: G_ZSH3_2

description:
Library name: G_ZSH3_2
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the peak stage of pathogen infection.


title: Z138_8h_DMSO Replicate 2

description:
Library name: CT8_2
Column name in matrixlogcpm.txt: CT8_2


title: HFpEF+SGLT2i #3

city: Tokyo

first: hidenori

last: tani

address: 1-1-4, Hanedakuko, Ota-ku, Haneda Innovation City Zone A

country: Japan

institute: Fujita Medical Innovation Center Tokyo, Fujita Health University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: human heart tissue

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Samples were disrupted and homogenised in TRIzol using a TissueLyser LT instrument. Total RNA was extracted using a ReliaPrep RNA Cell Miniprep System according to the manufacturer’s instructions.

value: hiPS-CM+hiPS-Epi+HUVEC

tag: strain

value: HFpEF+SGLT2i; HFpEF medium + 1 μM empagliflozin


title: MERFISH of Human liver cancer (HCC_8)

source_name: Liver

value: Human liver cancer (HCC)


title: HFpEF+SGLT2i #2


title: HFpEF+SGLT2i #1


title: G_ZSH3_1

description:
Library name: G_ZSH3_1
Transcriptome of potato tubers from the highly powdery scab-resistant cultivar "Zhongshuhong 3" at the peak stage of pathogen infection.


title: MERFISH of Human liver cancer (HCC_7)


title: Z138_8h_DMSO Replicate 1

description:
Library name: CT8_1
Column name in matrixlogcpm.txt: CT8_1

value: lymphoid

value: lymphoblast cell line


title: G_BF017_3

description:
Library name: G_BF017_3
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the peak stage of pathogen infection.


title: Z138_24h_AU-15330 Replicate 3

description:
Library name: AU24_3
Column name in matrixlogcpm.txt: AU24_3


title: MERFISH of Human liver cancer (HCC_6)


title: HFpEF #3

value: HFpEF; low-glucose DMEM + 2% AlbuMax + 1 mM L-NAME


title: HFpEF #2


title: HFpEF #1


title: Z138_24h_AU-15330 Replicate 2

description:
Library name: AU24_2
Column name in matrixlogcpm.txt: AU24_2


title: MERFISH of Human liver cancer (HCC_5)


title: Fibro #3

value: Fibro; Ctrl + 1 nM TGF-β


title: G_BF017_1

description:
Library name: G_BF017_1
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the peak stage of pathogen infection.


title: MERFISH of Human liver cancer (HCC_4)


title: G_BF017_2

description:
Library name: G_BF017_2
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "BF017" at the peak stage of pathogen infection.


title: Z138_24h_AU-15330 Replicate 1

description:
Library name: AU24_1
Column name in matrixlogcpm.txt: AU24_1


title: G_HX226_3

description:
Library name: G_HX226_3
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the peak stage of pathogen infection.


title: Z138_8h_AU-15330 Replicate 3

description:
Library name: AU8_3
Column name in matrixlogcpm.txt: AU8_3


title: MERFISH of Human liver cancer (HCC_3)


title: G_HX226_2

description:
Library name: G_HX226_2
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the peak stage of pathogen infection.


title: MERFISH of Human liver cancer (HCC_2)


title: Z138_8h_AU-15330 Replicate 2

description:
Library name: AU8_2
Column name in matrixlogcpm.txt: AU8_2


title: Fibro #2


title: Ctrl #3

value: Ctrl; low-glucose DMEM + FA-free BSA


title: G_HX226_1

description:
Library name: G_HX226_1
Transcriptome of potato tubers from the highly powdery scab-susceptible cultivar "Huangxin 226" at the peak stage of pathogen infection.


title: Z138_8h_AU-15330 Replicate 1

description:
Library name: AU8_1
Column name in matrixlogcpm.txt: AU8_1


title: MERFISH of Human liver cancer (HCC_1)


title: Fibro #1


title: S. Typhi transposon library responding to MUC2

status: Public on Jul 15 2026

city: Ithaca

first: Jeongmin

last: Song

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description: Library name: Tnseq

data_processing:
Reads containing the transposon sequence, AGACCGGGGACTTATCATCCAACCTGTTA, were isolated using seqkit amplicon and trimmed to 100 bp after the transposon.
Supplementary files format and content: fastq

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: S. Typhi

extract_protocol:
The plasmid pCat-mariner was transferred into S. Typhi PhilD-LacZ via conjugation, yielding approximately 50,000 colonies, representing 10-fold coverage of 4,688 S. Typhi genes. The library was grown in LB.3 medium with 0.2% MUC2 for 1 hour, then plated on LB.3 agar containing X-gal (80 µg/ml) and 0.05% GalNAc. A total of 143 white colonies from three independent biological replicates were collected. These colonies were pooled and cultured in LB medium until an optical density at 600 nm (OD600) of approximately 1.0 was reached. Two milliliters of this culture were used for gDNA extraction with the QIAamp DNA Blood Mini Kit (Qiagen, cat. #51106).
Three micrograms of gDNA were prepared with Ultra II End-prep mix (NEB, cat # E7546L), and a sequencing library was generated using the Nanopore Ligation Sequencing Kit (SQK-LSK114). Sequencing was performed with MinION flow cells (R10.4.1) using MinKNOW v21.06.0 (ONT), with base-calling done by Guppy v6.4.2 (minimum Q score > 7).

value: S. Typhi

value: S. Typhi PhilD-LacZ


title: S. Typhi treated with 0.2% MUC2. Exp 3.

description: Library name: STy_MUC2_3

data_processing:
The pooled libraries were sequenced using MinION flow cells (R9.4.1) or Flongle cells with MinKNOW v21.06.0 (ONT). Raw reads were base-called, filtered (minimum Q score > 7), debarcoded, and aligned with the S. Typhi ISP2825 genome using Guppy v5.0.11 (ONT, RRID:SCR_023196). Normalization was performed with DESeq2 (alpha = 0.01, a cutoff for read counts = 10), and data were visualized with Prism v10 (GraphPad, RRID:SCR_002798). Genes with an adjusted P value (Padj) < 0.01 and log2 fold change > 1 were considered statistically significant.
Supplementary files format and content: fastq

extract_protocol:
S. Typhi were cultured in LB.3 supplemented with or without 0.2% purified porcine MUC2 for 3 hours at 37 °C. After fixing the cells in 100% cold methanol for 1 hour at -20 °C, the pellet was washed with RNAprotect Bacteria Reagent (Qiagen, cat. #76506), followed by lysis in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) containing lysozyme (1 mg/ml). RNA extraction was performed using the Qiagen RNeasy Mini Kit (Qiagen, cat. #74104) with in-column DNase digestion (Qiagen, cat. #79254). The RNA concentration was measured using the Qubit RNA HS kit (Invitrogen, cat. # Q32852), and RNA quality was assessed by agarose gel electrophoresis.
4 µg of total RNA was hybridized with in-house oligomer mixes specific to S. Typhi rRNA (71 oligomers, 7 µM each, Table S4) and digested with thermostable RNase H (NEB, cat # M0523S) for 30 min at 60 °C, followed by DNase I digestion (DNase I-XT, NEB, cat # M0570S) for 30 min at 37 °C. Note that in-house oligomers were designed by using the Oligo-ASST program (Phelps et al., 2021). cDNA libraries were prepared using the Maxima H Minus Double-Stranded cDNA Synthesis Kit (ThermoFisher, cat # K2561) with random hexamers. The purified libraries were end-prepped with the Ultra II End-prep mix (NEB, cat # E7546L), barcoded (ONT, cat # EXP-NBD104687), and pooled for adaptor ligation (ONT, cat # EXP-NBD104). RNAclean XP beads (Beckman Coulter, cat # A63987) and AMPure XP beads (Beckman Coulter, cat # A63880) were used for RNA and DNA purification, respectively, at each required step.


title: Ctrl #2


title: S. Typhi treated with 0.2% MUC2. Exp 1.

description: Library name: STy_MUC2_1


title: S. Typhi treated with 0.2% MUC2. Exp 2.

description: Library name: STy_MUC2_2


title: S. Typhi untreated. Exp 3.

description: Library name: STy_untreated_3

value: untreated


title: S. Typhi untreated. Exp 2.

description: Library name: STy_untreated_2


title: S. Typhi untreated. Exp 1.

description: Library name: STy_untreated_1


title: Ctrl #1


title: cultured newborn microglia stimulated 3

city: Halle

first: Martin

middle: Sebastian

last: Staege

address: Ernst-Grube-Str. 40

department: Paediatrics I

institute: Martin Luther University Halle-Wittenberg

description: Gene expression of cultured cells

hyb_protocol: For hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used.

scan_protocol: Fluorescence signals on microarrays were detected by the SureScan Microarray Scanner (Agilent Technologies).

data_processing: Agilent’s Feature Extraction software version 11 was used to read and process the image files.

source_name: cultured newborn microglia stimulated replicate 3

label_protocol: For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) was used.

growth_protocol: FACS sorted microglia was used immediately. For cultured microglia, cells were seeded in complete DMEM/F12 in a 75 cm2 cell culture flask coated with 0.1% poly-L-ornithine. Flasks were washed with complete DMEM/F12 after overnight incubation and stimulated with 20% L-929 conditioned medium in complete DMEM/F12 on day 8, 13, 21 and 29 after isolation. Microglia were collected by shaking the flasks for 5.5 h at 70 rpm and subsequently aspirating the cell suspension.

extract_protocol: Total RNA was isolated from cell pellets or lysates using the Nucleospin RNA XS isolation kit (Machery-Nagel).

treatment_protocol: For stimulation, microglia were cultured in the presence of 100ng/mL human TGFbeta, 100 ng/mL human IL34 and 100 ng/mLCX3CL1.

value: brain

value: microglia


title: cultured newborn microglia stimulated 1

description: Gene expression of cultured cells

source_name: cultured newborn microglia stimulated replicate 1


title: cultured newborn microglia stimulated 2

description: Gene expression of cultured cells

source_name: cultured newborn microglia stimulated replicate 2


title: Patients 39

city: Milan

first: Orazio

last: Fortunato

address: Via Venezian 1

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: not provided

data_processing: The raw data were processed using geometric mean cartridge correction, mean background correction, TGM normalization, and non-parametric batch effect adjustment. To identify genes differentially expressed between the different statuses (dead or alive) after accounting for differences in expression among cartridges, an A+B ANOVA for fixed-effects models was applied. Statistical significance was set at p < 0.05.

label: Nanostring

source_name: Plasma EV

label_protocol: Mirna profile was done using NanoString nCounter Human miRNA v3 Panel. The analysis was performed following manufacturer's instruction: https://nanostring.com/wp-content/uploads/MAN-C0009-07_miRNA_Expression_Assay_User_Manual.pdf

growth_protocol: Extracellular vesicles and particles were isolated from 1 ml plasma diluted to 4.2 ml with sterile filtered PBS 1X to ensure proper tube filling. Samples were ultracentrifuged using TLA-100.3 fixed-angle rotor at 120,000×g for 90 minutes at 4°C in TL-100 ultracentrifuge. Supernatant was carefully removed, and the EV-enriched pellet was washed with filtered PBS at 120,000×g for 60 minutes at 4°C to remove residual contaminants. The final EV-enriched pellet was resuspended in 200 μl of sterile filtered PBS. After the protein quantification single-use aliquots 15 μg protein were prepared and stored at -80°C to avoid freeze-thaw cycles

extract_protocol: 90 µg of EVPs using Maxwell RSC Instrument with Maxwell RSC miRNA Tissue Kit (Promega) according to manufacturer's instructions with the addition of a spike in sequence (osa-miR-414) during the lysis process

value: M

tag: os (1=dead; 0=alive)

tag: Stage

value: IIA


title: Patients 40

value: IIB


title: cultured newborn microglia control 2

description: Gene expression of cultured cells

source_name: cultured newborn microglia control replicate 2

tag: tissue


title: Patients 38


title: Patients 37


title: Patients 36


title: FACS sorted newborn microglia 2

description: Gene expression of freshly isolated cells

source_name: FACS sorted newborn microglia replicate 2


title: cultured newborn microglia control 3

description: Gene expression of cultured cells

source_name: cultured newborn microglia control replicate 3


title: cultured newborn microglia control 1

description: Gene expression of cultured cells

source_name: cultured newborn microglia control replicate 1


title: FACS sorted newborn microglia 3

source_name: FACS sorted newborn microglia replicate 3


title: Patients 35


title: Patients 34


title: FACS sorted adult microglia 2

source_name: FACS sorted adult microglia replicate 2


title: FACS sorted adult microglia 1

source_name: FACS sorted adult microglia replicate 1


title: Patients 33


title: FACS sorted newborn microglia 1

source_name: FACS sorted newborn microglia replicate 1


title: Patients 32


title: Patients 30


title: Patients 29


title: Patients 27

value: F


title: Patients 26


title: Patients 28


title: Patients 31


title: Patients 25


title: Patients 24


title: Patients 22


title: Patients 19

value: IB


title: Patients 18


title: Patients 20


title: Patients 16


title: Patients 17


title: Patients 23


title: Patients 21


title: Patients 15

value: IA


title: Patients 14


title: Patients 13


title: Patients 12


title: Patients 11


title: Patients 10


title: Patients 9


title: Patients 8


title: Patients 7


title: Patients 6


title: Patients 3


title: Patients 5


title: Patients 1


title: Patients 2


title: iPS cell biol rep 3

city: Kanagawa

first: Ryosuke

last: Morozumi

state: --- Select One ---

address: 3-25-26 Tonomachi

institute: National Institte of Health Sciences

description:
Library name: iPS3
Biological replicate 3 of the iPS group; column name in all.tpm: iPS3

data_processing:
Raw sequencing reads were processed by the sequencing provider pipeline.
Reads were quality-controlled and aligned to the human reference genome. Gene-level expression values were summarized as TPM.
Differential expression analysis was performed for iPS versus HLO. P values were adjusted using the Benjamini-Hochberg method; differentially expressed genes were defined using |log2 fold change| >= 1.0 and adjusted FDR < 0.05.
Downstream visualization and GO enrichment analyses were performed in R using the scripts deposited with the manuscript.
Assembly: GRCh38/hg38
Supplementary files format and content: all.tpm.xlsx: gene-level TPM expression matrix for all six samples, including three iPS biological replicates and three HLO biological replicates.
Supplementary files format and content: iPS-VS-HLO_DE_anno.txt: differential expression result table for iPS versus HLO, including gene annotations, fold-change statistics, P values, and adjusted FDR values.

source_name: not applicable

growth_protocol: Human induced pluripotent stem cells were maintained and differentiated into human liver organoids according to the study protocol.

extract_protocol:
Total RNA was extracted from iPS cells and HLOs for bulk RNA-seq. RNA quality was assessed prior to library preparation.
RNA-seq libraries were prepared according to the provider's standard protocols and sequenced on the DNBSEQ platform to generate paired-end reads of 2 x 150 bp.

treatment_protocol: iPS cells and HLOs were compared as experimental groups. No additional treatment was applied unless described in the associated manuscript.

value: not applicable

value: iPS cell line

value: induced pluripotent stem cell

value: iPS


title: Patients 4


title: iPS cell biol rep 1

description:
Library name: iPS1
Biological replicate 1 of the iPS group; column name in all.tpm: iPS1


title: iPS cell biol rep 2

description:
Library name: iPS2
Biological replicate 2 of the iPS group; column name in all.tpm: iPS2


title: HLO biol rep 3

description:
Library name: HLO3
Biological replicate 3 of the HLO group; column name in all.tpm: HLO3

source_name: liver

value: liver

value: human liver organoid

value: differentiation to human liver organoid

value: HLO


title: HLO biol rep 2

description:
Library name: HLO2
Biological replicate 2 of the HLO group; column name in all.tpm: HLO2


title: HLO biol rep 1

description:
Library name: HLO1
Biological replicate 1 of the HLO group; column name in all.tpm: HLO1


title: H1299 cells, SiPFKFB4-2 3

city: Wuhan

first: Yunshang

last: Chen

address: No. 1277 Jiefang Avenue

institute: Wuhan Union Hospital

data_processing:
The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries sequencing20 with MGISEQ2000 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications.
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Analysis description: Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.
Assembly: hg38
Supplementary files format and content: txt file reports fpkm and read_count

source_name: Lung

growth_protocol: All the cells were cultured in RPMI1640 medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: H1299 cells transfected with Scrambled or SiRNAs targeting PFKFB4 for 48 hours.

value: Lung

value: Human lung adenocarcinoma cells

tag: genotype

value: SiPFKFB4-2 tranfected


title: H1299 cells, SiPFKFB4-2 1

tag: treatment


title: H1299 cells, SiPFKFB4-2 2

tag: cell line


title: H1299 cells, SiPFKFB4-1 3

tag: cell type

value: SiPFKFB4-1 tranfected


title: H1299 cells, SiPFKFB4-1 2


title: H1299 cells, SiPFKFB4-1 1


title: H1299 cells, Scramble 2

value: Scramble

value: Scramble tranfected


title: H1299 cells, Scramble 1


title: K562-RaPID, sgNTC', 18h, rep1, 25kbps

city: Zurich

first: Charles

middle: D

last: Yeh

state: ZH

address: Otto-stern-weg 7

department: D-BIOL

country: Switzerland

institute: ETH Zurich

description: Library name: RaPIDseq_sgNTC_25kbps_C3R5X135_18h

data_processing:
Illumina NGS adapter trimming (cutadapt)
DamID PCR adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
alignment to Lambda phage genome (bowtie2)
count reads into GATC tiles of human genome (htseq-count)
spike-in correction, coverage-normalization (FPKM), background subtraction, and binning (analyzeRaPID)
Assembly: hg38
Supplementary files format and content: bigWig with RaPID-FPKM normalization at 5kbps and/or 25kbps binning
Library strategy: DamID-Seq

source_name: blood

growth_protocol: RPMI 1640 base media supplemented to 10% with fetal bovine serum (tetracycline-screened), GlutaMAX, 1X PenStrep, 1ug/mL puromycin. Cells were cultured at +37C in 5%CO2 in log phase growth.

extract_protocol:
genomic DNA
RaPID-labelled fragments were enriched per the DamID PCR protocol with methylated Lambda gDNA spike-in.
Enriched DNA fragments (200-2000bps) were then sheared to 300-600bps.
NGS libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: pre-treatment with doxycycline (20-24h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with Shield1 treatment  wherein siRNA is used, pretreated at -2d prior to CRISPR/Cas9 Nucleofection and again simultaneously with CRISPR/Cas9 Nucleofection.

value: blood

value: myelogenous leukemia

value: CRISPR/Cas9, sgNTC


title: K562-RaPID, sgCCKBR-g3', 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g3__25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g3'


title: K562-RaPID, sgCCKBR-g4', 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g4__25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g4'


title: K562-RaPID, sgCCKBR-g2', 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g2__25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g2'


title: K562-RaPID, sgMulti1, RAD51-ChIPseq, 12h, DMSO, rep1

description: Library name: C3R5X136_ChIPseq_RAD51_sgMulti1, DMSO, 12h

library_source: other

data_processing:
Illumina NGS adapter trimming (cutadapt)
filtering for known amplicon contaminants (if any) (cutadapt)
alignment to human genome (bowtie2)
conversion to coverage (deepTools bamCoverage), separated by first-of-read-pair maaping strand.  Parameters: (--binSize 250 --normalizeUsing CPM --minMappingQuality 10 --extendReads) with either (--samFlagInclude 99) or (--samFlagInclude 83)
Assembly: hg38
Supplementary files format and content: bigWig with CPM normalization

molecule: protein

extract_protocol:
chromatin immunoprecipitation
xGen ssDNA & Low-Input DNA Library Prep Kit

treatment_protocol: pre-treatment with 100nM doxycycline (20h); DSB induction by CRISPR/Cas9 Nucleofection simultaneous with 1uM Shield1 treatment

value: K-562, RaPID, clone 12A3

value: CRISPR/Cas9, sgMulti1, DMSO


title: K562-RaPID, sgNTC, RAD51-ChIPseq, 12h, Mirin, rep1

description: Library name: C3R5X136_ChIPseq_RAD51_sgNTC, Mirin, 12h

value: CRISPR/Cas9, sgNTC, Mirin


title: K562-RaPID, sgNTC, RAD51-ChIPseq, 12h, DMSO, rep1

description: Library name: C3R5X136_ChIPseq_RAD51_sgNTC, DMSO, 12h

value: CRISPR/Cas9, sgNTC, DMSO


title: K562-RaPID, sgCCKBR-g4, 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g4_25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g4


title: K562-RaPID, sgCCKBR-g3, 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g3_25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g3


title: K562-RaPID, sgCCKBR-g2, 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g2_25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g2


title: K562-RaPID, sgCCKBR-g1, 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g1_25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g1


title: K562-RaPID, sgNTC, Mirin, 12h, rep1, 25kbps

description: Library name: RaPIDseq_sgNTC_25kbps_C3R5X136_Mirin_12h


title: K562-RaPID, sgMulti1, Mirin, 12h, rep1, 25kbps

description: Library name: RaPIDseq_sgMulti1_25kbps_C3R5X136_Mirin_12h

value: CRISPR/Cas9, sgMulti1, Mirin


title: K562-RaPID, sgMulti1, DMSO, 12h, rep1, 25kbps

description: Library name: RaPIDseq_sgMulti1_25kbps_C3R5X136_DMSO_12h


title: K562-RaPID, sgNTC, DMSO, 12h, rep1, 25kbps

description: Library name: RaPIDseq_sgNTC_25kbps_C3R5X136_DMSO_12h


title: C3R5X122, RaPID-BFP, clone A3.2-C8, sgBFP, AZD7648

description: Library name: LentiMap_RaPID-BFP_clone_A3.2-C8_sgBFP_AZD7648

value: K-562, RaPID-BFP, clone A3.2-C8

value: CRISPR/Cas9, sgBFP, AZD7648


title: C3R5X122, RaPID-BFP, clone A3.2-C8, baseline

description:
Library name: LentiMap_RaPID-BFP_clone_A3.2-C8_baseline
input sample for baseline/background

value: blood


title: H_sh_2

city: Beijing

first: Jianqiang

last: Cai

state: Beijing

address: No.17 Nanli, Panjiayuan

institute: Cancer Hospital, Chinese Academy of Medical Sciences

description: Library name: Sample8

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCh38
Supplementary files format and content: Excels
Supplementary files format and content: This table contains information on RNA modification sites identified in each sample, RNA counts, and standardized values.

source_name: HUVEC

extract_protocol:
RNA was hanvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libranies
RNA libranies for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's prolocols

value: HUVEC


title: H_OE_3

description: Library name: Sample6


title: H_sh_1

description: Library name: Sample7


title: H_sh_3

description: Library name: Sample9


title: H_NC_1

description: Library name: Sample1


title: Patient-derived GSC, ZH305, GFP, 1

city: Helsinki

first: Vasiliki

last: Gkini

address: Haartmaninkatu 8

department: HiLIFE/ Neuroscience Center

country: Finland

institute: University of Helsinki

description: Library name: ZH305_P25_250519_GFP_S7

data_processing:
RNA analysis up to raw gene counts was done using the Illumina Novaseq X on-board DRAGEN system (Illumina, San Diego, CA, USA; DRAGEN version 4.3.16, RNA app version 1.3.13; Reference GRCh38). Raw gene count data were processed in R (version 4.5.3) and were filtered to remove genes with counts per million (CPM) < 1 in fewer than 3 samples, TMM-normalized using edgeR (version 4.8.2), and log2-CPM expression values were obtained using voomWithQualityWeights from the limma package (version 3.66).
Supplementary files format and content: xlsx file with counts for each sample

source_name: Patient-derived glioblastoma stem cells

growth_protocol: BT12, BT13 and BT18 cells were cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham (11530566; Merk) supplemented with 2% B27 (11530536; Thermo Fisher Scientific), 1% glutamine, epidermal growth factor (EGF, 20 ng/ml; AF-100-15-500UG; PeproTech), and basic fibroblast growth factor (bFGF, 5 ng/ml; AF-100-18B-250UG; PeproTech). ZH305 were cultured in neurobasal medium supplemented with 2% B27, 1% glutamine, EGF (20 ng/ml), and bFGF (10 ng/ml). For passaging cells were dissociated with Accutase (25-058-CI; Corning)

extract_protocol:
Total RNA was isolated from lysed GFP-transduced cells using the NucleoSpin RNA plus kit (740984, Macherey-Nagel) according to the manufacturer’s instructions. To ensure that no residual DNA was left, the samples were digested with rDNAse using the NucleoSpin rDNAse set (740963, Macherey-Nagel) followed by a repurification of the RNA using the RNA Clean-up XS kit (740903, Macherey-Nagel). 200ng of total RNA was used for library construction.
Library preparation from 200 ng of total RNA was performed according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Instruction Manual, Section 1 - Protocol for use with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA). The number of PCR cycles was 10 in the library amplification step. Libraries were barcoded with NEBNext® Multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA, USA).

value: Patient-derived glioblastoma stem cells

value: EGFP lentiviral transduction


title: Patient-derived GSC, ZH305, GFP, 2

description: Library name: ZH305_P26_250526_GFP_S9


title: H_NC_2

description: Library name: Sample2


title: Patient-derived GSC, BT18, GFP, 3

description: Library name: BT18_P32_250604_GFP_S17


title: Patient-derived GSC, BT18, GFP, 2

description: Library name: BT18_P31_250530_GFP_S15


title: Patient-derived GSC, BT13, GFP, 2

description: Library name: BT13_P32_250512_GFP_S21


title: Patient-derived GSC, BT13, GFP, 3

description: Library name: BT13_P33_250519_GFP_S23


title: Patient-derived GSC, BT13, GFP,1

description: Library name: BT13_P29_250416_GFP_S19


title: Patient-derived GSC, BT12, GFP, 3

description: Library name: BT12_P20_250421_GFP_S3


title: Patient-derived GSC, BT12, GFP, 2

description: Library name: BT12_P19_250424_GFP_S5


title: Patient-derived GSC, BT12, GFP, 1

description: Library name: BT12_P19_250414_GFP_S1


title: BeWo, sFlt-1, Rep 3

city: Augusta

first: Jessica

last: Faulkner

state: Georgia

address: 1120 15th Street

department: Physiology

institute: Augusta Univeristy

description: Library name: SF3

data_processing:
Adapters were trimmed from the FASTQ sequence files using Cutadapt (version 4.0)
sequence files were aligned to the GRCh38 human reference genome using STAR (version 2.7.10a).
Subread (v2.0.3) was used for feature counting to create gene-level count matrices from the aligned reads.
Assembly: hg38
Supplementary files format and content: csv file including counts for each samples

source_name: BeWo

growth_protocol: Human BeWo trophoblasts (#CCL-98, ATCC, USA) were cultured in a complete medium (F12K media, 10 % fetal bovine serum, and 1 % penicillin streptomycin (#302004, ATCC, USA). HUVECs (# CC-2519, Lonza, Switzerland) were cultured in EBM2 media (#CC-3156, Lonza, Switzerland). The cells were seeded at 0.5-2×105 cells/well.

extract_protocol:
Total RNA from samples was extracted using PureLinkTM RNA Mini Kit (ref. No. 12183025; Thermo Fisher Scientific)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina

treatment_protocol: Twenty-four hours prior to treatment, cells were serum-starved (1%).  Cells were then incubated with sFlt-1 (1ng/mL) for 72 hours.

value: BeWo


title: BeWo, sFlt-1, Rep 1

description: Library name: SF1


title: BeWo, sFlt-1, Rep 2

description: Library name: SF2


title: BeWo, Control, Rep 3

description: Library name: Veh3

value: Control


title: BeWo, Control, Rep 2

description: Library name: Veh2


title: BeWo, Control, Rep 1

description: Library name: Veh1


title: K562-RaPID, sgHBB, 18h, rep1, 25kbps, siRAD54L

description:
Library name: RaPIDseq_sgHBB_siRAD54L_18h_rep1-25kbps_LZX6
LZX6_R-F3_binned-25kbps.bw

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB, siRAD54L


title: K562-RaPID, sgHBB, 18h, rep1, 25kbps, siBRCA2

description:
Library name: RaPIDseq_sgHBB_siBRCA2_18h_rep1-25kbps_LZX6
LZX6_R-B3_binned-25kbps.bw

value: CRISPR/Cas9, sgHBB, siBRCA2


title: K562-RaPID, sgHBB, 18h, rep1, 25kbps, siCTRL

description:
Library name: RaPIDseq_sgHBB_siCTRL_18h_rep1-25kbps_LZX6
LZX6_R-A3_binned-25kbps.bw

value: CRISPR/Cas9, sgHBB, siCTRL


title: K562-RaPID, sgBFP, 18h, rep1, 25kbps, siBRCA2

description:
Library name: RaPIDseq_sgBFP_siBRCA2_18h_rep1-25kbps_LZX6
LZX6_R-B3_binned-25kbps.bw

value: CRISPR/Cas9, sgBFP, siBRCA2


title: K562-RaPID, sgBFP, 18h, rep1, 25kbps, siRAD54L

description:
Library name: RaPIDseq_sgBFP_siRAD54L_18h_rep1-25kbps_LZX6
LZX6_R-F3_binned-25kbps.bw

value: CRISPR/Cas9, sgBFP, siRAD54L


title: K562-RaPID, sgBFP, 18h, rep1, 25kbps, siCTRL

description:
Library name: RaPIDseq_sgBFP_siCTRL_18h_rep1-25kbps_LZX6
LZX6_R-A3_binned-25kbps.bw

value: CRISPR/Cas9, sgBFP, siCTRL


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-095

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-095_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B8-A8_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B8-A8.bw

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-095


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-060

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-060_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B6-A6_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B6-A6.bw

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-060


title: K562-RaPID, sgMulti1, RAD51-ChIPseq, 12h, Mirin, rep1

description: Library name: C3R5X136_ChIPseq_RAD51_sgMulti1, Mirin, 12h

value: K-562, RaPID, clone 12A3

value: CRISPR/Cas9, sgMulti1, Mirin


title: H1299 cells, Scramble 3

value: Lung

value: Human lung adenocarcinoma cells

value: Scramble

value: Scramble tranfected


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-080

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-080_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B5-A5_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B5-A5.bw

value: blood

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-080


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-000

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-000_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B3-A3_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B3-A3.bw

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-000


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid12.5-HBB-100

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid12.5-HBB-100_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B2-A2_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B2-A2.bw

value: CRISPR/Cas9, sgHBB, plasmid12.5-HBB-100


title: K562-RaPID, sgCCKBR-g1', 18h, rep1, 25kbps

description: Library name: RaPIDseq_sgCCKBR-g1__25kbps_C3R5X135_18h

value: CRISPR/Cas9, sgCCKBR-g1'


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-095

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-095_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B8-A8_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B8-A8.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-095


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-099

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-099_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B7-A7_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B7-A7.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-099


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-060

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-060_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B6-A6_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B6-A6.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-060


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-090

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-090_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B4-A4_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B4-A4.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-090


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-080

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-080_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B5-A5_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B5-A5.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-080


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-000

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-000_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B3-A3_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B3-A3.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-000


title: K562-RaPID, hg38, sgBFP, 18h, rep1, 25kbps, plasmid12.5-HBB-100

description:
Library name: RaPIDseq_hg38_sgBFP_plasmid12.5-HBB-100_18h_rep1-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B2-A2_binned-25kbps.bw
C3R5X127_plasmid_bkgrdSubtracted_B2-A2.bw

value: CRISPR/Cas9, sgBFP, plasmid12.5-HBB-100


title: H_OE_2

description: Library name: Sample5

value: HUVEC


title: K562-RaPID, sgHBB, 18h, rep7, 25kbps

description:
Library name: RaPIDseq_sgHBB_18h_rep7-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B1-A1_binned-25kbps.bw
C3R5X127_hg38_bkgrdSubtracted_B1-A1_binned-5kbps_raw.bw

value: CRISPR/Cas9, sgHBB


title: C3R5X122, RaPID-BFP, clone A3.2-C8, sgBFP

description: Library name: LentiMap_RaPID-BFP_clone_A3.2-C8_sgBFP

value: K-562, RaPID-BFP, clone A3.2-C8

value: CRISPR/Cas9, sgBFP


title: K562-RaPID, sgBFP, 18h, rep7, 25kbps

description:
Library name: RaPIDseq_sgBFP_18h_rep7-25kbps_C3R5X127
C3R5X127_hg38_bkgrdSubtracted_B1-A1_binned-25kbps.bw
C3R5X127_hg38_bkgrdSubtracted_B1-A1_binned-5kbps_raw.bw

value: blood


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-095

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-095_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B8-A8_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B8-A8.bw

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-095


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-099

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-099_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B7-A7_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B7-A7.bw

value: myelogenous leukemia

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-099


title: H_OE_1

description: Library name: Sample4


title: H_NC_3

description: Library name: Sample3


title: Patient-derived GSC, ZH305, GFP, 3

description: Library name: ZH305_P27_250602_GFP_S11

value: Patient-derived glioblastoma stem cells

value: EGFP lentiviral transduction


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-060

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-060_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B6-A6_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B6-A6.bw

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-060


title: K562-RaPID, hg38, sgHBB, 18h, rep1, 25kbps, plasmid100-HBB-090

description:
Library name: RaPIDseq_hg38_sgHBB_plasmid100-HBB-090_18h_rep1-25kbps_C3R5X126
C3R5X126_hg38_bkgrdSubtracted_B4-A4_binned-25kbps.bw
C3R5X126_plasmid_bkgrdSubtracted_B4-A4.bw

value: CRISPR/Cas9, sgHBB, plasmid100-HBB-090