title: FLASH 1x10Gy_ID567_Cortex_Other_011

first: Marie-Catherine

last: Vozenin

address: Avenue de la Roseraie 53

institute: HUG

description:
Library name: DSP-1001660035574-F-E02
FFPE fixed samples GeoMx Nanostring

data_processing:
DSP data were analyzed in R 4.4.0 (2024) according to Nanostring recommendation, using their in-house tools, with the exception of normalization which was performed using the trimmed mean of M values (TMM) algorithm of edgeR. Other packages were used for data manipulation and plotting as well as gene set enrichment analysis.
First, quality control (QC) was performed for the segments using a set of thresholds on chosen descriptive statistics of the segment. Chosen parameters were used as recommended by Nanostring. Then a Grubb test was performed for gene QC, also using parameters recommended by Nanostring. Next, negative probes were used to evaluate the background of quantification and define limit of quantification thresholds for filtering. Segments that contain less than 5% of the genes above the gene detection threshold and genes that are found in less than 5% of the segments were removed from the analysis. After filtering, normalization was performed using the TMM method of the edgeR package. Robust gene detection rate within segments and cell type specificity were confirmed, enabling downstream analysis.
Data was split per region (CA1, CA3, DG, SO and Cortex) and differential gene expression was performed using a linear mixed model (LMM) with the irradiation modality set as the test variable and the slide number as the random intercept.
All scripts used for the analysis and plotting can be found at https://gitlab.unige.ch/lirr/nanostring_flash_mouse_brain.
Assembly: MW0R30722
Supplementary files format and content: dcc
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
24h post-treatment completion, whole brains were collected and stored at 4°C in 4% PFA for 48 hours before Formalin-Fixed Paraffin-Embedded (FFPE) before processing
FFPE tissue section of 5-µm were processed according to the provider standard protocol for the GeoMx Digital Spatial Profiler (DSP).Neurons were identified using NeuN  (1:100, Millipore ABN78) revealed with a secondary goat anti-rabbit Alexa 594 (1:1000, Abcam ab150080). Vessels and astrocytes were also stained using an antibodies cocktail composed of CD31 Alexa 488 (Vessels, 1/100, R&D FAB3628G) and GFAP Alexa 647 (Astrocytes, 1/100, Novus NBP2-3318). The nuclear marker Syto83 (Invitrogen 511364) was also used. Whole slides were imaged at x20 magnification and morphologic markers were used to select regions of interest (ROI). Automatic segmentation of ROI based on CD31, NeuN and GFAP markers was performed to define area of illumination (AOIs). AOIs were exposed to 385 nm light (UV), releasing the indexing oligonucleotides to be sequenced. Sequencing libraries were generated by PCR from the photo-released indexing oligos. Pooled libraries were single-sequenced at 27 base pairs and with the single-index workflow  on an Illumina NovaSeq S4 instrument.

value: Brain

tag: strain

value: Other

tag: genotype

value: Cortex

value: FLASH 1x10Gy


title: A15-PC

status: Public on Jul 07 2026

type: SRA

city: Bethesda

first: Aaron

middle: M

last: Cypess

state: Maryland

address: 10 Center Drive, 5N318A

department: NIDDK - DEOB

country: USA

institute: National Institutes of Health

description: Library name: sample_64

library_source: transcriptomic

data_processing:
Data quality check was performed using FastQC (v0.11.8). The adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5). Contamination removal was performed using Bowtie2 (v2.5.1). Alignment was performed using STAR (v2.7.3a). The raw read counts were estimated using HTSeq (v0.11.2). Read count data were normalized using DESeq2. Additionally the aligned reads were used for estimating expression of the genes using cufflinks (v2.2.1). The expression values are also reported in FPKM (Fragments per kilobase per million) units for each gene. Additionally, RNA-Seq quality control was performed using RNA-SeQC (v1.1.8), RSeQC (v3.0.1) and MultiQC (v1.7).
Assembly: GRCh38/hg38
Supplementary files format and content: Excel spreadsheet containing DESeq2-normalized count
Supplementary files format and content: Salmon-based raw counts as tab-separated value file

molecule: total RNA

organism: Homo sapiens

source_name: pericardial

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen, Germantown, MD) following the manufacturer’s protocol
Takara SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian

tag: tissue

value: pericardial


title: A15-O

description: Library name: sample_63

source_name: omental

value: omental


title: scRNA-Seq of homo sapiens: Sample (KS1-PRE) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

city: St. Louis

first: Lee

last: Ratner

state: Missouri

address: 4451 Clayton Ave, St. Louis

department: Department of Medicine

institute: Washington University in St. Louis

description: Library name: KS1A

data_processing:
Cell Ranger count and multi v7.1.0 were used for alignment and gene expression quantification.
Reads were aligned against a custom reference including the human genome (GRCh38/hg38), KSHV genome (Strain GK18, GCF_000838265.1), and HIV-1 genome (GCF_000864765.1).
Feature-barcode matrices were quality controlled, normalized, and scaled using Seurat v4.2.1.
Principal component analysis was performed using highly variable genes followed by clustering (resolution = 0.7).
Dimensionality reduction and visualization were performed using t-SNE and UMAP.
Cell type annotations were assigned using SingleR v2 with the Human Primary Cell Atlas reference dataset and refined manually.
Differential expression analysis was performed using Seurat FindMarkers with the Wilcoxon rank-sum test.
Assembly: GRCh38/hg38 human genome; KSHV genome (Strain GK18, GCF_000838265.1); HIV-1 genome (GCF_000864765.1)
Supplementary files format and content: KS_scRNAseq_seurat.rds: This file contains quality-controlled single-cell gene expression count matrices, normalized expression data, cell-level metadata, clustering assignments, dimensionality reduction embeddings (UMAP and PCA), cell type annotations, and KSHV-related annotations used in the published analyses. The Seurat (.rds) file is intended for use in R/Seurat workflows. The file contains the processed assays and metadata required to reproduce the downstream analyses and visualizations presented in the study.
Supplementary files format and content: KS_scRNAseq_seurat.h5ad: This file contains quality-controlled single-cell gene expression count matrices, normalized expression data, cell-level metadata, clustering assignments, dimensionality reduction embeddings (UMAP and PCA), cell type annotations, and KSHV-related annotations used in the published analyses. The AnnData (.h5ad) file is intended for use in Python/Scanpy workflows. The file contains the processed assays and metadata required to reproduce the downstream analyses and visualizations presented in the study.

source_name: Skin

extract_protocol:
Viably frozen (in Bambanker, serum-free cell freezing media. Sigma) single-cell suspensions were prepared from fresh primary skin biopsy samples using enzymatic digestion and gentle manual tissue dissociation (Whole Skin Dissociation Kit, Miltenyi Biotech) and thawed immediately prior to submission for single cell RNA sequencing. It should be noted that sample preparation without enzymatic digestion dramatically diminished the diversity and abundance of cell populations obtained from skin lesions. An estimated 50,000 cells were submitted for sequencing for each sample, though there was some variation between samples in the viable cells submitted. As for Peripheral blood mononuclear cell samples (PBMC), they were processed separately according to standard PBMC isolation procedures prior to single-cell RNA sequencing.
Single-cell libraries were prepared using the 10x Genomics 5′ or 3′ immune profiling/scRNA-seq protocol by GTAC@MGI. Resulting 10x libraries were sequenced on an Illumina NovaSeq 6000 using an S4 flow cell and 300-cycle sequencing, targeting approximately 100,000 reads per cell.

value: Skin

tag: cell type

value: Mixed skin lesion cells

tag: subject status

value: patient with Kaposi Sarcoma


title: A15-AD

description: Library name: sample_62

source_name: periadrenal

value: periadrenal


title: CHI209 Unknown WT

city: Memphis

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Pl, M2426

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Library name: CHI209

data_processing:
Adapter sequences were removed by TrimGalore (v0.6.3).
STAR (v2.7.9a) was then used for alignment to the mouse reference genome (GRCm38) in a splice-site aware manner based on Gencode M22 primary assembly annotations.
Gene level quantifications were derived using RSEM (v1.3.3).
Assembly: Mouse mm10
Supplementary files format and content: Processed data contains raw counts per gene for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: dorsal striatum

extract_protocol:
Cell contents were extracted using the recording electrode following patch-clamp recordings. Contents were directly lysed in buffer from the SMART-Seq mRNA Single Cell LP kit (Takara, 634787).
Libraries were constructed from single cells using the SMART-Seq mRNA Single Cell LP kit (Takara, 634787).

value: dorsal striatum

tag: group

value: Unknown

value: cholinergic interneuron

value: WT

tag: Sex

value: male

tag: batch

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist

tag: mouse id

tag: rt lot

tag: date lp

tag: lp lot

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: A14-SQ

description: Library name: sample_60

source_name: subcutaneous

tag: tissue

value: subcutaneous


title: CHI207 Active WT

description: Library name: CHI207

value: Active

tag: cell type

tag: genotype


title: A14-SCLV

description: Library name: sample_59

source_name: supraclavicular

value: supraclavicular


title: scRNA-Seq of homo sapiens: Sample (KS1-POST) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS1B

tag: subject status


title: scRNA-Seq of homo sapiens: Sample (KS18) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS18


title: A14-PV

description: Library name: sample_58

source_name: paravertebral

value: paravertebral


title: CHI205 Silent WT

description: Library name: CHI205

tag: group

value: Silent

tag: Sex


title: A14-PC

description: Library name: sample_57


title: scRNA-Seq of homo sapiens: Sample (KS16) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS16


title: A14-AD

description: Library name: sample_55


title: CHI204 Active WT

description: Library name: CHI204

tag: batch

tag: date ephys


title: scRNA-Seq of homo sapiens: Sample (KS15) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS15


title: A14-O

description: Library name: sample_56


title: CHI203 Unknown WT

description: Library name: CHI203

tag: dob

tag: age days


title: A13-SQ

description: Library name: sample_53


title: A13-SCLV

description: Library name: sample_52


title: scRNA-Seq of homo sapiens: Sample (KS13) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS13


title: CHI202 Active WT

description: Library name: CHI202

tag: electrophysiologist

tag: mouse id


title: scRNA-Seq of homo sapiens: Sample (KS12-PBMC) obtained from PBMC (non-tumor) of patient with Kaposi Sarcoma.

description: Library name: KS12-PBMC

source_name: PBMC

value: PBMC


title: A13-PC

description: Library name: sample_50

value: pericardial


title: scRNA-Seq of homo sapiens: Sample (KS12) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS12


title: A13-AD

description: Library name: sample_48


title: A13-O

description: Library name: sample_49

value: omental


title: A12-SQ

description: Library name: sample_46


title: scRNA-Seq of homo sapiens: Sample (KS11-PBMC) obtained from PBMC (non-tumor) of patient with Kaposi Sarcoma.

description: Library name: KS11-PBMC


title: CHI199 Active WT

description: Library name: CHI199

tag: rt lot

tag: date lp


title: CHI200 Active WT

description: Library name: CHI200

tag: lp lot

tag: index lot


title: A12-SCLV

description: Library name: sample_45


title: scRNA-Seq of homo sapiens: Sample (KS10-PRE) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS10A

value: Skin


title: A12-PV

description: Library name: sample_44


title: CHI198 Active WT

description: Library name: CHI198

tag: date seq

tag: seq srm_sample_id


title: A12-PC

description: Library name: sample_43

tag: tissue


title: scRNA-Seq of homo sapiens: Sample (KS10-POST) obtained from Skin (tumor) of patient with Kaposi Sarcoma.

description: Library name: KS10B

tag: cell type

value: Mixed skin lesion cells


title: CHI197 Unknown WT

description: Library name: CHI197

tag: genotype


title: scRNA-Seq of homo sapiens: Sample (KS10-PBMC) obtained from PBMC (non-tumor) of patient with Kaposi Sarcoma.

description: Library name: KS10-PBMC

tag: subject status

value: patient with Kaposi Sarcoma


title: A10-U

description: Library name: sample_41

source_name: urinary bladder

value: urinary bladder


title: A12-AD

description: Library name: sample_42

value: periadrenal


title: A10-SQ

description: Library name: sample_40


title: A10-SCLV

description: Library name: sample_39


title: A10-PV

description: Library name: sample_38


title: BCC7

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
Library name: LY081221
BCC7 (LY081221)

library_source: transcriptomic single cell

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina).
Raw sequencing data provided as fastq files were processed using the count function of the Cell Ranger pipeline (v. 5.0.1, 10x Genomics).
The count function allowed us to demultiplex reads to individual cells, to align the reads to the human GRCh38 reference (v. GRCh38-2020-A), and to generate filtered matrices of gene counts by cell barcodes.
Assembly: hg38
Supplementary files format and content: The processed data files consist of the 3 files generated by Cell Ranger v5.0.1, containing only detected cellular barcodes (filtered_feature_bc_matrix). The file "matrix.mtx.gz" is a sparse matrix containing number of UMIs per gene (in rows) per single cell (in columns). The file "barcodes.tsv.gz" contains the list of detected cellular barcodes (i.e. single cell identities) corresponding to the columns in "matrix.mtx.gz", and the file "features.tsv.gz" contains the genes corresponding to the rows in "matrix.mtx.gz".

source_name: skin biopsy

extract_protocol:
Fresh tumor tissue was minced and enzymatically digested to obtain a single cell suspension. Single living cells were then FACS sorted. The cells were resuspended to reach a target final concentration of approximately 1,000 cells/μl.  ScRNA-seq was performed using the Chromium Next GEM single cell 3' reagent kit v3.1 (10xGenomics) following the manufacturer's protocol with a target number of captured cells of 10,000.
Sequencing libraries were prepared after GEM generation and barcoding using the Chromium Next GEM single cell 3'reagent kit v3.1 (10xGenomics) the following manufacturer's protocol.

value: skin biopsy

value: Mohs specimen residual debulking piece of skin

tag: tumor type

value: infiltrative basal cell carcinoma

tag: location

value: upper lip


title: CHI195 Active WT

description: Library name: CHI195

value: dorsal striatum

tag: group

value: cholinergic interneuron

value: WT

tag: Sex

value: male

tag: batch

tag: date ephys


title: CHI194 Active Het

description: Library name: CHI194

value: Active

value: Het

tag: dob

tag: age days

tag: electrophysiologist

tag: mouse id


title: A9-U

description: Library name: sample_36


title: BCC6

description:
Library name: LY071221
BCC6 (LY071221)

value: ear


title: A9-SQ

description: Library name: sample_35

value: subcutaneous


title: HepG2 cells, strong-cloaked eGFP mRNA, biological rep 3

city: Beijing

first: Xiangdong

last: Zhang

state: Beijing

address: Tsinghua University

country: China

institute: Tsinghua Univercity

description:
Library name: HepG2_S_rep3
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-S-3

data_processing:
Raw sequencing reads were quality-trimmed to remove adaptor sequences and low-quality sequences.
Trimmed reads were aligned to the human reference genome GRCh38 using HISAT2.
Gene-level raw counts were generated using HTSeq. RPKM values were calculated for expression quantification.
Differential expression analysis was performed with DESeq2 (v1.46.0) in R (v4.4.2). Genes with >=10 counts in at least 3 samples were retained (18,404 expressed genes). Duplicate gene symbols were merged by summing raw counts. Seven pairwise Wald tests were performed (O vs UT, W vs UT, M vs UT, S vs UT, W vs O, M vs O, S vs O) with differentially expressed genes defined by FDR < 0.05 (Benjamini-Hochberg correction) and |log2 fold change| >= 1.
Variance-stabilizing transformation (VST, blind=TRUE) was applied for unsupervised transcriptome visualization. PCA was run on the top 2,000 most variable genes. Pairwise Spearman correlations were calculated across all 15 samples. Over-representation analysis (ORA) was conducted on DE gene lists via the Enrichr API using MSigDB Hallmark 2020, GO Biological Process 2023, and KEGG 2021 Human gene sets with adjusted p-value < 0.05 as the significance threshold.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw gene counts for all 15 samples (41,412 genes x 15 sample columns).

growth_protocol: HepG2 cells (RRID:CVCL_0027) were obtained from the Cell Resource Center, Peking Union Medical College (PCRC), STR-identified and mycoplasma-detected. Cells were cultured in DMEM complete medium (DMEM (C11995500BT, Thermo) supplemented with 10% FBS (40130ES76, YEASEN), 1x NEAA (60707ES60, YEASEN), 1x GlutaMAX (35050061, Thermo), and 1x penicillin-streptomycin (60162ES76, YEASEN)) in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
At 48 h post-transfection, cells were directly lysed with Trizol reagent (BN20537, BIORIGIN). The lysates were shipped to Genewiz (Azenta Life Sciences) for sequencing services, where total RNA was isolated and quality-verified with an RNA integrity number (RIN) cutoff of 7.0.
Strand-specific mRNA libraries were constructed via oligo(dT)-mediated poly(A) enrichment. Libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: HepG2 cells were seeded at 5x10^5 cells/well in 6-well plates and grown to 70-80% confluence. Cells were transfected with 1 ug of eGFP mRNA under five conditions using NanoLNP Transfection Reagent for RNA (CT0010, CYTOCH): (1) untransfected control (UT); (2) non-cloaked eGFP mRNA (O); (3) weak-cloaked eGFP mRNA (W, 0.1 M CR-3, 0.5 h, 25C); (4) medium-cloaked eGFP mRNA (M, 0.5 M CR-3, 1 h, 30C); (5) strong-cloaked eGFP mRNA (S, 1 M CR-3, 2 h, 37C). n=3 biological replicates per group. Cells were harvested at 48 h post-transfection.

tag: cell line

tag: treatment

value: transfected with 1 ug strong-cloaked eGFP mRNA (1 M CR-3, 2 h, 37C) via NanoLNP


title: A9-SCLV

description: Library name: sample_34

value: supraclavicular


title: CHI193 Active Het

description: Library name: CHI193

tag: rt lot

tag: date lp

tag: lp lot

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: A9-PV

description: Library name: sample_33

tag: tissue

value: paravertebral


title: HepG2 cells, strong-cloaked eGFP mRNA, biological rep 2

description:
Library name: HepG2_S_rep2
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-S-2

tag: genotype


title: A9-PC

description: Library name: sample_32

value: pericardial


title: A9-O

description: Library name: sample_31

value: omental


title: HepG2 cells, strong-cloaked eGFP mRNA, biological rep 1

description:
Library name: HepG2_S_rep1
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-S-1


title: A9-AD

description: Library name: sample_30

value: periadrenal


title: A8-U

description: Library name: sample_29

value: urinary bladder


title: HepG2 cells, medium-cloaked eGFP mRNA, biological rep 3

description:
Library name: HepG2_M_rep3
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-M-3

value: transfected with 1 ug medium-cloaked eGFP mRNA (0.5 M CR-3, 1 h, 30C) via NanoLNP


title: A8-SCLV

description: Library name: sample_28


title: CHI189 Active Het

description: Library name: CHI189

tag: group

tag: cell type

tag: Sex


title: HepG2 cells, medium-cloaked eGFP mRNA, biological rep 2

description:
Library name: HepG2_M_rep2
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-M-2


title: A8-PC

description: Library name: sample_26


title: A8-AD

description: Library name: sample_25


title: HepG2 cells, medium-cloaked eGFP mRNA, biological rep 1

description:
Library name: HepG2_M_rep1
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-M-1


title: A6-U

description: Library name: sample_24


title: A6-SQ

description: Library name: sample_23


title: HepG2 cells, weak-cloaked eGFP mRNA, biological rep 3

description:
Library name: HepG2_W_rep3
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-W-3

value: transfected with 1 ug weak-cloaked eGFP mRNA (0.1 M CR-3, 0.5 h, 25C) via NanoLNP


title: A6-SCLV

description: Library name: sample_22


title: CHI186 Active Het

description: Library name: CHI186

value: dorsal striatum

tag: batch

tag: date ephys

tag: dob


title: HepG2 cells, weak-cloaked eGFP mRNA, biological rep 2

description:
Library name: HepG2_W_rep2
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-W-2


title: A6-PC

description: Library name: sample_20


title: A6-O

description: Library name: sample_19


title: A8-PV

description: Library name: sample_27


title: CHI188 Active Het

description: Library name: CHI188

value: cholinergic interneuron

tag: age days

tag: electrophysiologist

tag: mouse id


title: HepG2 cells, weak-cloaked eGFP mRNA, biological rep 1

description:
Library name: HepG2_W_rep1
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-W-1

tag: cell line

value: WT

tag: treatment


title: A6-AD

description: Library name: sample_18


title: CHI187 Active Het

description: Library name: CHI187

value: male

tag: rt lot

tag: date lp

tag: lp lot


title: CHI184 Active Het

description: Library name: CHI184

value: Active

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: A5-U

description: Library name: sample_17

tag: tissue


title: HepG2 cells, non-cloaked eGFP mRNA, biological rep 3

description:
Library name: HepG2_O_rep3
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-O-3

tag: genotype

value: transfected with 1 ug non-cloaked eGFP mRNA via NanoLNP


title: A5-SQ

description: Library name: sample_16


title: CHI183 Active Het

description: Library name: CHI183

tag: group

tag: cell type

value: Het

tag: Sex


title: A5-SCLV

description: Library name: sample_15


title: A6-PV

description: Library name: sample_21


title: A14-U

description: Library name: sample_61


title: CHI208 Active WT

description: Library name: CHI208

tag: batch

tag: date ephys

tag: dob


title: HepG2 cells, non-cloaked eGFP mRNA, biological rep 2

description:
Library name: HepG2_O_rep2
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-O-2


title: A5-PC

description: Library name: sample_14


title: CHI182 Active Het

description: Library name: CHI182

tag: age days

tag: electrophysiologist

tag: mouse id


title: A5-O

description: Library name: sample_13


title: HepG2 cells, non-cloaked eGFP mRNA, biological rep 1

description:
Library name: HepG2_O_rep1
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-O-1

tag: cell line

tag: treatment


title: A13-U

description: Library name: sample_54


title: CHI185 Active Het

description: Library name: CHI185

tag: rt lot

tag: date lp

tag: lp lot


title: A5-AD

description: Library name: sample_12


title: CHI181 Silent Het

description: Library name: CHI181

value: Silent

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: A4-SQ

description: Library name: sample_11

tag: tissue

value: subcutaneous


title: A4-SCLV

description: Library name: sample_10

value: supraclavicular


title: HepG2 cells, untransfected control, biological rep 3

description:
Library name: HepG2_UT_rep3
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-3

tag: genotype

value: untransfected


title: CHI180 Active Het

description: Library name: CHI180

tag: group

tag: cell type

tag: Sex


title: A13-PV

description: Library name: sample_51

value: paravertebral


title: A4-PC

description: Library name: sample_9

value: pericardial


title: HepG2 cells, untransfected control, biological rep 2

description:
Library name: HepG2_UT_rep2
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-2


title: CHI201 Active WT

description: Library name: CHI201

tag: batch

tag: date ephys

tag: dob


title: A4-O

description: Library name: sample_8

value: omental


title: CHI178 Silent WT

description: Library name: CHI178

tag: age days

tag: electrophysiologist

tag: mouse id


title: A4-AD

description: Library name: sample_7

value: periadrenal


title: A12-U

description: Library name: sample_47

value: urinary bladder


title: A3-U

description: Library name: sample_6


title: HepG2 cells, untransfected control, biological rep 1

description:
Library name: HepG2_UT_rep1
Column name in 20260625-194448_gene_count_matrix_filtered.txt: HepG2-1

tag: cell line

tag: treatment


title: CHI177 Silent WT

description: Library name: CHI177

tag: rt lot

tag: date lp

tag: lp lot


title: A3-SQ

description: Library name: sample_5


title: PH5_Treat

city: Shenzhen

first: HE

middle: Mu

last: Hua

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

description: Library name: Sample20

data_processing:
Raw reads were trimmed and filtered using fastp (v0.23.4) to remove adapter sequences and low-quality reads, generating clean reads.
Clean reads were aligned to the human reference genome HG38 using STAR (v2.7) and Bowtie2 (v2.2.4), and BAM files were produced.
The pseudoU-BID-seq pipeline was applied to calculate sequencing depth and deletion rate of each base site, and candidate pseudouridine (Ψ) sites were identified.
Candidate Ψ sites were filtered by sequencing depth and deletion rate. Differential pseudouridine modification analysis was performed between treated and input groups.
Assembly: Human reference genome: HG38 (GRCh38)
Supplementary files format and content: mRNA_Profiling.xlsx

source_name: Lung tissue

extract_protocol:
Total RNA was extracted from human samples using TRIzol reagent. RNA concentration, purity and integrity were assessed via NanoDrop ND-1000 and agarose gel electrophoresis. Qualified RNA was used for BID-seq library construction.
3’ and 5’ adapters were sequentially ligated to fragmented RNA using the GenSeq Small RNA Library Prep Kit (GenSeq, Inc.). One portion of adapter-ligated RNA was used to construct Input libraries (Control1-Control5, PH1-PH5). The remaining RNA was incubated with bisulfite reagent at 70 °C for 3 hours, followed by desulfonation in RNA Desulphonation Buffer (Zymo Research) at room temperature for 1 hour to generate treated samples (Control1-Control5, PH1-PH5). Both Input and treated RNA were used for cDNA synthesis and PCR amplification. Libraries were purified by gel extraction and sequenced on Illumina platform with 150 bp single-end mode.

treatment_protocol: RNA Bisulfite-induced deletion sequencing (BID-seq) was performed by Cloudseq Biotech Inc. (Project ID: 2024042676; Shanghai, China) following published protocols with minor modifications. Total RNA was isolated from 5 pulmonary hypertension (PH) patient samples and 5 healthy control samples using TRIzol reagent (Invitrogen, USA). RNA quality and purity were quantified and qualified before subsequent experiments. Purified RNA was fragmented with RNA Fragmentation Reagents (Thermo Fisher Scientific, USA) at 70 °C for 14 minutes, then subjected to 3’-end repair and 5’-phosphorylation using T4 polynucleotide kinase (Thermo Fisher Scientific).

value: Lung tissue


title: A3-SCLV

description: Library name: sample_4


title: CHI175 Unknown WT

description: Library name: CHI175

value: dorsal striatum

value: Unknown

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: PH5_Input

description: Library name: Sample19

tag: tissue


title: A3-PC

description: Library name: sample_3


title: A3-O

description: Library name: sample_2


title: CHI171 Silent WT

description: Library name: CHI171

tag: group

tag: cell type

value: cholinergic interneuron

tag: genotype

value: WT


title: RNAseq, SMC1, aux, rep3

city: Tokyo

first: Shoin

last: Tei

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description: Library name: RNAseq_SMC1_aux_rep3

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR (version 2.7.10a). Transcript abundance was quantified using RSEM (version 1.3.3). Differential expression analysis was performed with edgeR (version 3.40.2; FDR < 0.05).
Assembly: hg38
Supplementary files format and content: BigWig

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium containing 10% FBS, penicillin, and streptomycin solution (Wako) at 37 C with 5% CO2.

extract_protocol:
Total RNA was extracted from HCT-116 cells with TRIzol reagent (Invitrogen) and purified with NucleoSpin RNA II kit (Macherey-Nagel), following the manufacturer’s instructions. rRNA was depleted with NEBNext rRNA Depletion Kit (New England BioLabs).
The library for sequencing was prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs)..

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete RAD21. RNA interference was performed with Lipofectamine RNAiMax (Invitrogen) using siRNA duplexes at a final RNA concentration of 50 nM, according to the manufacturer’s instructions. Cells were collected two days after transfection. The siRNA sequences are listed in the key resource table.

value: Auxin


title: CHI169 Unknown WT

description: Library name: CHI169

tag: Sex

value: male

tag: batch

tag: date ephys


title: A3-AD

description: Library name: sample_1


title: Control5_Treat

description: Library name: Sample18


title: CHI196 Silent WT

description: Library name: CHI196

tag: dob

tag: age days

tag: electrophysiologist


title: RNAseq, SMC1, ctrl, rep3

description: Library name: RNAseq_SMC1_ctrl_rep3

tag: cell line

tag: treatment

value: DMSO


title: Control5_Input

description: Library name: Sample17


title: RNAseq, SMC1, aux, rep2

description: Library name: RNAseq_SMC1_aux_rep2


title: CHI168 Unknown WT

description: Library name: CHI168

tag: mouse id

tag: rt lot

tag: date lp


title: RNAseq, SMC1, ctrl, rep2

description: Library name: RNAseq_SMC1_ctrl_rep2


title: Patient HGADF188, dermal fibroblasts, lamin A/C Gly608Gly

city: Cambridge

first: Sebastian

last: Sewerin

state: MA

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

description: Library name: LMNAIII_HGADF188

data_processing:
Demultiplexing and FASTQ file generation were performed using Illumina’s bcl2fastq2 software (v2.20.0).
RNA‐Seq data were analyzed using the Cologne Center for Genomics’ in‐house pipeline for RNA‐Seq analysis based on the Nextflow domain-specific language (v20.01.0, build 5264).
Sequence reads were adapter‐trimmed with Trimmomatic (v0.38), removing sequences of length < 18nt after trimming.
Sequence reads were then mapped against the hg38 human reference genome and the gene assembly v101 using STAR aligner (v2.6.1a) with the default settings.
The count matrix was generated using Subread (v1.6.4). Counts were normalized with DESeq2 (v1.20.0).
Assembly: hg38
Supplementary files format and content: .xlsx file containing raw counts, DESeq2 normalized values, and FPKM values for all samples in three separate tabs that correspond to the type of value

source_name: Human dermal fibroblasts

growth_protocol: Primary human dermal fibroblasts were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% v/v FBS and 1% v/v penicillin/ streptomycin in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was harvested from pelleted cells using Qiagen's RNeasy Plus Mini Kit, essentially according to the manufacturer’s instructions. RNA‐Seq libraries were prepared with 200ng total RNA inputs.
RNA‐Seq libraries were prepared with the Illumina TruSeq Stranded mRNA Library Prep assay based on the recommended protocol.

tag: individual

value: Patient HGADF188

value: Human dermal fibroblasts

value: LMNA p.(Gly608Gly)


title: RNAseq, SMC1, aux, rep1

description: Library name: RNAseq_SMC1_aux_rep1


title: CHI167 Unknown WT

description: Library name: CHI167

tag: lp lot

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: Patient HGADF164, dermal fibroblasts, lamin A/C Gly608Gly

description: Library name: LMNAIII_HGADF164

value: Patient HGADF164

tag: cell type

tag: genotype


title: RNAseq, aux, XRN2, KD, rep3

description: Library name: RNAseq_aux_XRN2_KD_rep3

value: Auxin, XRN2 knockdown


title: CHI166 Active WT

description: Library name: CHI166

tag: tissue

tag: group

value: Active

tag: Sex

tag: batch


title: RNAseq, SMC1, ctrl, rep1

description: Library name: RNAseq_SMC1_ctrl_rep1


title: Patient 3.9.1, dermal fibroblasts, lamin A/C Arg482Trp

description: Library name: LMNA_391II

value: Patient 3.9.1

value: LMNA p.(Arg482Trp)


title: RNAseq, XRN2, KD, rep3

description: Library name: RNAseq_XRN2_KD_rep3

value: XRN2 knockdown


title: RNAseq, aux, XRN2, KD, rep2

description: Library name: RNAseq_aux_XRN2_KD_rep2


title: CHI164 Silent WT

description: Library name: CHI164

value: Silent

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist


title: Patient 3.8.1, dermal fibroblasts, lamin A/C Arg482Trp

description: Library name: LMNA_381II

value: Patient 3.8.1


title: RNAseq, XRN2, KD, rep2

description: Library name: RNAseq_XRN2_KD_rep2

tag: cell line

tag: treatment


title: RNAseq, aux, XRN2, KD, rep1

description: Library name: RNAseq_aux_XRN2_KD_rep1


title: CHI163 Silent WT

description: Library name: CHI163

value: dorsal striatum

tag: mouse id

tag: rt lot

tag: date lp


title: RNAseq, XRN2, KD, rep1

description: Library name: RNAseq_XRN2_KD_rep1


title: CHI162 Silent Het

description: Library name: CHI162

value: cholinergic interneuron

value: Het

value: female

tag: lp lot

tag: index lot

tag: date seq


title: RNAseq, aux, rep2

description: Library name: RNAseq_aux_rep2

value: Auxin


title: CHI161 Silent Het

description: Library name: CHI161

tag: cell type

tag: genotype

tag: seq srm_sample_id


title: Patient 3.3.1, dermal fibroblasts, lamin A/C Arg349Trp, biological replicate 2

description: Library name: LMNA_331bI

tag: individual

value: Patient 3.3.1

value: LMNA p.(Arg349Trp)


title: RNAseq, aux, rep1

description: Library name: RNAseq_aux_rep1


title: CHI160 Silent Het

description: Library name: CHI160

tag: tissue

tag: group

tag: Sex

tag: batch


title: Patient 3.10.1, dermal fibroblasts, lamin A/C Arg349Trp

description: Library name: LMNA_3101I

value: Patient 3.10.1

value: Human dermal fibroblasts


title: RNAseq, ctrl, rep1

description: Library name: RNAseq_ctrl_rep1

value: DMSO


title: RNA-seq_SCC13,p63 siRNA,rep2

city: Stanford

first: Namyoung

last: Jung

state: CA

address: 269 Campus Dr. CCSR Room 2150

department: Medicine

institute: Stanford University

data_processing:
Single-end reads were aligned using STAR aligner (2.5.4b) using GENCODE v19 gene annotation in hg19 with default settings.
To obtain raw expected read counts, RSEM (1.3.0) was used, and these raw counts were subjected to differential expression analysis with DESeq2 (1.26.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes expected counts from RSEM for each sample

growth_protocol: CAL27 human squamous cell carcinoma cells were obtained from ATCC (CRL-2095) and cultured in DMEM F:12 (ThermoFisher) supplemented with 10% FBS. SCC-13 human squamous cell carcinoma cells were obtained from J.G.Rheinwald, Dana-Farber/Harvard Cancer Center as a generous gift and cultured in Keratinocyte-SFM (ThermoFisher) supplemented with 25 ug/ml BPE, 0.2ng/ml EGF (GIBCO, Thermofisher) and 0.3mM CaCl2 (Sigma-Aldrich). Primary human keratinocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Keratinocytes were cultured in 1:1 Keratinocyte-SFM (ThermoFisher) and Medium 154 (ThermoFisher) supplemented with HKGS (ThermoFisher). Keratinocytes were induced to differentiate by the addition of 1.2mM calcium for 3 days at full confluence.

extract_protocol:
Cells were harvested and pellets were flash frozen on dry ice. RNA was extracted using the RNeasy Mini Kit (QIAGEN).
RNA-seq libraries were generated on two biological replicates for each group using the Lexogen Quant-seq 3’ mRNA -seq Library Prep Kit FWD (Lexogen) according to the manufacturer’s protocol. The libraries were sequenced as single-end 1X101bp reads on an Illumina HiSeq2000 or 1X150bp reads on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Dharmacon siStable siRNA was designed to target PAN-p63 with the sequences as follows: sense (5’-CGACAGUCUUGUACAAUUUUU-3’) and antisense (5’-AAAUUGUACAAGACUGUCGUU-3’) or FOXK1 with si1 sense (5’-GAACGGAAAGCAUGCGGUU-3’), antisense (5’-AACCGCAUGCUUUCCGUUC-3’) and si2 sense (5'-GCAGUGUACCUUCCGGUUU-3’) and antisense (5’-AAACCGGAAGGUACACUGC-3’). 1-1.5nmol of siRNA was electroporated into 1 million keratinocytes and 2 million SCC cells using the human keratinocyte Nucleofector kit (Lonza) according to the manufacturer’s protocol. After 24 hours, fresh media was added to the cells and cells were subsequentially seeded for differentiation after 48 h transfection or maintained at subconfluence. The negative control was the ON-TARGET Smart pool negative control (Horizon, D-001810-10-20).

value: Squamous cell carcinoma

value: p63 knockdown


title: CHI159 Silent Het

description: Library name: CHI159

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist


title: RNA-seq_SCC13,p63 siRNA,rep1

tag: cell line

tag: treatment


title: CHI158 Silent Het

description: Library name: CHI158

tag: mouse id

tag: rt lot

tag: date lp

tag: lp lot


title: Control subject pa01, dermal fibroblasts

description: Library name: Control2_pa01

value: Control subject pa01

tag: cell type

tag: genotype

value: LMNA WT


title: RNA-seq_SCC13,control siRNA,rep1

value: WT


title: RNA-seq_CAL27,p63 siRNA,rep2


title: CHI157 Silent Het

description: Library name: CHI157

value: Silent

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: RNA-seq_CAL27,p63 siRNA,rep1


title: Control subject 3.3.3, dermal fibroblasts, parent of patient 3.3.1

description: Library name: Cntrl333

tag: individual

value: Control subject 3.3.3


title: RNA-seq_CAL27,control siRNA,rep2


title: CHI156 Active Het

description: Library name: CHI156

tag: tissue

value: dorsal striatum

tag: group

value: Active

tag: Sex

tag: batch


title: crTMPRSS2 knockout rat lung, biological replicate 3

city: Berlin

first: Yue

last: Qiu

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center - Berlin

description:
Library name: seq7
Novogene sample seq7; library ID ERRA250001433-1a; group KO; raw reads 42,435,952; clean reads 39,547,728.

data_processing:
Raw sequencing data were converted to FASTQ format by Illumina CASAVA/base calling and filtered by Novogene to generate clean reads.
Clean reads were aligned to the Rattus norvegicus reference genome GCF_015227675.2/mRatBN7.2 using HISAT2 v2.2.1.
Transcripts were assembled with StringTie v2.2.3 and gene-level read counts were quantified with featureCounts v2.0.6. FPKM values were calculated for expression profiling.
Differential expression between crTMPRSS2 knockout and WT lung samples was analyzed with DESeq2 v1.42.0 using padj <= 0.05 and |log2FoldChange| >= 1 as the significance threshold.
GO and KEGG enrichment analyses were performed using clusterProfiler v4.8.1.
Assembly: Rattus norvegicus mRatBN7.2, NCBI RefSeq assembly GCF_015227675.2
Supplementary files format and content: gene_count.txt: tab-delimited gene-level raw read count matrix for seq1, seq2, seq3, seq5, seq6, and seq7, with gene annotations.
Supplementary files format and content: gene_fpkm.txt: tab-delimited gene-level FPKM expression matrix for all six lung samples. KOvsWT_deg_all.txt: differential expression result table for crTMPRSS2 knockout versus WT lung tissue, including fold change and statistical results.

organism: Rattus norvegicus

source_name: lung

growth_protocol: WT and crTMPRSS2 knockout rats on a Sprague-Dawley background were used. The crTMPRSS2 rat line was generated by CRISPR/Cas9-mediated genome editing targeting the rat Tmprss2 gene. Lung tissue was collected for transcriptomic profiling.

extract_protocol:
Total RNA was extracted from lung tissues of WT and crTMPRSS2 rats using TRIzol™ reagent. The isolated RNA was submitted to Novogene in Munich, Germany, where RNA integrity assessment, library preparation, sequencing, and initial data processing were performed according to the provider’s standard workflow.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, PCR amplification, purification, library QC by Qubit/qPCR/Bioanalyzer, pooling, and sequencing on an Illumina platform. Layout: paired-end, 150 bp reads.

treatment_protocol: No experimental treatment was applied; samples were compared by genotype (crTMPRSS2 knockout vs wild type).

value: lung

value: crTMPRSS2 knockout


title: RNA-seq_CAL27,control siRNA,rep1


title: CHI155 Active Het

description: Library name: CHI155

value: cholinergic interneuron

value: Het

value: female

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist


title: Control subject 1.4.3, dermal fibroblasts

description: Library name: Cntrl143

value: Control subject 1.4.3


title: mNETseq, aux, rep3

description: Library name: mNETseq_aux_rep3

data_processing:
Reads were aligned to the human genome (hg38) with BWA-MEM (version 0.75) using the following parameters: -5SP -T0 -t16.70 Ligation-junction detection, read sorting, PCR-duplicate removal, and pair-file generation were performed using Pairtools (version 0.3.0). Matrix files were generated from the pairs files using Juicer (version 1.22.01) at 5 kb, 2 kb, and 1 kb resolutions. Loops were identified using Juicer Tools HiCCUPS and Mustache (version 1.2.0) at the same resolutions. Loops detected by both tools were combined to generate a set of Micro-C loops. TADs were identified using Juicer Tools Arrowhead at a 25 kb resolution. The intensity of Micro-C loops was quantified using Chromosight (version 1.6.1). For visualization, contact maps were generated using HiCExplorer (version 3.7.2), and aggregate plots were created using coolpup.py (version 1.0.0).
Assembly: hg38
Supplementary files format and content: BigWig

molecule: nuclear RNA

extract_protocol:
mNET-seq was performed as described by Nojima et al with minor modifications. A total of 1 x 108 HCT-116 cells were collected, divided into four aliquots, and washed with cold PBS. After collection by centrifugation,  cells were suspended in 4 mL of HLB+N buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 1x cOmplete EDTA-free (Roche), 1x PhosSTOP (Roche)] and incubated on ice form 5min, followed by the addition of 1 mL of HLB+NS buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 1x cOmplete EDTA-free, 1x PhosSTOP, 10% sucrose]. The supernatant was discarded after centrifugation, and the pellet was suspended in 125 μL of NUM1 lysis buffer [20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA (pH 8.0), 50% glycerol, 1x cOmplete EDTA-free, 1x PhosSTOP]. After the addition of 1.2 mL of NUM2 lysis buffer [20 mM HEPES (pH 7.5), 300 mM NaCl, 0.2 mM EDTA (pH 8.0), 7.5 mM MgCl2, 1% NP-40, 1M urea, 1x cOmplete EDTA-free, 1x PhosSTOP], the suspension was incubated on ice for 15 min with occasional vortexing. The supernatant was removed after centrifugation, and the pellet was washed with MNase buffer (1x MNase buffer, 1x BSA). Then, 100 μL of MNase reaction buffer [1x MNase buffer, 1x BSA, 400 gel units/μL MNase (New England BioLabs)] was added and incubated at 37°C for 90 min with shaking at 1400 rpm, followed by treatment with 25 mM EGTA. Supernatants from four aliquots were pooled after centrifugation and diluted with NET-2 buffer [50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 0.05% NP-40]. Fifty μL of Dynabeads Protein G (Invitrogen) were washed twice with mNET-2 buffer and resuspended in the same buffer. The beads were incubated with 5 μg of Pol II CTD antibody (mAb) (Monoclonal research institute Inc.) for 1 hour at 4°C with rotation. The beads were washed twice with mNET-2 buffer and added to the chromatin fraction. The mixture was rotated for 90 min at 4°C, and the beads were washed with mNET-2 buffer and PNKT buffer (1x T4 PNK buffer, 0.1% Tween20), followed by incubation for 6 min at 37°C in 200 mL of PNK reaction mixture [0.5 units/μL T4 Polynucleotide Kinase (New England BioLabs), 1.5 mM ATP]. RNA was eluted from the beads with TRIzol and purified using Direct-zol RNA Miniprep. To prepare Drosophila S2 mRNA as a spike-in control, total RNA was extracted from S2 cells using TRIzol (Invitrogen) and purified with the NucleoSpin RNA II kit (Macherey-Nagel), followed by mRNA purification using the Dynabeads mRNA Purification Kit (Invitrogen). The purified mRNA was fragmented using the First Strand Synthesis Reaction Buffer provided in the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs), followed by purification with RNAClean XP (Beckman Coulter) and phosphorylation using T4 Polynucleotide Kinase (New England BioLabs). The S2 mRNA was then purified using the Direct-zol RNA Miniprep Kit (ZYMO Research), and 2.5 ng was added to the mNET samples.
The library for sequencing was prepared with NEBNext Small RNA Library Prep Set for Illumina (New England BioLabs).

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete RAD21.

tag: cell line

tag: treatment

value: Auxin


title: CHI154 Active Het

description: Library name: CHI154

tag: mouse id

tag: rt lot

tag: date lp

tag: lp lot


title: crTMPRSS2 knockout rat lung, biological replicate 1

description:
Library name: seq5
Novogene sample seq5; library ID ERRA250001431-1a; group KO; raw reads 40,855,564; clean reads 38,707,378.

tag: genotype


title: mNETseq, ctrl, rep3

description: Library name: mNETseq_ctrl_rep3

value: DMSO


title: Control subject 1.4.2, dermal fibroblasts, biological replicate 1

description: Library name: Cntrl142

value: Control subject 1.4.2

tag: cell type

value: Human dermal fibroblasts


title: Patient 3.3.1, dermal fibroblasts, lamin A/C Arg349Trp, biological replicate 1

description: Library name: LMNA_331I

tag: individual

value: Patient 3.3.1

value: LMNA p.(Arg349Trp)


title: Patient 3.7.1, dermal fibroblasts, lamin A/C Arg482Trp

description: Library name: LMNA_371II

value: Patient 3.7.1

value: LMNA p.(Arg482Trp)


title: RNAseq, aux, rep3

description: Library name: RNAseq_aux_rep3


title: CHI153 Silent Het

description: Library name: CHI153

tag: tissue

value: Silent

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: WT rat lung, biological replicate 3

description:
Library name: seq3
Novogene sample seq3; library ID ERRA250001430-1a; group WT; raw reads 49,488,334; clean reads 47,275,392.

value: wild type

tag: batch


title: RNAseq, ctrl, rep2

description: Library name: RNAseq_ctrl_rep2


title: PH4_Treat

description: Library name: Sample16

value: Lung tissue


title: mNETseq, aux, rep2

description: Library name: mNETseq_aux_rep2


title: WT rat lung, biological replicate 2

description:
Library name: seq2
Novogene sample seq2; library ID ERRA250001429-1a; group WT; raw reads 43,341,494; clean reads 41,469,344.

value: lung


title: CHI152 Active Het

description: Library name: CHI152

value: dorsal striatum

tag: group

value: Active

tag: Sex

tag: date ephys

tag: dob


title: PH4_Input

description: Library name: Sample15


title: mNETseq, ctrl, rep2

description: Library name: mNETseq_ctrl_rep2

tag: cell line

tag: treatment


title: CHI151 Silent Het

description: Library name: CHI151

value: cholinergic interneuron

value: Het

tag: age days

tag: electrophysiologist

tag: mouse id

tag: rt lot


title: RNA-seq_SCC13,control siRNA,rep2

tag: cell type

value: Squamous cell carcinoma

tag: genotype

value: WT


title: WT rat lung, biological replicate 1

description:
Library name: seq1
Novogene sample seq1; library ID ERRA250001428-1a; group WT; raw reads 41,646,196; clean reads 40,443,968.

tag: tissue


title: PH3_Treat

description: Library name: Sample14


title: Control subject 1.4.2, dermal fibroblasts, biological replicate 2

description: Library name: Control1_142

tag: individual

value: LMNA WT


title: mNETseq, aux, rep1

description: Library name: mNETseq_aux_rep1

value: Auxin


title: CHI145 Silent WT

description: Library name: CHI145

value: female

tag: date lp

tag: lp lot

tag: index lot

tag: date seq


title: V2 Pool 2 RNA Replicate 10

city: Boston

first: Jeerthi

last: Kannan

address: 401 Park Dr

department: Nephrology

institute: Boston Children's Hospital

description:
Library name: V2_Pool2_RNA10
rna.r10 column in mpra_qtigc_pgl4v2_pool2.txt

library_source: other

data_processing:
For oligo sequencing, we preprocessed the raw  data using the NGMerge tool (Gaspar, BMC BIoinformatics, 2018)  to combine paired reads and remove flanking adaptor sequences. We then aligned the merged reads to the designed oligo sequences using the Bowtie2 in the end-to-end mode, with the --very-sensitive option. Next, we identified perfectly aligned reads using the optional tag AS=0. We also extracted mismatch information from the XM tags and INDEL information from the XG tags.
For barcode sequencing (both RNA and DNA), we combined the paired-end reads using the NGMerge tool and used only the 13 bp barcode sequences. We used only perfect matches of the designed barcodes for both DNA and mRNA quantification.
Supplementary files format and content: tab-separated value text files

molecule: other

growth_protocol: Mouse cardiomyocyte HL-1 cells were cultured in Claycomb medium (Sigma)

extract_protocol:
The two 200-mer oligo pools (Twist Bioscience) were first cloned into pLS-mP vector backbone, before sub-cloning into pGL4.23 (Promega) vector backbone. pLS-mP was digested with SbfI and EcoRI (New England Biolabs) to release the minimal promoter-driven eGFP gene. Oligo pools were PCR amplified using primers that are specific to the 5’ and 3’ flanking sequences and introduce overhangs complementary to the SbfI and EcoRI digested pLS-mP vector backbone. Post gel extraction cleanup (Zymo Research), amplified products were cloned using HiFi DNA Assembly master mix (New England Biolabs). The overhangs complementary to the vector backbone were designed to disrupt the original SbfI and EcoRI sites in the vector post-assembly. The cloning reaction was transformed into electrocompetent Stable cells, and transformants (>5 million/pool)  were pooled, grown overnight and maxi-prepped (Thermo Fisher Scientific) to generate the pre-reporter MPRA plasmid libraries for each of the two oligo pools (Pre-reporter/pLS-mP/Stable). These plasmid libraries were then used to generate the oligo sequencing Illumina libraries and sub-cloning of oligos into pGL4.23 vector backbone. We generated these cloned oligo libraries for potential use in future for lentiviral delivery-based MPRA.
For sub-cloning of oligos into pGL4.23, pGL4.23 DNA was first digested with KpnI and XbaI (New England Biolabs) to release the minimal promoter-driven firefly luciferase gene and generate the vector backbone for cloning of MPRA oligos. The cloned oligos in the two pre-reporter MPRA plasmid libraries in pLS-mP backbone were PCR amplified using primers that are specific to the 5’ and 3’ flanking sequences and introduce overhangs complementary to the KpnI and XbaI digested pGL4.23 vector backbone. Post gel extraction cleanup (Zymo Research), amplified products were cloned using HiFi DNA Assembly master mix (New England Biolabs). The cloning reaction was transformed into electrocompetent Stable and DH10β cells, and transformants (>5 million/pool) were pooled, grown overnight and maxi-prepped (Thermo Fisher Scientific) to generate two versions, V1 and V2, of the pre-reporter MPRA plasmid libraries for each of the two oligo pools (V1: Pre-reporter/pGL4.23/Stable; V2: Pre-reporter/pGL4.23/DH10β). Two different E. coli host cells were used for library propagation to maximize representation and recovery of test elements. These pre-reporter plasmid libraries were digested with SbfI and EcoRI (New England Biolabs), sites for which are present only in the deigned oligos, and ligated with the minimal promoter-driven eGFP reporter cassette from pLS-mP, released by SbfI and EcoRI digestion. Like above, the cloning reaction was transformed into electrocompetent Stable and DH10β cells, and transformants (>5 million/pool) were pooled, grown overnight and maxi-prepped (Thermo Fisher Scientific) to generate two versions, V1 and V2, the post-reporter MPRA plasmid libraries for each of the two oligo pools (V1: Post-reporter/pGL4.23/Stable; V2: Post-reporter/pGL4.23/DH10β).
Quality of the synthesized oligos and their representation was assessed by high throughput sequencing. For each of the two oligo pools, oligos cloned in the pre-reporter MPRA plasmid libraries (Pre-reporter/pLS-mP/Stable) were amplified using custom primers that include P5 and P7 Illumina adapter sequences to generate custom amplicon single-indexed oligo sequencing libraries. These two libraries were pooled and sequenced on Illumina MiSeq platform (2×170 + 8 base index) using custom sequencing primers to cover the entire oligo except for the 5’ and 3’ constant flanking sequences.
The post-reporter MPRA plasmid libraries (V1 and V2) were transfected using FuGENE HD Transfection Reagent (Promega) into HL-1 cells, 24h post seeding of 5 million cells in 10 cm dishes, in 10 parallel replicates per pool to ensure robustness and reproducibility. To preserve library complexity, the number of cells at the time of transfection ensures that at least 50× more cells get transfected as compared to the number of unique oligos after adjusting for ~40% transfection efficiency. Forty-eight hours post- transfection cells were harvested, and total RNA was isolated using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen). All RNA isolated was used to isolate mRNA using oligo-dT based Magnetic mRNA Isolation Kit (New England Biolabs), which was then treated with TURBO DNase (Thermo Fisher Scientific) to remove contaminating DNA. 500 ng of mRNA from each replicate was reverse transcribed with SuperScript III First-Strand Synthesis System (Thermo Fisher Scientific) in two parallel reactions using a primer downstream of the barcode, which contained a sample index and P7 Illumina adapter sequence. The two cDNA preparations for each replicate transfection were combined, and used as a template in PCR to generate the cDNA (RNA) -based MPRA barcode sequencing library with the same reverse primer and a forward primer complementary to the 3’ end of eGFP with a P5 Illumina adapter sequence. Similarly, the post-reporter MPRA plasmid libraries (V1 and V2) for each oligo pool were used as templates in PCR to generate the input plasmid (DNA) -based MPRA barcode sequencing libraries in three replicates. In total, we generated 26 (3 replicates for input plasmid DNA and 10 transfection replicates for RNA for each of the two oligo pools) custom amplicon single-indexed barcode libraries for V1, which were pooled and sequenced on the Illumina NextSeq 550 platform (2×26 + 8 base index; high-output kit) using custom sequencing primers. The same was repeated for V2.

value: cardiac muscle cell


title: PH3_Input

description: Library name: Sample13


title: mNETseq, ctrl, rep1

description: Library name: mNETseq_ctrl_rep1

value: DMSO


title: CHI142 Silent WT

description: Library name: CHI142

tag: group

tag: Sex

tag: batch

tag: seq srm_sample_id


title: PH2_Treat

description: Library name: Sample12


title: V2 Pool 2 RNA Replicate 9

description:
Library name: V2_Pool2_RNA9
rna.r9 column in mpra_qtigc_pgl4v2_pool2.txt

tag: cell line


title: CHI141 Silent WT

description: Library name: CHI141

tag: date ephys

tag: dob

tag: age days


title: EUseq, aux, rep2

data_processing:
Low-quality reads were removed with Trimmomatic (version 0.39) using the parameters LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:20. Single-end 65-bp reads were aligned to dm6 with Bowtie2 (version 2.4.5) in “--very-sensitive-“ mode and the unmapped reads were aligned to hg38 in the same mode. The removal of redundant reads and the normalization of the read number for each sample were performed with parse2wig (version 3.7.2). For visualization, we used deeptools (version 3.5.1.)
Assembly: hg38
Supplementary files format and content: BigWig files generated by parse2wig (version 3.7.2)
Library strategy: EU-seq

source_name: Colorectal carcinoma

extract_protocol:
Total RNA from HCT116 cells and drosophila S2 cells was isolated with Trizol (Invitrogen) and Nucleospin RNA II (Macherey-Nagel) following the manufacturer’s instructions. rRNA was depleted from total RNA from HCT116 cells with NEBNext rRNA Depletion Kit (NEB). mRNA was purified from total RNA from S2 cells with Dynabeads mRNA Purification Kit (Invitrogen). 200 μg of rRNA-depleted RNA of HCT116 cells and 20 μg of mRNA of S2 cells were mixed, and EU-labelled RNA was isolated with Click-iT Nascent RNA Capture Kit (Thermo Fisher). Single-strand cDNA was synthesized from the isolated RNA by SuperScript VILO cDNA synthesis kit (Thermo Fisher).
Second-strand cDNA synthesis and the subsequent steps to create library were conducted with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs).

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete Rad21. For labeling of nascent transcripts, HCT116 cells and S2 cells were incubated in 0.5 mM 5-ethynyl uridine (Thermo Fisher) for 20 min and 0.2 mM for 2 hr.

value: Colorectal carcinoma

tag: treatment


title: V2 Pool 2 RNA Replicate 8

description:
Library name: V2_Pool2_RNA8
rna.r8 column in mpra_qtigc_pgl4v2_pool2.txt

tag: cell type


title: PH2_Input

description: Library name: Sample11


title: EUseq, ctrl, rep2

tag: genotype


title: Control subject 3.3.2, dermal fibroblasts, parent of patient 3.3.1

description: Library name: Cntrl332

value: Control subject 3.3.2

value: Human dermal fibroblasts


title: CHI140 Silent WT

description: Library name: CHI140

tag: tissue

value: Silent

tag: electrophysiologist

tag: mouse id

tag: rt lot


title: V2 Pool 2 RNA Replicate 7

description:
Library name: V2_Pool2_RNA7
rna.r7 column in mpra_qtigc_pgl4v2_pool2.txt


title: PH1_Treat

description: Library name: Sample10

value: Lung tissue


title: EUseq, aux, rep1


title: CHI139 Active WT

description: Library name: CHI139

tag: date lp

tag: lp lot

tag: index lot


title: crTMPRSS2 knockout rat lung, biological replicate 2

description:
Library name: seq6
Novogene sample seq6; library ID ERRA250001432-1a; group KO; raw reads 41,284,206; clean reads 39,586,178.

value: lung

value: crTMPRSS2 knockout


title: V2 Pool 2 RNA Replicate 6

description:
Library name: V2_Pool2_RNA6
rna.r6 column in mpra_qtigc_pgl4v2_pool2.txt


title: PH1_Input

description: Library name: Sample9


title: CHI138 Silent WT

description: Library name: CHI138

value: dorsal striatum

tag: group

tag: Sex

tag: date seq


title: EUseq, ctrl, rep1

tag: cell line


title: V2 Pool 2 RNA Replicate 5

description:
Library name: V2_Pool2_RNA5
rna.r5 column in mpra_qtigc_pgl4v2_pool2.txt


title: Control4_Treat

description: Library name: Sample8


title: ChIPseq, Input, NELFCD, flav, aux

library_source: genomic

data_processing:
Sequenced reads were aligned to hg38 and mm10 using bowtie (version 1.2.3) with “-n2-m1” parameters. The removal of redundant reads and the normalization of the read number for each sample were performed with parse2wig (version 3.7.2). For peak-calling, we used drompa_peakcall (version 3.7.2) in “PC_SHARP” mode, and for visualization, we used drompa+ PC_SHARP (version 1.17.2) and deeptools (version 3.5.1.)
Assembly: hg38
Supplementary files format and content: BigWig files generated by parse2wig (version 3.7.2)

molecule: genomic DNA

extract_protocol:
HCT116 and C2C12 cells were crosslinked with 1% formaldehyde for 10 min, quenched with 125 mM glycine for 5 min, and washed with PBS. After collection by centrifugation, the fixed cells were frozen and stored at -80 C. The thawed cells resuspended with LB1 Buffer (50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton-X, 1 mM PMSF, 10 mM DTT, 1x cOmplete EDTA-free (Roche)) and incubated on ice for 10 min. After collection by centrifugation, the pellet was resuspended with LB2 Buffer (20 mM Tris-HCl (pH7.5), 200 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1x cOmplete EDTA-free) and incubated on ice for 10 min. After centrifugation, the pellet was resuspended with LB3 Buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Na-Deoxycholate, 0.1 % SDS, 1x cOmplete EDTA-free) and incubated on ice for 10 min. Then, we repeated the centrifugation and resuspension with LB3 Buffer. For shearing chromatin, sonication was performed for 12 sec 6 times with amplitude setting at 17 % of the maximum amplitude using Sonifier 250D. Between each cycle, chromatin was collected by centrifugation. After the step of sonication, cell debris was removed by centrifugation at 19000 g for 15 min. 50 μl of Dynabeads Protein A or Dynabeads Protein G (Invitrogen) was washed with 5 mg/ml BSA/PBS twice and resuspended with BSA/PBS. 4 μg antibody was added to the beads, and the mixture was rotated for 3 h at 4 C. The beads was washed with BSA/PBS twice and with LB3 Buffer once and resuspended with LB3 Buffer. Chromatin from HCT116 and from C2C12 cells were mixed and incubated with antibody beads for 14 h at 4 C. The beads was washed with LB3 Buffer once, with LB3 High Buffer ( 20 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Na-Deoxycholate, 0.1 % SDS) twice, with RIPA wash Buffer (50 mM HEPES-KOH (pH 7.4), 0.25 M LiCl, 1 mM EDTA, 0.5 % Na-Deoxycholate, 1 % NP-40) 3 times and with TE50 Buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA) once. Chromatin bound to beads was eluted with Elution Buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1 % SDS). The eluates were incubated at 65 °C for 6 h to reverse crosslinks and then treated with RNaseA and then with proteinase K. The samples were purified with QIAquick PCR purification kit (QIAGEN).  Methods Mol Biol, 2017. 1515: p. 257-271).
The library for sequencing was prepared with NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete Rad21.

tag: chip antibody

value: Flavopiridol,Auxin


title: CHI137 Silent WT

description: Library name: CHI137

value: cholinergic interneuron

tag: batch

tag: date ephys

tag: dob

tag: seq srm_sample_id


title: V2 Pool 2 RNA Replicate 4

description:
Library name: V2_Pool2_RNA4
rna.r4 column in mpra_qtigc_pgl4v2_pool2.txt

tag: cell type


title: Control4_Input

description: Library name: Sample7

tag: tissue


title: ChIPseq, Input, NELFCD, flav, ctrl

tag: genotype

tag: treatment

value: Flavopiridol


title: CHI136 Active WT

description: Library name: CHI136

value: Active

value: WT

tag: age days

tag: electrophysiologist

tag: mouse id

tag: rt lot


title: Control3_Treat

description: Library name: Sample6


title: V2 Pool 2 RNA Replicate 3

description:
Library name: V2_Pool2_RNA3
rna.r3 column in mpra_qtigc_pgl4v2_pool2.txt


title: CHI135 Active WT

description: Library name: CHI135

tag: group

tag: date lp

tag: lp lot

tag: index lot


title: ChIPseq, NELFCD, flav, aux

tag: chip antibody

value: NELFCD

tag: cell line


title: Control3_Input

description: Library name: Sample5


title: V2 Pool 2 RNA Replicate 2

description:
Library name: V2_Pool2_RNA2
rna.r2 column in mpra_qtigc_pgl4v2_pool2.txt


title: ChIPseq, NELFCD, flav, ctrl


title: CHI134 Active WT

description: Library name: CHI134

tag: Sex

value: female

tag: batch

tag: date ephys

tag: date seq


title: V2 Pool 2 RNA Replicate 1

description:
Library name: V2_Pool2_RNA1
rna.r1 column in mpra_qtigc_pgl4v2_pool2.txt

tag: cell type

value: cardiac muscle cell


title: Control2_Treat

description: Library name: Sample4

tag: tissue


title: ChIPseq, Input, RPB1, GFP, WaplKD

tag: genotype

tag: treatment

value: Wapl siRNA


title: CHI133 Silent WT

description: Library name: CHI133

tag: dob

tag: age days

tag: electrophysiologist

tag: seq srm_sample_id


title: Control2_Input

description: Library name: Sample3


title: V2 Pool 1 RNA Replicate 10

description:
Library name: V2_Pool1_RNA10
rna.r10 column in mpra_qtigc_pgl4v2_pool1.txt


title: ChIPseq, Input, RPB1, GFP, ctrlKD

value: Colorectal carcinoma

value: control


title: CHI132 Active WT

description: Library name: CHI132

tag: group

tag: mouse id

tag: rt lot

tag: date lp


title: V2 Pool 1 RNA Replicate 9

description:
Library name: V2_Pool1_RNA9
rna.r9 column in mpra_qtigc_pgl4v2_pool1.txt

tag: cell line


title: ChIPseq, GFP, WaplKD

tag: chip antibody

value: GFP


title: Control1_Treat

description: Library name: Sample2


title: CHI131 Silent WT

description: Library name: CHI131

value: Silent

tag: Sex

tag: batch

tag: lp lot

tag: index lot


title: Control1_Input

description: Library name: Sample1

tag: tissue

value: Lung tissue


title: V2 Pool 1 RNA Replicate 8

description:
Library name: V2_Pool1_RNA8
rna.r8 column in mpra_qtigc_pgl4v2_pool1.txt

tag: cell type


title: ChIPseq, GFP, ctrlKD

tag: genotype

tag: treatment


title: CHI126 Silent Het

description: Library name: CHI126

value: Het

tag: date ephys

tag: dob

tag: age days

tag: date seq


title: PH3

description: Library name: Sample6

data_processing:
Raw reads were quality-controlled using Fastp software. Feature-barcode matrices were generated using the 10× Genomics Cell Ranger pipeline, including alignment to the human reference genome GRCh38 (hg38) and cell calling.
Secondary quality filtering was performed to remove low-quality cells and potential doublets. Normalization, dimensionality reduction, and cell clustering were performed to identify distinct cell populations.
Assembly: Human reference genome assembly: GRCh38 (hg38)
Supplementary files format and content: filtered_feature_bc_matrix.rar

extract_protocol:
Single-cell suspensions were generated by mincing lung tissues into fine fragments followed by enzymatic digestion at 37 °C for ~30 minutes. Cell pellets were harvested by centrifugation, resuspended in RPMI 1640 medium supplemented with 2% fetal bovine serum, and filtered through a 30 μm cell strainer. Cell viability was assessed by AOPI staining, and the final cell concentration was adjusted to 700–1200 cells/μL.
Libraries were constructed using the 10× Genomics Chromium Controller platform. Briefly, single cells were partitioned into Gel Bead-In-EMulsions (GEMs), followed by cDNA synthesis, purification with Dynabeads MyOne SILANE magnetic beads, and PCR amplification. Libraries were then subjected to fragmentation, end repair, A-tailing, and adapter ligation. All libraries were sequenced on the Illumina NovaSeq platform in paired-end mode.

tag: disease state

value: PF-associated PH


title: CHI125 Silent Het

description: Library name: CHI125

value: dorsal striatum

tag: group

tag: electrophysiologist

tag: mouse id

tag: rt lot

tag: seq srm_sample_id


title: ChIPseq, RPB1, WaplKD

tag: chip antibody

tag: cell line


title: V2 Pool 1 RNA Replicate 7

description:
Library name: V2_Pool1_RNA7
rna.r7 column in mpra_qtigc_pgl4v2_pool1.txt


title: V2 Pool 1 RNA Replicate 6

description:
Library name: V2_Pool1_RNA6
rna.r6 column in mpra_qtigc_pgl4v2_pool1.txt


title: PH2

description: Library name: Sample5


title: ChIPseq, RPB1, ctrlKD


title: CHI124 Silent Het

description: Library name: CHI124

tag: Sex

tag: batch

tag: date lp

tag: lp lot

tag: index lot


title: PH1

description: Library name: Sample4

tag: tissue


title: V2 Pool 1 RNA Replicate 5

description:
Library name: V2_Pool1_RNA5
rna.r5 column in mpra_qtigc_pgl4v2_pool1.txt

tag: cell type


title: ChIPseq, Input, RPB1, KL1, aux

tag: genotype

tag: treatment

value: KL-1, Auxin


title: CHI123 Silent Het

description: Library name: CHI123

value: cholinergic interneuron

tag: date ephys

tag: dob

tag: age days

tag: date seq


title: V2 Pool 1 RNA Replicate 4

description:
Library name: V2_Pool1_RNA4
rna.r4 column in mpra_qtigc_pgl4v2_pool1.txt


title: con3

description: Library name: Sample3

tag: disease state

value: healthy


title: ChIPseq, Input, RPB1, KL1, ctrl


title: CHI122 Active Het

description: Library name: CHI122

tag: group

value: Active

tag: electrophysiologist

tag: mouse id

tag: rt lot

tag: seq srm_sample_id


title: V2 Pool 1 RNA Replicate 3

description:
Library name: V2_Pool1_RNA3
rna.r3 column in mpra_qtigc_pgl4v2_pool1.txt

tag: cell line


title: ChIPseq, RPB1, KL1, aux

tag: chip antibody


title: con2

description: Library name: Sample2


title: CHI121 Silent Het

description: Library name: CHI121

tag: Sex

tag: batch

tag: date lp

tag: lp lot

tag: index lot


title: V2 Pool 1 RNA Replicate 2

description:
Library name: V2_Pool1_RNA2
rna.r2 column in mpra_qtigc_pgl4v2_pool1.txt

tag: cell type


title: con1

description: Library name: Sample1

tag: tissue


title: CHI120 Active Het

description: Library name: CHI120

tag: genotype

tag: date ephys

tag: dob

tag: age days


title: ChIPseq, RPB1, KL1, ctrl

tag: treatment


title: V2 Pool 1 RNA Replicate 1

description:
Library name: V2_Pool1_RNA1
rna.r1 column in mpra_qtigc_pgl4v2_pool1.txt


title: PAECs_PUS7

city: Guangdong, Shenzhen

first: Xiaolin

last: Chen

address: No. 1088 Xueyuan Avenue, Nanshan District

description: Library name: Sample2

data_processing:
Raw reads were filtered using fastp v0.23.4 to remove adapter sequences and low-quality reads; reads shorter than 75 bp were discarded. Clean reads were used for subsequent analysis.
Clean reads were aligned to human reference genome GRCh38 using HISAT2 v2.5.4.
Peak calling for PUS7 RNA binding sites was performed using MACS3 v3.0.2 with q-value < 0.05 as the threshold.
Peak annotation was conducted using ChIPseeker. GO and KEGG enrichment analyses of peak-associated genes were performed. Motif analysis was carried out using Homer v4.11.1.
Gene-level read counts were calculated, and binding difference analysis was performed using DESeq2 v1.34.0 and edgeR v3.36.0.
Assembly: Human reference genome assembly: GRCh38 (hg38)
Supplementary files format and content: HPAEC_PUS7_peaks_gene.txt

source_name: Primary human pulmonary artery endothelial cells (PAECs)

extract_protocol:
RNA was purified from RIP eluates using standard RNA extraction method. RNA concentration, purity and integrity were assessed for subsequent library construction and sequencing.
RNA samples were fragmented and reverse transcribed into cDNA. Sequencing adapters were ligated, and libraries were amplified by PCR. Qualified libraries were sequenced on Illumina NovaSeq 6000 platform using paired-end 150 bp strategy.

value: WT

value: anti-PUS7 antibody (6 µg/mg lysate; Cat#A305-147A, Bethyl, USA)


title: ChIPseq, Input, AFF4, DRB, aux

value: DRB, Auxin


title: CHI118 Silent Het

description: Library name: CHI118

tag: group

value: female

tag: electrophysiologist

tag: mouse id

tag: date seq


title: V1 Pool 2 RNA Replicate 10

description:
Library name: V1_Pool2_RNA10
rna.r10 column in mpra_qtigc_pgl4v1_pool2.txt

tag: cell line

value: cardiac muscle cell


title: PAECs_IgG

description: Library name: Sample1

value: Primary human pulmonary artery endothelial cells (PAECs)

value: IgG (5 µg; 12-370, Sigma-Aldrich)


title: ChIPseq, Input, AFF4, DRB, ctrl

tag: chip antibody

value: Colorectal carcinoma

value: DRB


title: CHI117 Active Het

description: Library name: CHI117

tag: Sex

tag: batch

tag: rt lot

tag: seq srm_sample_id


title: ChIPseq, AFF4, DRB, aux

tag: cell type


title: PAECs_siPUS7_rep3

description: Library name: Sample6

data_processing:
Raw reads were filtered using Cutadapt to remove adapters and low-quality reads with average quality scores < Q20. All downstream analyses were performed using high-quality clean reads.
Clean reads were aligned to the human reference genome using HISAT2 v2.0.5 with default parameters.
Gene-level read counts were calculated using HTSeq v0.9.1, and gene expression was normalized to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments).
Differential expression analysis between siPUS7 and NC groups was performed using DESeq v1.20.0. Genes with |log2FoldChange| > 1 and P-value < 0.05 were considered significantly differentially expressed.
Gene Ontology (GO) enrichment analysis was performed using topGO, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using clusterProfiler v3.4.4, with a significance threshold of P-value < 0.05.
Assembly: Human reference genome assembly: GRCh38 (hg38)
Supplementary files format and content: PAECs_siPUS7_Expression.xlsx

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific), and integrity was verified by agarose gel electrophoresis and an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent Technologies).
Strand-specific RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, mRNA was enriched from 1 μg total RNA using Oligo(dT) magnetic beads, fragmented, and reverse-transcribed into cDNA. After end-repair, A-tailing, and adapter ligation, 400-500 bp fragments were selected using AMPure XP beads, amplified by PCR, and purified. Library quality was evaluated using an Agilent 2100 Bioanalyzer with the High Sensitivity DNA Kit, and concentration was quantified using the PicoGreen assay and qPCR. Libraries were sequenced on an Illumina platform in paired-end 150 bp mode.


title: CHI116 Silent Het

description: Library name: CHI116

tag: tissue

value: Silent

tag: date lp

tag: lp lot

tag: index lot


title: V1 Pool 2 RNA Replicate 9

description:
Library name: V1_Pool2_RNA9
rna.r9 column in mpra_qtigc_pgl4v1_pool2.txt


title: V1 Pool 2 RNA Replicate 8

description:
Library name: V1_Pool2_RNA8
rna.r8 column in mpra_qtigc_pgl4v1_pool2.txt


title: ChIPseq, AFF4, DRB, ctrl

tag: genotype


title: CHI114 Silent WT

description: Library name: CHI114

tag: date ephys

tag: dob

tag: age days


title: PAECs_siPUS7_rep2

description: Library name: Sample5


title: V1 Pool 2 RNA Replicate 7

description:
Library name: V1_Pool2_RNA7
rna.r7 column in mpra_qtigc_pgl4v1_pool2.txt


title: PAECs_siPUS7_rep1

description: Library name: Sample4


title: CHI109 Silent WT

description: Library name: CHI109

tag: group

tag: electrophysiologist

tag: mouse id


title: RNAseq, ctrl, rep3

description: Library name: RNAseq_ctrl_rep3

tag: cell line

tag: treatment

value: DMSO


title: ChIPseq, Input, RPB1, aux, SMC1

tag: chip antibody

value: Auxin


title: V1 Pool 2 RNA Replicate 6

description:
Library name: V1_Pool2_RNA6
rna.r6 column in mpra_qtigc_pgl4v1_pool2.txt


title: ChIPseq, Input, RPB1, ctrl, SMC1


title: CHI108 Active WT

description: Library name: CHI108

value: dorsal striatum

tag: Sex

tag: batch

tag: rt lot

tag: date seq


title: PAECs_NC_rep3

description: Library name: Sample3


title: V1 Pool 2 RNA Replicate 5

description:
Library name: V1_Pool2_RNA5
rna.r5 column in mpra_qtigc_pgl4v1_pool2.txt

tag: cell type


title: ChIPseq, RPB1, aux, SMC1


title: PAECs_NC_rep2

description: Library name: Sample2


title: V1 Pool 2 RNA Replicate 4

description:
Library name: V1_Pool2_RNA4
rna.r4 column in mpra_qtigc_pgl4v1_pool2.txt


title: CHI107 Silent WT

description: Library name: CHI107

tag: tissue

tag: date lp

tag: lp lot

tag: seq srm_sample_id


title: PAECs_NC_rep1

description: Library name: Sample1

tag: genotype


title: ChIPseq, RPB1, ctrl, SMC1


title: CHI106 Active WT

description: Library name: CHI106

tag: date ephys

tag: dob

tag: age days

tag: index lot


title: V1 Pool 2 RNA Replicate 3

description:
Library name: V1_Pool2_RNA3
rna.r3 column in mpra_qtigc_pgl4v1_pool2.txt

tag: cell line


title: CRC11,Irinotecan sensitivity

city: Jinhua

first: Yi

last: Pan

state: Zhejiang Province

address: No. 365, Renmin East Road, Wucheng District

department: Central Laboratory and Precision Medicine Center

institute: Affiliated Jinhua Hospital, Zhejiang University School of Medicine

description:
Library name: sample2
10x Genomics

data_processing:
After obtaining raw data from sequencing, the raw data is first filtered using the default parameters of the fastp tool to remove adapter sequences and low-quality sequences. Then, CellRanger v7.2.0 is used to align the sequences against the human genome (GRCh38-2020-A), yielding a feature barcode matrix. Downstream sample analysis was performed for each cell in every sample, ultimately yielding a merged feature barcode matrix. Cell quality control was then applied, retaining cells expressing over 200 genes and exhibiting a mitochondrial unique molecular identifier (UMI) proportion below 20%. Subsequently, mitochondrial genes were removed from the expression matrix.
Assembly: human genome (GRCh38-2020-A)
Supplementary files format and content: barcodes,features and matrix files

source_name: patient-derived organoid

extract_protocol:
Isolate PBMCs using LeucoSep tubes pre-filled with Ficoll-Paque Plus according to the manufacturer's instructions. Centrifuge samples at 700g for 20 minutes and collect PBMCs from the interface between Ficoll-Paque Plus and plasma. Then resuspend cells in red blood cell lysis buffer (Miltenyi Biotec) to lyse remaining red blood cells. After erythrocyte lysis, PBMCs were washed twice to remove peripheral RNA and resuspended in 1× PBS (calcium- and magnesium-free) containing 0.04% bovine serum albumin (BSA). The cell suspension was passed through a 30-μm Flowmi cell filter to ensure a single-cell suspension. Only cells with viability exceeding 90% were selected for subsequent processing and maintained on ice prior to fixation and single-cell RNA analysis.
scRNA-Seq libraries were generated using the Chromium Controller instrument and Chromium Single Cell 3’ V3.1 Reagent Kit (10× Genomics, Pleasanton, CA). Briefly, cells were concentrated to 1,000 cells/µL, and approximately 15,000 cells were loaded into each channel to generate single-cell gel bead emulsions (GEMs), yielding an expected 1,000 mRNA barcodes per single-cell sample. Following reverse transcription, GEMs were disrupted, and barcoded cDNAs were purified and amplified. Amplified barcoded cDNA was sheared, A-tailed, ligated with adapters, and subjected to index PCR amplification. The final library was quantified using Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific) and analyzed for size distribution via high-sensitivity DNA chips on the Qsep100 (Bioptic). All libraries were sequenced using 150 bp paired-end reads on the NovaSeq 6000 (Illumina, San Diego, CA).

value: patient-derived organoid

value: Organoids derived from colorectal cancer patients


title: ChIPseq, Input, AFF4, aux

tag: treatment


title: CHI105 Active WT

description: Library name: CHI105

tag: group

value: cholinergic interneuron

tag: electrophysiologist

tag: mouse id


title: V1 Pool 2 RNA Replicate 2

description:
Library name: V1_Pool2_RNA2
rna.r2 column in mpra_qtigc_pgl4v1_pool2.txt


title: CRC5,Irinotecan resistance

description:
Library name: sample1
10x Genomics


title: CHI104 Active WT

description: Library name: CHI104

value: Active

tag: Sex

tag: batch

tag: rt lot


title: ChIPseq, Input, AFF4, ctrl

tag: chip antibody

tag: cell type


title: V1 Pool 2 RNA Replicate 1

description:
Library name: V1_Pool2_RNA1
rna.r1 column in mpra_qtigc_pgl4v1_pool2.txt


title: Neurons replicate 2 derived from iPSC replicate 3

city: Toronto

first: Shreejoy

last: Tripathy

address: 250 College Street

country: Canada

institute: Centre for Addiction and Mental Health

description: Library name: CN_3_2_S14_L001

data_processing:
Raw reads from short-read RNAseq were aligned to the GRCh38.p13 (hg38) reference genome via STAR v2.4.2a using comprehensive gene annotations from Gencode v47 (Dobin et al., 2013). BAM files were produced in both genomic and transcriptomic coordinates and sorted using samtools v1.3. Splice junctions from SJ.out.tab files produced by STAR were mapped to splice junctions in the long-read RNAseq dataset, with default parameters for splice junction output filtering in STAR.
Assembly: GRCh38
Supplementary files format and content: SJ.out.tab contains high confidence collapsed splice junctions in tab-delimited format. Note that STAR defines the junction start/end as intronic bases, while many other software define them as exonic bases.

growth_protocol: PGPC17_11-CLYBL-TetO-NGN2 iPSCs were grown in 6-well plates coated with Matrigel (#354234, Corning) in mTeSR Plus media (#100-0276, STEMCELL) and passaged with ReLeSR (#100-0483, STEMCELL) for routine maintenance. All cells were kept at 37°C, 95% humidity and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol™ Reagent according to the manufacturer's instructions
Sequencing libraries were prepared using the stranded rRNA-depletion workflow (Ribo-Zero Plus rRNA Kit; Illumina), which removes bacterial and mammalian rRNA as well as human globin transcripts. Sequencing was performed on an Illumina NovaSeq 6000 platform using an S4 flowcell to generate paired-end 150 bp reads, with a target depth of approximately 100 million reads per sample.

treatment_protocol: iPSCs were dissociated from maintenance culture plates with Accutase and seeded on Matrigel-coated 6-well plates at a density of 260,00 cells/cm² in custom complete neuron media with 10 μM ROCK inhibitor (Y-27632, #AB144494, Abcam) and 2 μM/mL doxycycline hyclate (DOX, #D9891, Sigma Aldrich) to induce NGN2 over-expression. ROCK inhibitor was removed after 24 hours. Media was changed every 24 hours with fresh complete neuron media with DOX.  On day 4 (t04), cells were passaged by Accutase and plated at 260,00 cells/cm² on PEI-coated 6-well plates in complete neuron medium with ROCK inhibitor and DOX. ROCK inhibitor was removed after 24 hours. Media was changed every 24 hours with fresh complete neuron media with DOX continued until day 7 (t07). After t07, DOX was removed, and media was changed daily until day 30 (t30).  Samples for RNA-seq were collected at day 0 (t00, iPSC), day 4 (t04, intermediate), and day 30 (t30, neuron).

value: Neuron


title: ChIPseq, AFF4, aux


title: CHI103 Silent WT

description: Library name: CHI103

data_processing:
Adapter sequences were removed by TrimGalore (v0.6.3).
STAR (v2.7.9a) was then used for alignment to the mouse reference genome (GRCm38) in a splice-site aware manner based on Gencode M22 primary assembly annotations.
Gene level quantifications were derived using RSEM (v1.3.3).
Assembly: Mouse mm10
Supplementary files format and content: Processed data contains raw counts per gene for each sample.

extract_protocol:
Cell contents were extracted using the recording electrode following patch-clamp recordings. Contents were directly lysed in buffer from the SMART-Seq mRNA Single Cell LP kit (Takara, 634787).
Libraries were constructed from single cells using the SMART-Seq mRNA Single Cell LP kit (Takara, 634787).

tag: tissue

value: WT

tag: date lp

tag: lp lot

tag: date seq


title: V1 Pool 1 RNA Replicate 10

description:
Library name: V1_Pool1_RNA10
rna.r10 column in mpra_qtigc_pgl4v1_pool1.txt


title: Neurons replicate 1 derived from iPSC replicate 3

description: Library name: CN_3_1_S13_L001


title: ChIPseq, AFF4, ctrl

tag: genotype


title: CHI102 Active WT

description: Library name: CHI102

tag: date ephys

tag: dob

tag: age days

tag: seq srm_sample_id


title: V1 Pool 1 RNA Replicate 9

description:
Library name: V1_Pool1_RNA9
rna.r9 column in mpra_qtigc_pgl4v1_pool1.txt

tag: cell line


title: Neurons replicate 2 derived from iPSC replicate 2

description: Library name: CN_2_2_S9_L001


title: ChIPseq, Input, Ser2P, NELFCD, aux

tag: treatment


title: CHI101 Silent WT

description: Library name: CHI101

tag: group

tag: electrophysiologist

tag: mouse id

tag: index lot


title: V1 Pool 1 RNA Replicate 8

description:
Library name: V1_Pool1_RNA8
rna.r8 column in mpra_qtigc_pgl4v1_pool1.txt


title: Neurons replicate 1 derived from iPSC replicate 2

description: Library name: CN_2_1_S8_L001


title: CHI100 Silent WT

description: Library name: CHI100

tag: Sex

tag: batch

tag: rt lot


title: ChIPseq, Input, Ser2P, NELFCD, ctrl

tag: chip antibody

tag: cell type


title: V1 Pool 1 RNA Replicate 7

description:
Library name: V1_Pool1_RNA7
rna.r7 column in mpra_qtigc_pgl4v1_pool1.txt


title: Neurons replicate 2 derived from iPSC replicate 1

description: Library name: CN_1_2_previous_tube_label_CN_1_3_S4_L001


title: ChIPseq, NELFCD, aux, rep1

value: NELFCD


title: CHI097 Silent Het

description: Library name: CHI097

tag: tissue

value: Het

value: male

tag: date lp

tag: lp lot

tag: date seq


title: Neurons replicate 1 derived from iPSC replicate 1

description: Library name: CN_1_1_previous_tube_label_CN_1_2_S3_L001


title: V1 Pool 1 RNA Replicate 6

description:
Library name: V1_Pool1_RNA6
rna.r6 column in mpra_qtigc_pgl4v1_pool1.txt

value: cardiac muscle cell


title: ChIPseq, NELFCD, ctrl, rep1

tag: genotype


title: CHI094 Silent Het

description: Library name: CHI094

tag: date ephys

tag: dob

tag: age days

tag: seq srm_sample_id


title: V1 Pool 1 RNA Replicate 5

description:
Library name: V1_Pool1_RNA5
rna.r5 column in mpra_qtigc_pgl4v1_pool1.txt

tag: cell line


title: Intermediate cells replicate 2 derived from iPSC replicate 3

description: Library name: NPC_3_2_previous_tube_label_NPC_3_3_S12_L001

value: Intermediate


title: ChIPseq, Input, H3K4me3, aux

value: Colorectal carcinoma

tag: treatment


title: V1 Pool 1 RNA Replicate 4

description:
Library name: V1_Pool1_RNA4
rna.r4 column in mpra_qtigc_pgl4v1_pool1.txt


title: CHI093 Active Het

description: Library name: CHI093

tag: group

tag: electrophysiologist

tag: mouse id

tag: index lot


title: Intermediate cells replicate 1 derived from iPSC replicate 3

description: Library name: NPC_3_1_S11_L001


title: ChIPseq, Input, H3K4me3, ctrl

tag: chip antibody


title: CHI092 Active Het

description: Library name: CHI092

tag: cell type

tag: Sex

tag: batch

tag: rt lot


title: V1 Pool 1 RNA Replicate 3

description:
Library name: V1_Pool1_RNA3
rna.r3 column in mpra_qtigc_pgl4v1_pool1.txt


title: ChIPseq, H3K4me3, aux


title: CHI091 Silent Het

description: Library name: CHI091

tag: tissue

tag: date lp

tag: lp lot

tag: date seq


title: Intermediate cells replicate 2 derived from iPSC replicate 2

description: Library name: NPC_2_2_S7_L001


title: V1 Pool 1 RNA Replicate 2

description:
Library name: V1_Pool1_RNA2
rna.r2 column in mpra_qtigc_pgl4v1_pool1.txt


title: Intermediate cells replicate 1 derived from iPSC replicate 2

description: Library name: NPC_2_1_S6_L001


title: ChIPseq, H3K4me3, ctrl

tag: genotype


title: CHI090 Silent Het

description: Library name: CHI090

tag: date ephys

tag: dob

tag: age days

tag: seq srm_sample_id


title: V1 Pool 1 RNA Replicate 1

description:
Library name: V1_Pool1_RNA1
rna.r1 column in mpra_qtigc_pgl4v1_pool1.txt

tag: cell line


title: Intermediate cells replicate 2 derived from iPSC replicate 1

description: Library name: NPC_1_2_previous_tube_label_NPC_1_3_S2_L001


title: CHI089 Silent Het

description: Library name: CHI089

tag: group

tag: electrophysiologist

tag: mouse id


title: ChIPseq, Input, H3K4me1, aux

tag: chip antibody

tag: cell type

tag: treatment


title: LN, CD8, KP, CD11c_IRF4, ADT

city: Paris

first: Nathan

last: Vaudiau

address: 25 rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

description:
Library name: LN_CD8_KP_CD11c_IRF4_ADT
10x genomics
Antibody-derived oligonucleotide (ADT)
LN_CD8_feature_reference.csv
LN_CD8_KP_CD11c_IRF4_barcodes.tsv.gz
LN_CD8_KP_CD11c_IRF4_features.tsv.gz
LN_CD8_KP_CD11c_IRF4_matrix.mtx.gz

data_processing:
Raw sequencing reads were processed using the 10x Genomics software Cellranger. To obtain a cell count matrix, reads were mapped to the mouse mm10 reference genome. scRNA-seq analysis was performed using Seurat v4. For each dataset, cells with low genes per cell or with a high percentage of mitochondrial genes were removed from downstream analyses. Following data QC we obtained 4421 cells from the lungs KP CD8+ T cells dataset, 1404 cells for the tdLN KP WT CD8+ T cells dataset, 3340 cells for the tdLN KP CD11cIRF4 CD8+ T cells dataset, 2076 cells for the tdLN KP WT CD11c+MHCII+ cells dataset and 3150 cells for the tdLN KP CD11cIRF4 CD11c+MHCII+ cells dataset. RNA and ADT expression were normalized separately using the default Seurat LogNormalize and Centered Log Ratio (CLR) approaches, respectively. Top 2000 most variable genes were then determined by applying a VST (Variance Stabilizing Transformation). Datasets were analyzed separately or were integrated together before analysis. For integration, top 2000 most variable genes across datasets were used as anchors with the LogNormalize method. Dimensionality reduction was performed using PCA and the top informative principle components were determined after visualization with an elbow plot and dimensional reduction heatmaps, and used for the non-linear dimensionality reduction technique UMAP. Louvain clustering of the data was performed across a range of resolution parameters visualized using a clustree. Cluster of cells with low number of genes and in which no T lymphocyte cell identifying genes could be detected were not considered in the analysis. Subsequent analyses were performed using Seurat default parameters.
Assembly: mm10
Supplementary files format and content: Cellranger output files: Tab-separated values and matrix files
Supplementary files format and content: For ADT data: feature_reference.csv files
Library strategy: CITE-seq

molecule: protein

source_name: Lymph node

extract_protocol:
The droplet-based approach of 10X Genomics platform was used to perform scRNA-seq. For each scRNA-seq sample, cell suspension from three individual mice were pooled and sorted in PBS containing 0,04%BSA.
10 000 cells were loaded on a Chromium Controller using the Chromium Next GEM Single Cell 3 Reagent Kits v3.1 according to manufacturer instructions.

treatment_protocol: In this project, we have worked in the KP (KRASG12D; p53-/-) model of murine lung cancer. 14 days after intravenous injection of the KP cell line, CD8+ T cells or CD11c+MHCII+ cells were stained with CITE-Seq antibodies then sorted by flow cytometry from pooled lungs or lymph nodes of 3 C57BL/6J mice before scRNA-seq analysis.Single cells were isolated using a 10X Chromium droplet-based approach and sequenced.

value: Lymph node

value: KP

value: CD8+ T cells

tag: strain

value: CD11ccre x Irf4fl/fl

tag: age

value: 8-12 weeks

tag: library type

value: ADT

tag: adt

value: TotalSeq-B0004 anti-mouse PD1, TotalSeq-B0201 anti-mouse CD103, TotalSeq-B0197 anti-mouse CD69, TotalSeq-B0378 anti-mouse Lag3


title: LN, CD8, KP, WT, ADT

description:
Library name: LN_CD8_KP_WT_ADT
10x genomics
Antibody-derived oligonucleotide (ADT)
LN_CD8_feature_reference.csv
LN_CD8_KP_WT_barcodes.tsv.gz
LN_CD8_KP_WT_features.tsv.gz
LN_CD8_KP_WT_matrix.mtx.gz

tag: tissue


title: Intermediate cells replicate 1 derived from iPSC replicate 1

description: Library name: NPC_1_1_resub_S15_L001


title: CHI088 Active Het

description: Library name: CHI088

value: dorsal striatum

value: cholinergic interneuron

tag: genotype

tag: Sex

tag: batch

tag: rt lot

tag: date lp

tag: lp lot

tag: index lot

tag: date seq


title: Induced pluripotent stem cells replicate 3

description: Library name: iPSC_3_S10_L001

tag: cell line

value: iPSC


title: ChIPseq, Input, H3K4me1, ctrl

tag: chip antibody

value: DMSO


title: ChIPseq, H3K4me1, aux

tag: cell type

value: Auxin


title: CHI087 Active Het

description: Library name: CHI087

tag: group

value: Active

value: Het

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist

tag: mouse id

tag: seq srm_sample_id


title: Lung, CD8, KP, WT, ADT

description:
Library name: Lung_CD8_KP_WT_ADT
10x genomics
Antibody-derived oligonucleotide (ADT)
Lung_CD8_feature_reference.csv
Lung_CD8_KP_WT_barcodes.tsv.gz
Lung_CD8_KP_WT_features.tsv.gz
Lung_CD8_KP_WT_matrix.mtx.gz

source_name: Lungs

tag: tissue

value: Lungs

tag: strain

tag: genotype

value: WT

tag: age

tag: library type

tag: adt

value: TotalSeq-B0004 anti-mouse PD1, TotalSeq-B0201 anti-mouse CD103, TotalSeq-B0197 anti-mouse CD69, TotalSeq-B0378 anti-mouse Lag3, TotalSeq-B0073 anti-mouse CD44, TotalSeq-B0112 anti-mouse CD62L


title: ChIPseq, H3K4me1, ctrl

value: Colorectal carcinoma

tag: treatment


title: Induced pluripotent stem cells replicate 2

description: Library name: iPSC_2_S5_L001

tag: cell line


title: CHI086 Silent Het

description: Library name: CHI086

value: Silent

tag: Sex

value: male

tag: batch

tag: rt lot

tag: date lp

tag: lp lot

tag: index lot

tag: date seq


title: LN, CD8, KP, CD11c_IRF4, RNA

description:
Library name: LN_CD8_KP_CD11c_IRF4_RNA
10x genomics
RNA

data_processing:
Raw sequencing reads were processed using the 10x Genomics software Cellranger. To obtain a cell count matrix, reads were mapped to the mouse mm10 reference genome. scRNA-seq analysis was performed using Seurat v4. For each dataset, cells with low genes per cell or with a high percentage of mitochondrial genes were removed from downstream analyses. Following data QC we obtained 4421 cells from the lungs KP CD8+ T cells dataset, 1404 cells for the tdLN KP WT CD8+ T cells dataset, 3340 cells for the tdLN KP CD11cIRF4 CD8+ T cells dataset, 2076 cells for the tdLN KP WT CD11c+MHCII+ cells dataset and 3150 cells for the tdLN KP CD11cIRF4 CD11c+MHCII+ cells dataset. RNA and ADT expression were normalized separately using the default Seurat LogNormalize and Centered Log Ratio (CLR) approaches, respectively. Top 2000 most variable genes were then determined by applying a VST (Variance Stabilizing Transformation). Datasets were analyzed separately or were integrated together before analysis. For integration, top 2000 most variable genes across datasets were used as anchors with the LogNormalize method. Dimensionality reduction was performed using PCA and the top informative principle components were determined after visualization with an elbow plot and dimensional reduction heatmaps, and used for the non-linear dimensionality reduction technique UMAP. Louvain clustering of the data was performed across a range of resolution parameters visualized using a clustree. Cluster of cells with low number of genes and in which no T lymphocyte cell identifying genes could be detected were not considered in the analysis. Subsequent analyses were performed using Seurat default parameters.
Assembly: mm10
Supplementary files format and content: Cellranger output files: Tab-separated values and matrix files
Supplementary files format and content: For ADT data: feature_reference.csv files

value: Lymph node

value: KP

tag: cell type

value: CD8+ T cells

value: CD11ccre x Irf4fl/fl

value: RNA


title: Induced pluripotent stem cells replicate 1

description: Library name: iPSC_1_S1_L001


title: ChIPseq, Input, H3K27ac, aux, rep2

tag: chip antibody