title: ChemPerturb-Seq Screen of EndoC-betaH1 cells (GEX)

first: Shuibing

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
For ChemPerturb-Seq assay, the sequencing data was analyzed using the 10X Cell Ranger pipeline (v.7.1.0). The Cell Ranger multi pipeline was employed to assign cell multiplexing oligos (CMOs) to cell-associated barcodes and align the FASTQ files to the 10X human reference genome (GRCh38 v3.0.0), which was modified to incorporate internal barcodes corresponding to the 23 unique barcoded lines. The barcode sequences were trimmed to 250 bp around the barcode region. Running the Cell Ranger pipeline enabled us to extract the gene expression UMI counts matrix. We manually corrected the sample barcode UMI matrix by extracting alignment entries of barcode reads and reviewing these entries to correct barcodes, ensuring no more than one mismatch.
For Fixed RNA profiling assay, the sequencing data was analyzed using the 10X Cell Ranger pipeline (v.7.2.0). The Cell Ranger multi pipeline was employed to extract the gene expression UMI counts matrix.
Assembly: GRCh38
Supplementary files format and content: cellranger output files: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz
Supplementary files format and content: seurat object; cell annotation metadata file in .csv format

extract_protocol:
For ChemPerturb-Seq, we generated twenty-three NLuc-EndoC-betaH1-BC-BFP cell lines, each treated with a different small molecule from our in-house small molecule library  for 48 hours. After 48 hours, NLuc-EndoC-betaH1-BC-BFP cells were trypsinized using 0.25% trypsin-EDTA and pooled. For Fixed RNA profiling, NLuc-EndoC-betaH1-mCherry cells were treated with the LIP cocktail for 48 hours, and 5 million treated or untreated cells were subcutaneously transplanted into male or female SCID-Beige mice. After one week, grafts were removed from the mice and dissociated into single cells using 1 μg/μl of collagenase D for 1 hour at 37C . The mCherry+ cells were purified using either the Becton-Dickinson Influx or Becton-Dickinson Symphony S6 instruments. The cells were then fixed using standard protocols for the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics).
For ChemPerturb-Seq, three different libraries were prepared, and treated and control cells were labeled using the cell multiplexing oligonucleotides from the 3ʹ CellPlex Kit Set A (10X Genomics), specifically, CMO301, CMO302, and CMO303. Libraries were prepared following standard protocols for Chromium Single Cell 3’ Reagent Kits with feature barcoding technology for cell multiplexing (10X Genomics) and sequenced on the Illumina NovaSeq 6000 platform. For Fixed RNA profiling, libraries were prepared using the Chromium Fixed RNA Profiling Reagent Kit for Multiplexed Samples (10X Genomics). Samples were multiplexed using the Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 4 BC (10X Genomics), and libraries were sequenced using the Illumina NovaSeq 6000 platform.

value: Human pancreatic beta cell line

value: In house small molecule screening library

tag: library type

value: GEX


title: AD_159

status: Public on May 26 2025

type: SRA

city: New York

first: Madeline

last: Kim

state: NY

address: 1 Gustave Levy Place

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: AD_159

library_source: transcriptomic

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genomic features with <10 counts in at least 7 (n of smallest group) samples were filtered out (filterByExpr [edgeR R package] default parameters)
Data was then transfomed to log2-counts per million by voom-transform
Fold changes (FCHs) vs. normals and between LS (lesional) and NL (non-lesional) were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Assembly: GRCh37
Supplementary files format and content: expression matrix (csv file) of voom-transformed counts in log2 counts per million

molecule: total RNA

organism: Homo sapiens

source_name: Skin tape strip

extract_protocol:
Total RNA was extracted from skin tape stip samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 5ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragmented mRNA by reverse transcription, second strand synthesis and ligation of specific adapters.

tag: tissue

value: Skin tape strip

tag: patient id

tag: disease

value: AD

tag: tissue type

value: Non-Lesional


title: AD_16

description: Library name: AD_16


title: Control_79

description: Library name: Control_79

value: Control


title: AD_158

description: Library name: AD_158

value: Lesional


title: Human Podocyte, Yap5SA, No treatment, rep3

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

data_processing:
The oriented cDNA produced from the poly-A+ fraction were sequenced on a NovaSeq6000 from Illumina (Paired-End reads 100 bases + 100 bases). A total of ~50 millions of passing filter paired-end reads was produced per library.
The alignments were made by Dragen (https://support-docs.illumina.com/SW/DRAGEN_v38/Content/SW/DRAGEN/GPipelineAlign_fDG.htm)
The counts were carried out using featurecount from the subread package (https://subread.sourceforge.net/featureCounts.html).
Batch correction was carried out using the “removeBatchEffect” function from the Limma package to adjust for variations attributable to an outlier experiment.
Differential expression analysis was executed using DESeq2.
Assembly: GRCh38 / hg38
Supplementary files format and content: teb-delimited text file includes raw count for each sample

source_name: Conditionally immortalized podocyte cell line with temperature-sensitive SV40 large-T antigen

growth_protocol: The human podocyte cell line (Moin A. Saalem) that is transormed by a a thermolabile large-T antigen (ts SV40LT) was maintained in RPMI-1640 (Gibco) medium supplemented with 10% FBS (Sigma-Aldrich), 1% Insulin-Transferrin-Selenium (Gibco) and 1% Penicillin-Streptomycin (Gibco) on collagen I-coated (Sigma-Aldrich) cell culture vessels. These cells, which proliferate at 33 °C (active large-T antigen), were cultured for 12 days at 37 °C prior to treatment, during which they halt proliferation (inactive large-T antigen) and re-differentiate into podocytes.

extract_protocol:
RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel).
RNAseq libraries were prepared starting from 1000 ng of total RNA using the Universal Plus mRNA-Seq kit (Nugen) as recommended by the manufacturer (libraries can be prepared from 10 ng to 1µg of starting total RNA).

treatment_protocol: Podocytes were then treated with ± Doxycycline (Dox) 0.1 µg/ml for 24 hours to induce FLAG-NLS-YAP5SA or GFP expression.

tag: cell line

tag: cell type

value: Human podocyte

tag: genotype

tag: treatment

value: No


title: AD_143

description: Library name: AD_143


title: Human Podocyte, GFP Control, Dox treated, rep3

value: Conditionally immortalized podocyte cell line with temperature-sensitive SV40 large-T antigen

value: pCW-eGFP

value: Doxycyline 0.1 µg for 24 hours


title: Human Podocyte, GFP Control, No treatment, rep3


title: AD_142

description: Library name: AD_142


title: Human Podocyte, Yap5SA, Dox treated, rep2


title: Human Podocyte, Yap5SA, No treatment, rep2


title: AD_12

description: Library name: AD_12


title: AD_113

description: Library name: AD_113


title: Human Podocyte, GFP Control, Dox treated, rep2


title: AD_112

description: Library name: AD_112


title: AD_10

description: Library name: AD_10


title: Human Podocyte, Yap5SA, No treatment, rep1


title: Human Podocyte, Yap5SA, Dox treated, rep1


title: Human Podocyte, GFP Control, Dox treated, rep1


title: Fixed RNA profiling of EndoC-betaH1 cells transplanted in vivo

last: Chen

library_source: transcriptomic single cell

value: LIP cocktail


title: ChemPerturb-Seq Screen of EndoC-betaH1 cells (CMO)

molecule: polyA RNA

value: CMO


title: Human Podocyte, GFP Control, No treatment, rep2


title: Case73

city: Tianjin

first: xiangqian

last: zheng

address: Huan-hu-xi Road, He-xi District

department: Department of Thyroid and Neck Tumor

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

library_source: genomic

data_processing:
Quality control, including removing of low-quality sequences, filtering out low-complexity sequences, and removing adapter sequences.
Sequence Mapping,  the sequencing data is aligned to a reference genome.
Methylation extraction, extract DNA methylation information from the aligned sequencing data.
Assembly: hg38
Supplementary files format and content: Tab-separated txt file，contains information on every single cytosine in the genome irrespective of its context, the columns are chromosome, position, strand, count methylated, count unmethylated, C-context, trinucleotide context.

molecule: genomic DNA

source_name: thyroid tissues

extract_protocol: Not provided

value: thyroid tissues

tag: sample type

value: Benign

value: thyroid nodules


title: Case71


title: Case72


title: AD-MSCs, Donor 3, INFy_24h, Passage 7

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

description:
Library name: V350118750_L02_128
AD-MSCs, Donor 3, INFy_24h, Passage 7

data_processing:
Raw reads were processed using the nf-core/rnaseq pipeline (v3.11.1) implemented in Nextflow. Reads were assessed for quality with FastQC, trimmed using Fastp and pseudoaligned to the GRCh38 reference genome (Ensembl v109) with Salmon. The resulting data were imported into R (v4.4.0) as a SummarizedExperiment object. Non-coding genes were excluded based on gene annotations queried from BioMart. The raw counts were included in the processed data, without nromalization nor transformation.
Assembly: GRCh38
Supplementary files format and content: tsv file. The first column is gene, the rest of columns store the raw counts for each sample

source_name: adipose-derived mesenchymal stromal cells

growth_protocol: Adipose-derived mesenchymal stromal cells (AD-MSCs) were isolated from human subcutaneous adipose tissue obtained from three donors. Cells were plated in T-175 flasks in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% pooled human platelet lysate and passaged every 6–7 days upon reaching approximately 80% confluence. Culture conditions were maintained at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
At each passage, cells were trypsinized, washed with phosphate-buffered saline, counted, and then pelleted by centrifugation. Total RNA was extracted from the cell pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
High-quality RNA (RIN ≥7) from each sample was used to construct cDNA libraries using a mRNA-focused approach. Libraries were indexed and pooled.

treatment_protocol: Cells were cultured under three conditions: (1) DMEM alone (non-inflamed control), (2) DMEM supplemented with 25 ng/mL IFNγ added 24 hours prior to harvesting at each passage, and (3) DMEM supplemented continuously with 25 ng/mL IFNγ throughout all passages. Treatment was replenished with media changes every 3 days, and cell pellets were collected at passages 0 through 7.

tag: passage

tag: donor


title: Human Podocyte, Yap5SA, Dox treated, rep3


title: AD-MSCs, Donor 3, INFy_C, Passage 7

description:
Library name: V350118750_L02_127
AD-MSCs, Donor 3, INFy_C, Passage 7

value: adipose-derived mesenchymal stromal cells


title: AD_15

description: Library name: AD_15


title: Human Podocyte, GFP Control, No treatment, rep1


title: AD-MSCs, Donor 3, DMEM, Passage 7

description:
Library name: V350118750_L02_126
AD-MSCs, Donor 3, DMEM, Passage 7

value: DMEM


title: Case70


title: Case69

value: Malignant


title: AD-MSCs, Donor 2, INFy_24h, Passage 7

description:
Library name: V350118750_L02_125
AD-MSCs, Donor 2, INFy_24h, Passage 7


title: Case68


title: AD-MSCs, Donor 2, DMEM, Passage 7

description:
Library name: V350118750_L02_123
AD-MSCs, Donor 2, DMEM, Passage 7


title: Case66


title: Case64


title: AD-MSCs, Donor 1, INFy_24h, Passage 7

description:
Library name: V350118750_L02_122
AD-MSCs, Donor 1, INFy_24h, Passage 7


title: AD-MSCs, Donor 1, INFy_C, Passage 7

description:
Library name: V350118750_L02_121
AD-MSCs, Donor 1, INFy_C, Passage 7


title: AD-MSCs, Donor 1, DMEM, Passage 7

description:
Library name: V350118750_L02_104
AD-MSCs, Donor 1, DMEM, Passage 7


title: Case62


title: AD-MSCs, Donor 3, INFy_24h, Passage 6

description:
Library name: V350118750_L02_103
AD-MSCs, Donor 3, INFy_24h, Passage 6


title: Case60


title: AD-MSCs, Donor 3, INFy_C, Passage 6

description:
Library name: V350118750_L02_102
AD-MSCs, Donor 3, INFy_C, Passage 6


title: AD-MSCs, Donor 3, DMEM, Passage 6

description:
Library name: V350118750_L02_101
AD-MSCs, Donor 3, DMEM, Passage 6


title: Case59


title: AD-MSCs, Donor 2, INFy_C, Passage 6

description:
Library name: V350118750_L02_99
AD-MSCs, Donor 2, INFy_C, Passage 6


title: AD-MSCs, Donor 2, INFy_24h, Passage 6

description:
Library name: V350118750_L02_100
AD-MSCs, Donor 2, INFy_24h, Passage 6


title: Case56


title: Case55


title: AD-MSCs, Donor 1, INFy_24h, Passage 6

description:
Library name: V350118750_L01_97
AD-MSCs, Donor 1, INFy_24h, Passage 6


title: Case67


title: Case53


title: Case54


title: Case63


title: Case52


title: Case50


title: Case51


title: Case49


title: Case58


title: AD-MSCs, Donor 2, DMEM, Passage 6

description:
Library name: V350118750_L02_98
AD-MSCs, Donor 2, DMEM, Passage 6


title: AD-MSCs, Donor 3, DMEM, Passage 5

description:
Library name: V350118750_L01_92
AD-MSCs, Donor 3, DMEM, Passage 5


title: AD-MSCs, Donor 2, INFy_24h, Passage 5

description:
Library name: V350118750_L01_91
AD-MSCs, Donor 2, INFy_24h, Passage 5


title: Case48


title: AD-MSCs, Donor 2, INFy_C, Passage 7

description:
Library name: V350118750_L02_124
AD-MSCs, Donor 2, INFy_C, Passage 7


title: AD-MSCs, Donor 2, INFy_C, Passage 5

description:
Library name: V350118750_L01_90
AD-MSCs, Donor 2, INFy_C, Passage 5


title: AD-MSCs, Donor 1, DMEM, Passage 6

description:
Library name: V350118750_L01_95
AD-MSCs, Donor 1, DMEM, Passage 6


title: AD-MSCs, Donor 2, DMEM, Passage 5

description:
Library name: V350118750_L01_89
AD-MSCs, Donor 2, DMEM, Passage 5


title: AD-MSCs, Donor 1, INFy_24h, Passage 5

description:
Library name: V350118750_L01_88
AD-MSCs, Donor 1, INFy_24h, Passage 5


title: Case46


title: Case45


title: AD-MSCs, Donor 3, INFy_24h, Passage 5

description:
Library name: V350118750_L01_94
AD-MSCs, Donor 3, INFy_24h, Passage 5


title: AD-MSCs, Donor 1, INFy_C, Passage 5

description:
Library name: V350118750_L01_87
AD-MSCs, Donor 1, INFy_C, Passage 5


title: AD-MSCs, Donor 1, DMEM, Passage 5

description:
Library name: V350118750_L01_86
AD-MSCs, Donor 1, DMEM, Passage 5


title: Case44


title: AD-MSCs, Donor 3, INFy_24h, Passage 4

description:
Library name: V350118750_L01_85
AD-MSCs, Donor 3, INFy_24h, Passage 4


title: Case43


title: Case42


title: Case41


title: Case40


title: AD-MSCs, Donor 2, INFy_C, Passage 4

description:
Library name: V350118564_L04_81
AD-MSCs, Donor 2, INFy_C, Passage 4


title: Case39


title: AD-MSCs, Donor 3, DMEM, Passage 4

description:
Library name: V350118750_L01_83
AD-MSCs, Donor 3, DMEM, Passage 4


title: Case36


title: AD-MSCs, Donor 2, INFy_24h, Passage 4

description:
Library name: V350118564_L04_82
AD-MSCs, Donor 2, INFy_24h, Passage 4


title: AD-MSCs, Donor 1, INFy_C, Passage 4

description:
Library name: V350118564_L04_78
AD-MSCs, Donor 1, INFy_C, Passage 4


title: AD-MSCs, Donor 2, DMEM, Passage 4

description:
Library name: V350118564_L04_80
AD-MSCs, Donor 2, DMEM, Passage 4


title: Case47


title: Case35


title: Case38


title: AD-MSCs, Donor 1, INFy_24h, Passage 4

description:
Library name: V350118564_L04_79
AD-MSCs, Donor 1, INFy_24h, Passage 4


title: Case37


title: Case34


title: Case33


title: Case32


title: Case31


title: AD-MSCs, Donor 1, DMEM, Passage 4

description:
Library name: V350118564_L04_77
AD-MSCs, Donor 1, DMEM, Passage 4


title: AD-MSCs, Donor 3, INFy_24h, Passage 3

description:
Library name: V350118564_L04_76
AD-MSCs, Donor 3, INFy_24h, Passage 3


title: AD-MSCs, Donor 2, INFy_C, Passage 3

description:
Library name: V350118564_L04_72
AD-MSCs, Donor 2, INFy_C, Passage 3


title: Case28


title: AD-MSCs, Donor 2, DMEM, Passage 3

description:
Library name: V350118564_L04_71
AD-MSCs, Donor 2, DMEM, Passage 3


description:
Library name: V350118564_L04_70
AD-MSCs, Donor 1, INFy_24h, Passage 3, technical rep 1


description:
Library name: V350118641_L01_70
AD-MSCs, Donor 1, INFy_24h, Passage 3, technical rep 2


title: AD-MSCs, Donor 3, INFy_C, Passage 3

description:
Library name: V350118564_L04_75
AD-MSCs, Donor 3, INFy_C, Passage 3


title: Case24


title: Case25


title: AD-MSCs, Donor 3, INFy_C, Passage 2

description:
Library name: V350118564_L02_66
AD-MSCs, Donor 3, INFy_C, Passage 2


title: AD-MSCs, Donor 3, INFy_C, Passage 4

description:
Library name: V350118750_L01_84
AD-MSCs, Donor 3, INFy_C, Passage 4


title: AD-MSCs, Donor 2, INFy_24h, Passage 3

description:
Library name: V350118564_L04_73
AD-MSCs, Donor 2, INFy_24h, Passage 3


title: Case30


title: Case27


title: Case29


title: Case21


title: AD-MSCs, Donor 3, DMEM, Passage 3

description:
Library name: V350118564_L04_74
AD-MSCs, Donor 3, DMEM, Passage 3


title: AD-MSCs, Donor 3, DMEM, Passage 2

description:
Library name: V350118564_L02_65
AD-MSCs, Donor 3, DMEM, Passage 2


title: AD-MSCs, Donor 1, DMEM, Passage 3

description:
Library name: V350118564_L02_68
AD-MSCs, Donor 1, DMEM, Passage 3


title: AD-MSCs, Donor 1, INFy_C, Passage 3

description:
Library name: V350118564_L04_69
AD-MSCs, Donor 1, INFy_C, Passage 3


title: Case26


title: Case20


title: AD-MSCs, Donor 2, INFy_24h, Passage 2

description:
Library name: V350118564_L02_64
AD-MSCs, Donor 2, INFy_24h, Passage 2


title: Case23


title: AD-MSCs, Donor 2, INFy_C, Passage 2

description:
Library name: V350118564_L02_63
AD-MSCs, Donor 2, INFy_C, Passage 2


title: Case19


title: Case18


title: AD-MSCs, Donor 2, DMEM, Passage 2

description:
Library name: V350118564_L02_62
AD-MSCs, Donor 2, DMEM, Passage 2


title: Case17


title: AD-MSCs, Donor 3, INFy_24h, Passage 2

description:
Library name: V350118564_L02_67
AD-MSCs, Donor 3, INFy_24h, Passage 2


title: AD-MSCs, Donor 1, INFy_24h, Passage 2

description:
Library name: V350118564_L02_61
AD-MSCs, Donor 1, INFy_24h, Passage 2


title: AD-MSCs, Donor 1, INFy_C, Passage 2

description:
Library name: V350118564_L02_60
AD-MSCs, Donor 1, INFy_C, Passage 2


title: Case22


title: Case14


title: AD-MSCs, Donor 1, DMEM, Passage 2

description:
Library name: V350118564_L02_59
AD-MSCs, Donor 1, DMEM, Passage 2


title: Case16


title: AD-MSCs, Donor 3, INFy_24h, Passage 1

description:
Library name: V350118564_L02_58
AD-MSCs, Donor 3, INFy_24h, Passage 1


title: Case57


title: Case15


title: AD-MSCs, Donor 3, DMEM, Passage 1

description:
Library name: V350118564_L02_48
AD-MSCs, Donor 3, DMEM, Passage 1


title: AD-MSCs, Donor 2, INFy_24h, Passage 1

description:
Library name: V350118564_L02_47
AD-MSCs, Donor 2, INFy_24h, Passage 1


title: Case12


title: Case11


title: Case9


title: AD-MSCs, Donor 2, DMEM, Passage 1

description:
Library name: V350118564_L01_45
AD-MSCs, Donor 2, DMEM, Passage 1


title: AD-MSCs, Donor 2, INFy_C, Passage 1

description:
Library name: V350118564_L01_46
AD-MSCs, Donor 2, INFy_C, Passage 1


title: AD-MSCs, Donor 1, INFy_C, Passage 6

description:
Library name: V350118750_L01_96
AD-MSCs, Donor 1, INFy_C, Passage 6


title: Case8


title: AD-MSCs, Donor 1, INFy_24h, Passage 1

description:
Library name: V350118564_L01_44
AD-MSCs, Donor 1, INFy_24h, Passage 1


title: AD-MSCs, Donor 1, INFy_C, Passage 1

description:
Library name: V350118564_L01_43
AD-MSCs, Donor 1, INFy_C, Passage 1


title: Case7


title: AD-MSCs, Donor 1, DMEM, Passage 1

description:
Library name: V350118564_L01_42
AD-MSCs, Donor 1, DMEM, Passage 1


title: AD-MSCs, Donor 3, INFy_24h, Passage 0

description:
Library name: V350118564_L01_41
AD-MSCs, Donor 3, INFy_24h, Passage 0


title: Case4


title: Case5


title: AD-MSCs, Donor 3, DMEM, Passage 0

description:
Library name: V350118564_L01_15
AD-MSCs, Donor 3, DMEM, Passage 0


title: Case6


title: AD-MSCs, Donor 3, INFy_C, Passage 1

description:
Library name: V350118564_L02_57
AD-MSCs, Donor 3, INFy_C, Passage 1


title: AD-MSCs, Donor 2, INFy_24h, Passage 0

description:
Library name: V350118564_L01_14
AD-MSCs, Donor 2, INFy_24h, Passage 0


title: AD-MSCs, Donor 3, INFy_C, Passage 0

description:
Library name: V350118564_L01_16
AD-MSCs, Donor 3, INFy_C, Passage 0


title: AD-MSCs, Donor 2, INFy_C, Passage 0

description:
Library name: V350118564_L01_13
AD-MSCs, Donor 2, INFy_C, Passage 0


title: Case3


title: Case2


title: Case13


title: Case10


title: Tumor tissue_3

first: Xiukun

last: Hou

address: Huanhu Road

institute: Tianjin Cancer Institute and Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Tumor tissue

extract_protocol:
Tissues were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: patient diagnosis

value: papillary thyroid carcinoma

tag: subject number

value: Tumor tissue

tag: chip antibody


title: Normal tissue_3

source_name: Normal tissue

value: Normal tissue


title: AD-MSCs, Donor 2, DMEM, Passage 0

description:
Library name: V350118564_L01_4
AD-MSCs, Donor 2, DMEM, Passage 0


title: AD-MSCs, Donor 1, DMEM, Passage 0

description:
Library name: V350118564_L01_1
AD-MSCs, Donor 1, DMEM, Passage 0


title: AD-MSCs, Donor 1, INFy_24h, Passage 0

description:
Library name: V350118564_L01_3
AD-MSCs, Donor 1, INFy_24h, Passage 0


title: Normal tissue_2


title: Tumor tissue_2


title: AD-MSCs, Donor 1, INFy_C, Passage 0

description:
Library name: V350118564_L01_2
AD-MSCs, Donor 1, INFy_C, Passage 0


title: TMA DLBCL F6 [FVP93]

type: RNA

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 7455 Fannin St

institute: MD Anderson Cancer Center

description:
F6_3_exprMat_file.csv
F6_3_fov_positions_file.csv
F6_3_metadata_file.csv
F6_3_tx_file.csv
F6_3-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.

hyb_protocol: ISH probes were incubated at 95°C for 2 min and placed on ice. The ISH probe mix (1nM 980 plex ISH probe, 10nM Attenuation probes, 1X Buffer R, 0.1 U/μL RNAse inhibitor in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight.

scan_protocol: Over forty fields of view (FOVs, 0.509mm × 0.509mm) were selected for data collection on each slice. The commercial CosMx optical system has an epifluorescent configuration based on a customized water objective (22.7x, NA 1.1), and uses widefield illumination, with a mix of lasers and light-emitting diodes (385nm 750mW, 488 nm 1W, 530nm 1W, 590nm 150mW, 647nm 1W) that allow imaging of DAPI, Alexa Fluor-488, Atto-532, Dyomics Dy-605 and Alexa Fluor-647, as well as removal of photocleavable dye components. The camera used was a Lucid Atlas10 ATX CMOS sensor (pixel size 120nm). A 3D multichannel image stack (8 frames) was obtained at each FOV location per imaging round, with the step size of 0.8um. Image registration, feature extraction, localization, decoding of individual transcripts, and machine-learning based cell segmentation (developed upon Cellpose [PMID: 33318659]) were performed as previously described. [PMID: 36203011] The final segmentation mapped each transcript in the registered images to the corresponding cell, as well as to subcellular compartments (nuclei, cytoplasm, membrane), where the transcript was located.

data_processing: Images were segmented to obtain cell boundaries, assign transcripts at the cell-level, and obtain a transcript by cell count matrix. Cells with an average negative control count greater than 0.5 and less than 20 detected features were filtered out. After quality control, a mean of 95,3% of cells across samples and FoVs was retained, corresponding to ~46,160 cells per sample on average.

label: SMI imaging barcodes

source_name: Diffuse large B-cell lymphoma (DLBCL), NOS

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in PBS at 40°C for 30 minutes. Tissue sections were then washed twice with diethylpyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 0.00075% fiducials  0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 1 min at room temperature. Fixed samples were rinsed twice with NBF stop buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min and subsequently blocked with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber  was placed over the tissue.

extract_protocol: To obtain a quasi-3D transcriptomic dataset, FFPE tissue blocks were sectioned to 5um slices using a microtome. The sample processing, staining, imaging, and cell segmentation were performed as previously described.[PMID: 36203011] Briefly, Tissue sections were placed to on VWR Superfrost Plus Micro Slide (Cat# 48311-703) for optimal adherence. Slides were then dried at 37°C overnight, followed by deparaffinization and heat-induced epitope retrieval (HIER).

tag: anatomic sampling location

value: Extranodal

tag: ebv status


title: Normal tissue_1


title: Splenic cells isolated from mouse, new RNA, 100 G,  scFLUENT-seq

city: Beijing

first: Xiaohua

last: Shen

state: Beijing

address: China, Tsinghua university, school of medicine

department: Medical School

institute: Tsinghua University

description: Library name: Sample 13

data_processing:
the SeekSoul Tools (http://seeksoul.seekgene.com/zh/v1.2.2/index.html) was used to to process the cleaned reads. Number of cells detected using the SeekSoul Tools pipeline was used as the input for UMI-tools v1.1.2. whitelist command with options: --bc-pattern=CCCCCCCCCCCCCCCCCNNNNNNNNNNNN --set-cell-number. Reads with matched cell barcodes in the whitelist file were retained for subsequent analysis using UMI-tools extract command. Each RNA read was tagged with the cell barcode (base 1-17 of Read1) and UMI (base 18-29 of Read1). Cell barcodes were extracted using UMI-tools extract command. Reads were trimmed of TSO sequences and adapters using Cutadapt v0.6.6 and aligned to the mouse (mm10, GENCODE release vM22 reference genome assembly using STAR v2.7.3a.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Nuclei of mouse ESCs were extracted using cytolysis buffer (0.1% BSA, 200 U RNase inhibitor, 0.2% NP-40, 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2) and fixed using 1% formaldehyde. Fixed nuclei were used for biotin-tagging reaction using in-situ click working solution (50 mM Hepes pH 7.5, 2.5 mM THPTA, 2.5 mM CuSO4, 4 mM Biotin-PEG3-azide, 10 mM Sodium ascorbate) and incubated at 25°C,350 rpm with 10 s on and 10s off on a ThermoMixer for 0.5 h. The nuclei were sent to single-cell sequencing.
cDNA products were amplified by PCR following 98℃ 3 min, (98℃ 10 sec, 63℃ 15 sec, 72℃ 1min) for 10 cyles, 72℃ 5 min, 4℃ Hold. The products were purified, checked for cDNA amount, and served as the template of the second PCR. Finally, after purification, one-fourth volume of cDNA was amplified by index PCR. The reaction was set on a thermal cycler with the following program: 98℃ 3 min, (98℃ 10 sec, 54℃ 15 sec, 72℃ 1min) for 7cyles, 72℃ 5 min, 4℃ Hold. The indexed sequencing libraries were purified using 0.8 DNA clean beads. Specifically, for supernatant fraction, rRNA/mtRNA blocking probes were added to the first round of PCR to remove cDNA from rRNA and mtRNA.

value: spleen


title: Splenic cells isolated from mouse, old RNA, 100 G,  scFLUENT-seq

description: Library name: Sample 14


title: Tumor tissue_1


title: MEF, new RNA, 100 G,  scFLUENT-seq

description: Library name: Sample 15

source_name: embryonic fibroblasts

value: embryonic fibroblasts


title: 2C_CasRX-KD polq_4_10hpi_20hphCG

city: Xuhui, Shanghai

first: Jie

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai

institute: Center for Excellence in Brain Science and Intelligence Technology (Institute of Neuroscience), Chinese Academy of Sciences

description:
Library name: 2C_Poql_4
Column name in counts_allsample.txt: 2C_Poql_4

data_processing:
Raw reads were firstly processed through Trim Galore (v0.6.10) with the default parameters. In this step, clean reads were obtained by removing reads containing adapter and low-quality reads from raw data. Reference genome (GRCm38) and gene model annotation files (Release M25) were downloaded from GENCODE database (http://gencodegenes.org/mouse/release_M25.html). Paired-end clean reads were aligned to the reference genome using STAR (v2.7.3a). The abundance of transcripts and genes was estimated from the aligned reads using RSEM (v1.2.28). RSEM provided quantification of gene expression metrics including expected read counts, TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads).
Assembly: GRCm10/mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

source_name: embryo

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: To investigate the transcriptome-wide effects of Polq knockdown using CasRX in mouse embryos, one-cell stage embryos were microinjected at 20 hours post-hCG administration, and total RNA was extracted 10 hours later when the embryos had reached the 2-cell stage. Each sample consisted of five embryos, and four biological replicates were included for both the Polq knockdown (CasRX/KD-Polq) and control (CasRX) groups.

value: embryo

value: mouse 2-Cell embryo

value: polq knockdown

value: One-cell stage embryos were microinjected with CasRX and a Polq-targeting gRNA at 20 hours post-hCG administration, and total RNA was extracted 10 hours later at the 2-cell stage.


title: TMA DLBCL F6 [FVP99]


title: Case1


title: TMA DLBCL F6 [FVP80]


title: 2C_CasRX-KD polq_3_10hpi_20hphCG

description:
Library name: 2C_Poql_3
Column name in counts_allsample.txt: 2C_Poql_3


title: 2C_CasRX-KD Ctrl_4_10hpi_20hphCG

description:
Library name: 2C_Ctrl_4
Column name in counts_allsample.txt: 2C_Ctrl_4

value: WT

value: One-cell stage embryos were microinjected with CasRX  at 20 hours post-hCG administration, and total RNA was extracted 10 hours later at the 2-cell stage.


title: TMA DLBCL F6 [FVP89]

source_name: T-cell/histiocyte-rich large B-cell lymphoma

value: Nodal


title: TMA DLBCL F6 [FVP87]

source_name: Primary mediastinal (thymic) large B-cell lymphoma


title: 2C_CasRX-KD polq_2_10hpi_20hphCG

description:
Library name: 2C_Poql_2
Column name in counts_allsample.txt: 2C_Poql_2


title: 2C_CasRX-KD polq_1_10hpi_20hphCG

description:
Library name: 2C_Poql_1
Column name in counts_allsample.txt: 2C_Poql_1


title: 2C_CasRX-KD Ctrl_3_10hpi_20hphCG

description:
Library name: 2C_Ctrl_3
Column name in counts_allsample.txt: 2C_Ctrl_3


title: TMA DLBCL F6 [FVP97]

value: Negative


title: 2C_CasRX-KD Ctrl_1_10hpi_20hphCG

description:
Library name: 2C_Ctrl_1
Column name in counts_allsample.txt: 2C_Ctrl_1


title: TMA DLBCL F6 [FVP94]

source_name: EBV+ DLBCL, NOS

value: Positive


title: TMA DLBCL F6 [FVP82]


title: MEF, old RNA, 100 G,  scFLUENT-seq

description: Library name: Sample 16


title: Primary Normal Fibroblast, Tumor cell-conditioned medium without lipids treatment 3

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: Ludwig Cancer Institute, UNIL

description:
Library name: T-L3
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCMwoLipid_3

data_processing:
Raw reads were trimmed using TrimGalore (v.0.6.6) according to quality from FastQC and adaptor.
The trimmed reads were mapped to the mm10 using STAR (v.2.7.9a).
The summarizeOverlaps function from the GenomicAlignments package (v.1.30.0) in R/Bioconductor (v.3.13) was used to define gene expression level by counting the alignments to exons
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: normalized counts from DEseq2

source_name: skin

growth_protocol: Primary normal fibroblasts were isolated from skin fragments of new-born mice. The obtained NFs were cultured and maintained in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol:
RNA were collected by Qiagen RNeasy Kits
The sequencing library was prepared by illumine Truseq Stranded RNA kit

treatment_protocol: YUMM1.7 tumor cell-conditioned medium was obtained by seeding 2×106 YUMM1.7 cells on a 10cm dish with DMEM supplemented with 10% FBS for 24h. To generate TCM without lipids, the collected TCM, as described above, was treated with Cleanascite reagent.

value: skin

value: fibroblast

value: wild-type

value: TCM w/o Lipids


title: Primary Normal Fibroblast, Tumor cell-conditioned medium without lipids treatment 1

description:
Library name: T-L1
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCMwoLipid_1


title: TMA DLBCL F6 [FVP85]


title: 2C_CasRX-KD Ctrl_2_10hpi_20hphCG

description:
Library name: 2C_Ctrl_2
Column name in counts_allsample.txt: 2C_Ctrl_2


title: TMA DLBCL F6 [FVP84]


title: TMA DLBCL F6 [FVP81]


title: Primary Normal Fibroblast, Tumor cell-conditioned medium treatment 2

description:
Library name: T2
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCM_2

value: TCM


title: Primary Normal Fibroblast, Tumor cell-conditioned medium without lipids treatment 2

description:
Library name: T-L2
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCMwoLipid_2


title: TMA DLBCL F6 [FVP98]

value: Extranodal


title: Primary Normal Fibroblast, Tumor cell-conditioned medium treatment 3

description:
Library name: T3
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCM_3


title: TMA DLBCL F6 [FVP95]


title: TMA DLBCL F6 [FVP96]


title: TMA DLBCL F6 [FVP92]


title: TMA DLBCL F6 [FVP86]

source_name: Sample 1. EBV+ DLBCL, NOS; Sample 2. Diffuse large B-cell lymphoma (DLBCL), NOS

value: Sample 1. Extranodal; Sample 2. Extranodal


title: Mouse olfactory bulb, OPL,rep3

city: qingdao

first: Xue

last: Dong

address: 238 songling road

institute: Ocean University of China

description:
Library name: sample46
FF, OPL,rep3

data_processing:
Drop-seq software
Assembly: hg38, mm10
Supplementary files format and content: GETD.summary

source_name: olfactory bulb

extract_protocol:
After tissue enzymatic digestion, the biotinylated cDNA was enriched using streptavidin-coated magnetic beads. The enriched cDNA was then amplified and prepared for sequencing
smart-seq2

value: olfactory bulb

value: in situ reaction

tag: batch


title: TMA DLBCL F6 [FVP79]


title: TMA DLBCL F6 [FVP102]


title: TMA DLBCL F5 [FVP62]

description:
F5_5_exprMat_file.csv
F5_5_fov_positions_file.csv
F5_5_metadata_file.csv
F5_5_tx_file.csv
F5_5-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.

value: Spleen


title: Primary Normal Fibroblast, treatment control 2

description:
Library name: C2
Column name in XYL_RNAseq_normalized_count_allSample.txt: Ctrl_2

tag: tissue

value: control


title: Mouse olfactory bulb, OPL,rep2

description:
Library name: sample45
FF, OPL,rep2


title: TMA DLBCL F6 [FVP88]


title: Primary Normal Fibroblast, Tumor cell-conditioned medium treatment 1

description:
Library name: T1
Column name in XYL_RNAseq_normalized_count_allSample.txt: TCM_1


title: TMA DLBCL F5 [FVP59]

source_name: Post-transplant lymphoproliferative disorder (PTLD)


title: Mouse olfactory bulb, OPL,rep1

description:
Library name: sample44
FF, OPL,rep1


title: Primary Normal Fibroblast, treatment control 3

description:
Library name: C3
Column name in XYL_RNAseq_normalized_count_allSample.txt: Ctrl_3


title: TMA DLBCL F6 [FVP83]

description:
F6_3_exprMat_file.csv
F6_3_fov_positions_file.csv
F6_3_metadata_file.csv
F6_3_tx_file.csv
F6_3-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.


title: TMA DLBCL F5 [FVP60]


title: Primary Normal Fibroblast, treatment control 1

description:
Library name: C1
Column name in XYL_RNAseq_normalized_count_allSample.txt: Ctrl_1


title: TMA DLBCL F5 [FVP78]


title: TMA DLBCL F5 [FVP61]


title: Mouse olfactory bulb, MCL,rep1

description:
Library name: sample41
FF, MCL,rep1


title: Mouse olfactory bulb, MCL,rep3

description:
Library name: sample43
FF, MCL,rep3


title: Mouse embryo, veterbra target,rep4

description:
Library name: sample34
FFPE section, veterbra,rep4

source_name: E15.5 mouse embryo

value: E15.5 mouse embryo


title: Mouse embryo, veterbra target,rep3

description:
Library name: sample33
FFPE section, veterbra,rep3


title: TMA DLBCL F5 [FVP70]


title: Mouse embryo, vertebra target,rep2

description:
Library name: sample32
FFPE section, veterbra,rep2


title: Mouse embryo, vertebra target,rep1

description:
Library name: sample31
FFPE section, veterbra,rep1


title: TMA DLBCL F5 [FVP68]


title: TMA DLBCL F5 [FVP73]


title: Mouse embryo, digit target,rep4

description:
Library name: sample30
FFPE section, digit,rep4


title: TMA DLBCL F5 [FVP69]


title: TMA DLBCL F5 [FVP76]


title: Mouse embryo, digit target,rep3

description:
Library name: sample29
FFPE section, digit,rep3


title: TMA DLBCL F5 [FVP74]


title: TMA DLBCL F5 [FVP58]


title: Mouse olfactory bulb, MCL,rep2

description:
Library name: sample42
FF, MCL,rep2


title: Mouse embryo, PAX6 negative,rep4

description:
Library name: sample26
PAX6 negative target, rep4

source_name: E13.5 mouse embryo

value: E13.5 mouse embryo


title: Mouse embryo, digit target,rep2

description:
Library name: sample28
FFPE section, digit,rep2


title: Mouse embryo, PAX6 negative,rep3

description:
Library name: sample25
PAX6 negative target, rep3


title: TMA DLBCL F5 [FVP72]


title: TMA DLBCL F5 [FVP66]


title: TMA DLBCL F5 [FVP65]

source_name: B-cell lymphoma, NOS


title: TMA DLBCL F5 [FVP77]


title: TMA DLBCL F5 [FVP67]


title: Mouse embryo, PAX6 negative,rep2

description:
Library name: sample24
PAX6 negative target, rep2


title: TMA DLBCL F5 [FVP71]


title: TMA DLBCL F5 [FVP75]


title: Mouse embryo, PAX6 negative,rep1

description:
Library name: sample23
PAX6 negative target, rep1


title: TMA DLBCL F4 [FVP57]

description:
F4_1_exprMat_file.csv
F4_1_fov_positions_file.csv
F4_1_metadata_file.csv
F4_1_tx_file.csv
F4_1-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.


title: Mouse embryo, PAX6 positive,rep4

description:
Library name: sample22
PAX6 positive target, rep4


title: Mouse embryo, PAX6 positive,rep3

description:
Library name: sample21
PAX6 positive target, rep3


title: Mouse embryo, PAX6 positive,rep2

description:
Library name: sample20
PAX6 positive target, rep2


title: TMA DLBCL F4 [FVP53]


title: Mouse embryo, PAX6 positive,rep1

description:
Library name: sample19
PAX6 positive target, rep1


title: TMA DLBCL F4 [FVP56]


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/10000, rep2

description:
Library name: sample17
HEK293 vs NIH/3T3=10000:1,rep2

source_name: cell line

value: cell line

value: HEK293 and NIH/3T3

value: wide


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/10000, rep1

description:
Library name: sample16
HEK293 vs NIH/3T3=10000:1,rep1


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/1000, rep3

description:
Library name: sample15
HEK293 vs NIH/3T3=1000:1,rep3


title: TMA DLBCL F3 [FVP52]

description:
F3_1_exprMat_file.csv
F3_1_fov_positions_file.csv
F3_1_metadata_file.csv
F3_1_tx_file.csv
F3_1-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/10000, rep3

description:
Library name: sample18
HEK293 vs NIH/3T3=10000:1,rep3


title: TMA DLBCL F4 [FVP55]


title: TMA DLBCL F3 [FVP45]


title: TMA DLBCL F3 [FVP47]


title: TMA DLBCL F3 [FVP51]

value: Positive


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/100, rep3

description:
Library name: sample12
HEK293 vs NIH/3T3=100:1,rep3


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/1000, rep1

description:
Library name: sample13
HEK293 vs NIH/3T3=1000:1,rep1


title: TMA DLBCL F3 [FVP48]

value: Nodal

value: Negative


title: Mouse embryo, digit target,rep1

description:
Library name: sample27
FFPE section, digit,rep1


title: AD-MSCs, Donor 3, INFy_C, Passage 5

description:
Library name: V350118750_L01_93
AD-MSCs, Donor 3, INFy_C, Passage 5

source_name: adipose-derived mesenchymal stromal cells


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/1000, rep2

description:
Library name: sample14
HEK293 vs NIH/3T3=1000:1,rep2


title: TMA DLBCL F3 [FVP43]


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/100, rep2

description:
Library name: sample11
HEK293 vs NIH/3T3=100:1,rep2


title: TMA DLBCL F3 [FVP50]


title: HEK293 and NIH/3T3 cells, 3T3 target, 1/100, rep1

description:
Library name: sample10
HEK293 vs NIH/3T3=100:1,rep1


title: HEK293 and NIH/3T3 cells, 293 target, 1/10000, rep3

description:
Library name: sample9
HEK293 vs NIH/3T3=1:10000,rep3


title: TMA DLBCL F3 [FVP49]


title: HEK293 and NIH/3T3 cells, 293 target, 1/10000, rep1

description:
Library name: sample7
HEK293 vs NIH/3T3=1:10000,rep1


title: TMA DLBCL F3 [FVP38]

source_name: High-grade B-cell lymphoma, with MYC and BCL2 and/or BCL6 rearrangements


title: HEK293 and NIH/3T3 cells, 293 target, 1/1000, rep2

description:
Library name: sample5
HEK293 vs NIH/3T3=1:1000,rep2


title: TMA DLBCL F3 [FVP42]

source_name: Diffuse large B-cell lymphoma (DLBCL), NOS


title: TMA DLBCL F3 [FVP40]


title: TMA DLBCL F3 [FVP41]


title: TMA DLBCL F3 [FVP46]

source_name: Sample 1. Diffuse large B-cell lymphoma (DLBCL), NOS; Sample 2. Diffuse large B-cell lymphoma (DLBCL), NOS

value: Sample 1. Nodal; Sample 2. Extranodal


title: HEK293 and NIH/3T3 cells, 293 target, 1/10000, rep2

description:
Library name: sample8
HEK293 vs NIH/3T3=1:10000,rep2


title: TMA DLBCL F3 [FVP39]


title: HEK293 and NIH/3T3 cells, 293 target, 1/100, rep2

description:
Library name: sample2
HEK293 vs NIH/3T3=1:100,rep2


title: HEK293 and NIH/3T3 cells, 293 target, 1/100, rep3

description:
Library name: sample3
HEK293 vs NIH/3T3=1:100,rep3


title: HEK293 and NIH/3T3 cells, 293 target, 1/100, rep1

description:
Library name: sample1
HEK293 vs NIH/3T3=1:100,rep1


title: TMA DLBCL F2 [FVP22]

description:
F2_1_exprMat_file.csv
F2_1_fov_positions_file.csv
F2_1_metadata_file.csv
F2_1_tx_file.csv
F2_1-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.


title: mtRNAP_2d

city: Bern

first: Torsten

last: Ochsenreiter

state: Bern

address: Blatzerstrasse 4

department: Biology

institute: Institute of Cell Biology

description:
Library name: AEKC-2
Standard mode

data_processing:
Unique Molecular Identifiers (UMI)s-tools were used to detect UMI sequences and remove bases corresponding to illumina adapters.
Assembly: MK584625 (https://www.ncbi.nlm.nih.gov/nuccore/MK584625 [ncbi.nlm.nih.gov]) and annotated_mOs_T.brucei_EATRO1125_AnTat1.1.gbk (https://figshare.com/articles/dataset/Trypanosoma_brucei_EATRO1125_AnTat1_1_assembled_and_annotated_minicircle_genome/7756808/1?file=15352502)
Supplementary files format and content: Excel files containing the counts and normalized counts. The normalization factor was determined based on mapping to the nuclear genome of TbruceiLister427 (Trypanosoma_brucei_Lister_strain_427_2018; https://tritrypdb.org/tritrypdb/app/search/genomic- sequence/SequencesByTaxon)

organism: Trypanosoma brucei

growth_protocol: Transgenic T. brucei cell lines were generated using the procyclic form (PCF) strain 29-13 and the bloodstream form (BSF) strain NYsm and yL262P (Dean et al., 2013; Motyka & Englund, 2004; Wirtz et al., 1999). The PCF were grown in exponential phase (up to 1×107 cells/ml) in semi-defined medium 79 (SDM-79, Bioconcept, #9-04V01-M) supplemented with 10% fetal calf serum (FCS) at 27 °C. BSF were grown in exponential phase (up to 1×106 cells/ml) in Hirumi’s modified Iscove’s medium 9 (HMI-9) at 37° C (with 5% CO2 and water) (Hirumi & Hirumi, 1989).

extract_protocol:
A total of 1x108 cells were harvested by centrifugation at 2500 rpm for 8 min at room temperature. The pellet was washed with 1 ml PBS, transferred to a 1.5 ml tube and centrifuged again at 2500 rpm for 8 min at room temperature. After removing the supernatant, the cell pellet was resuspended in 1 ml TRIzol (Tri-Reagent, Merck, #9424). Subsequently, 200 µl of chloroform was added and the samples were vortexed vigorously. The mixture was then centrifuged at 12000 rpm for 15 min at 4°C. The upper aqueous phase (400 µl) was carefully transferred to a new tube containing 500 µl of ice-cold isopropanol, ensuring that the interphase was not disturbed. The tube was inverted several times to mix the solution. RNA was precipitated by centrifugation at 12000 rmp for 15 min at 4°C. Subsequently, the supernatant was removed and discarded. The RNA pellet was washed twice with 1 ml 70% ethanol followed by centrifugation at 7500 rpm for 5 min at 4°C. The ethanol was removed, and the tube was inverted and left open at room temperature to air-dry for at least 5 min. Finally, the RNA pellet was resuspended in 50 µl RNase-free water and incubated at 55°C for 5 min on a heating block. RNA concentration was determined using a Nanodrop spectrophotometer and RNA integrity was assessed by running 1 µg of RNA on a 1% agarose gel for 40 min at 100 V. RNA was stored at -80°C or used directly for DNase treatment and cDNA synthesis.
Total RNA are processd into short fragments (150-200 bp) and treatet with kinase. Libraries are prepared using the QIAseq-miRNA kit

treatment_protocol: RNAi targets the open reading frame of mtRNAP (position: 575-1045) or mtTF1 (position: 98- 567) , respectively and was induced with tetracycline

tag: strain

value: mtRNAP RNAi +Tet


title: mtRNAP_0d

description:
Library name: AEKC-1
Standard mode

value: mtRNAP RNAi -Tet


title: TMA DLBCL F2 [FVP33]

source_name: Sample 1. T-cell/histiocyte-rich large B-cell lymphoma; Sample 2. T-cell/histiocyte-rich large B-cell lymphoma

value: Sample 1. Nodal; Sample 2. Nodal


title: oocyte rep 1

city: Lexington

first: Jeramiah

middle: James

last: Smith

state: KY

address: 101 Morgan Building

institute: University of Kentucky

data_processing:
RNAseq reads from this study and a previous studies targeting meiotic testes (SRP009181) were aligned to the reference genome using HISAT2 v.2.2.1
The resulting alignments were used to quantify the expression of annotated genes using Stringtie v.2.2.3.
Differential gene expression was assessed using median of ratios normalization in R.
Assembly: kPetMar1.pri
Supplementary files format and content: tab dellimited text fille showing normalized values (FKPM) for oocyte and published tesstes ( ) data.
Supplementary files format and content: .gff file showing the ocation of gene bodies that were considered for analyses. This is an updated set of gene models that builds on the current RefSeq annotation sest by integrating data from several new studies.

organism: Petromyzon marinus

source_name: oocyte

extract_protocol:
Standard Trizol extraction
Illumina PE 150

value: oocyte


title: P8 Wild Type scATAC-Seq Replicate 2

city: Baltimore

first: Dong Won

middle: Thomas

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description:
Library name: TK89
10x Genomics scATAC-Seq

library_source: genomic single cell

data_processing:
For sc/snRNA-Seq:Libraries for scRNA-Seq and snRNA-Seq were prepared using the 10x Genomics Chromium. Single Cell 3’ v3.0 and v3.1 platforms (Table S1), following the manufacturer’s protocols. Sequencing was conducted on an Illumina NovaSeq 6000, targeting a depth of 500 million reads per sample. Raw data were processed with the 10x Genomics Cell Ranger Software (v5) and aligned to the mm10 mouse genome reference (refdata-gex-mm10-2020-A).
For scATAC-Seq: scATAC-Seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC v1.1 platform (Table S1), with one-hour tagmentation and 9-10 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000, at a target depth of 600 million reads per sample. Raw data were processed with Cell Ranger ATAC (v2) and aligned to the mm10 mouse genome reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).
Assembly: mm10
Supplementary files format and content: sc/snRNA-Seq: matrix file in H5 format
Supplementary files format and content: scATAC-Seq: inside zip file contains matrix file (H5 format), fragments.tsv, singlecell.csv

source_name: Hypothalamus and Prethalamus

extract_protocol:
Animal model  Time-mated wild-type (WT) CD1 mice were obtained from Charles River Laboratories. Transgenic mouse lines were maintained on a mixed C67BL6/CD1 background. The following transgenic mouse lines were used in the study:  1) Foxd1-Cre (B6;129S4-Foxd1tm1(GFP/cre)Amc/J, JAX#012463), 2) Isl1-flox (gift from Dr. Lin Gan, (Pan et al. 2008)), 3) Lhx1-flox gift from Dr. Richard R Behringer (Kwan and Behringer 2002), 4) Nkx2.2-Cre (B6.129S6(Cg)-Nkx2-2tm4.1(cre/EGFP)Suss/J, JAX#026880), 5) Dlx1/2-flox (gift from Dr. Jay Lee, (B. Lee et al. 2018)).  Animals were housed in a temperature-controlled facility with a 14-hour dark/10-hour light cycle and had ad libitum access to food and water. All animal procedures followed the National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the Johns Hopkins University Animal Care and Use Committee.
Tissue Collection and Dissections  Dissection of WT Mice  Tissues were collected from WT mice representing a random but equal mix of males and females across postnatal ages. For embryonic stages, 10-30 embryos were harvested from 3-4 pregnant dams, depending on the gestational age. Brain dissections followed previously established protocols(D. W. Kim et al. 2020). Meninges were removed, and dissections were completed in cold HBSS (#14170112, ThermoFisher Scientific) within 30 minutes for each age group.  Dissection of Mutant Mice  Embryos from mutant mice were collected from a minimum of five pregnant dams. Hypothalamic and prethalamic regions were dissected, and the remaining tissues of embryos were used for rapid genotyping (#4359187, Thermo Fischer Scientific), and grouped by genotype for further analysis. Dissected hypothalamic and prethalamic tissues were stored in HABG buffer (Hibernate-E (#A1247601, Thermo Fisher Scientific) for embryos or Hibernate-A (#A1247501, Thermo Fisher Scientific) for postnatal stages, both supplemented with 2% B-27 Supplement (#17504044, Thermo Fischer Scientific), and 0.5 mM GlutaMAX Supplement (#35050061, Thermo Fisher Scientific) until cell dissociation.   Preparations of cells and nuclei  Cell Dissociation for scRNA-Seq  To prepare samples for scRNA-Seq, tissues were dissociated in Hibernate medium (Hibernate-E Minus Calcium (#HECA500, BrainBits) for embryos or Hibernate-A Minus Calcium (#HACA500, BrainBits) for postnatal stages), supplemented with 2 mg/ml papain (#LS003119, Worthington Biochemical) and 0.5 mM Glutamax. The enzyme mixture was pre-incubated for 15 minutes, then added to tissues for 5 - 30 minutes with 0.1 U/μl RNase inhibitor (N2615, Promega). Toward the end of digestion, 100 μg/ml final DNase I (#4716728001, Sigma-Aldrich) was added. Cells were subsequently centrifuged, resuspended in HABG buffer, filtered through a 40 μm cell strainer (BAH136800040-50EA, Sigma-Aldrich), and resuspended in HABG buffer containing RNase inhibitor (0.5 U/μl). Cell viability and counts were assessed with Trypan Blue staining (#15250061, Thermo Fisher Scientific) and a hemocytometer.  Nuclei Preparation for scATAC-Seq  Nuclei for scATAC-Seq were extracted following post-cell dissociation and purified following a 10x Genomics protocol. Nuclei count and yield were verified with Trypan Blue staining and a hemocytometer.  Nuclei Preparation for snRNA-Seq  For snRNA-Seq, adult mouse brains were rapidly dissected, and 100 um coronal sections were prepared using a mouse brain matrice. Regions spanning the ZI, TRN, and thalamus were microdissected under a dissection microscope. Nuclei were extracted following a 10x Genomics protocol.
Sequencing Library Preparation and Data Processing  sc/snRNA-Seq  Libraries for scRNA-Seq and snRNA-Seq were prepared using the 10x Genomics Chromium. Single Cell 3’ v3.0 and v3.1 platforms (Table S1), following the manufacturer’s protocols. Sequencing was conducted on an Illumina NovaSeq 6000, targeting a depth of 500 million reads per sample. Raw data were processed with the 10x Genomics Cell Ranger Software (v5) and aligned to the mm10 mouse genome reference (refdata-gex-mm10-2020-A).  scATAC-Seq  scATAC-Seq libraries were prepared using the 10x Genomics Chromium Single Cell ATAC v1.1 platform (Table S1), with one-hour tagmentation and 9-10 cycles of PCR. Libraries were sequenced on Illumina NovaSeq 6000, at a target depth of 600 million reads per sample. Raw data were processed with Cell Ranger ATAC (v2) and aligned to the mm10 mouse genome reference (refdata-cellranger-arc-mm10-2020-A-2.0.0).

value: Hypothalamus and Prethalamus

tag: library type

value: scATAC-Seq

tag: age

value: Wild Type

tag: Sex

value: pooled male and female


title: P8 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK88
10x Genomics scATAC-Seq


title: TMA DLBCL F3 [FVP37]

description:
F3_1_exprMat_file.csv
F3_1_fov_positions_file.csv
F3_1_metadata_file.csv
F3_1_tx_file.csv
F3_1-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.

value: Extranodal


title: HEK293 and NIH/3T3 cells, 293 target, 1/1000, rep1

description:
Library name: sample4
HEK293 vs NIH/3T3=1:1000,rep1

tag: cell line

tag: cell type

value: in situ reaction


title: TMA DLBCL F2 [FVP28]


title: IgG rep 2, Vg6+ gd T

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

description: Library name: IgG_rep2

data_processing:
Raw paired-end FASTQ sequences were aligned to the mm10 reference genome using Bowtie2 v2.4.4 with the parameters --very-sensitive-local, --dovetail, and fragment length constraints of 10-700 bp to maximize alignment sensitivity while preserving correct fragment pairing. The resulting SAM files were converted to BAM format using Samtools v1.14 and subsequently sorted to optimize downstream processing.
Mapped reads were extracted (-F 4 -F 8 in Samtools), and duplicate reads were marked using Picard v2.18.2 (MarkDuplicates function) before being removed (-F 1024 in Samtools). Low-confidence regions and artifacts were further eliminated by filtering against the ENCODE mm10 blacklist using BEDTools v2.30.0.
Narrow peak calling was performed using MACS2 v2.2.7.1 with a q-value threshold of 0.05 (-q 0.05)
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: cut&run

source_name: mesenteric lymph node

growth_protocol: Mesenteric lymph nodes were harvested from IL-17A-cre Rosa26-lox-Stop-lox-ZsGreen mice and Tgd17 cells were expanded for five days in vitro.

extract_protocol:
Vg6+ Tgd17 cells were sorted from day 5 mLN cultures as CD3+ CD4- CD8- gdTCR+ ZS-Green+ Vg4-.
Epicypher CUTANA CUT&RUN kit protocol was followed starting with 500,000 Vg6+ Tgd17 cells for each sample (JunB, Fosl2, or IgG control).
Epicypher CUTANA CUT&RUN library prep kit (Primer Set 1) protocol was followed for preparing sequencing ready libraries.

value: mesenteric lymph node

value: Vg6+ZS+gdT (CD3+CD4-CD8-gdTCR+ZS+Vg4-)

tag: genotype

value: IL-17A-cre Rosa26-lox-Stop-lox-ZsGreen

value: Rabbit IgG Negative Control (Epicypher 13-0042)


title: Fosl2 rep 3, Vg6+ gd T

description: Library name: Fosl2_rep3

value: Fosl2 (Sigma HPA004817)


title: TMA DLBCL F2 [FVP25]

source_name: T-cell/histiocyte-rich large B-cell lymphoma

value: Nodal


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/flox scATAC-Seq Replicate 2

description:
Library name: TK48
10x Genomics scATAC-Seq

value: CD1 & C57BL6

value: Foxd1-Cre/+ ; Isl1-flox/flox


title: P4 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK87
10x Genomics scATAC-Seq


title: IgG rep 1, Vg6+ gd T

description: Library name: IgG_rep1


title: P4 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK86
10x Genomics scATAC-Seq


title: oocyte rep 2


title: JunB rep 3, Vg6+ gd T

description: Library name: JunB_rep3

value: JunB (C37F9) Rabbit mAb #3753 Cell Signaling


title: HEK293 and NIH/3T3 cells, 293 target, 1/1000, rep3

description:
Library name: sample6
HEK293 vs NIH/3T3=1:1000,rep3

value: cell line

value: HEK293 and NIH/3T3

value: wide

tag: treatment


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/flox scATAC-Seq Replicate 1

description:
Library name: TK44
10x Genomics scATAC-Seq

value: Hypothalamus and Prethalamus

value: scATAC-Seq


title: TMA DLBCL F2 [FVP29]

value: Negative


title: IgG rep 3, Vg6+ gd T

description: Library name: IgG_rep3


title: C_t3_3

city: Pamplona

first: Mirja

last: Rotinen

state: Navarre

address: Avenida Barañain s/n

department: Health Sciences

country: Spain

institute: Public University of Navarre

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode v42 release were used to obtain read counts at gene level considering only those reads aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

growth_protocol: NCI-H510A cells were grown in RPMI-1640 media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA was subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 7. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Lentiviral particles were generated by cotransfection of the pCMV-Delta-8.2 packaging plasmid, the pCMV-VSVG plasmid and the OC2 inducible expression plasmid into HEK-293 cells. NCI-H510A cells were transduced and selected with geneticin. NCI-H510A cells were cultured with 50 ng/mL doxycycline (dox) for 5 days (first induction). Subsequently, the medium was replaced with complete RPMI for 6 days (off-phase). Finally, doxycycline was added again for 5 days (second induction).

value: induction/off-phase/induction of OC2 expression

tag: time point


title: TMA DLBCL F2 [FVP26]


title: JunB rep 2, Vg6+ gd T

description: Library name: JunB_rep2


title: TMA DLBCL F2 [FVP23]


title: Fosl2 rep 1, Vg6+ gd T

description: Library name: Fosl2_rep1


title: TMA DLBCL F2 [FVP34]

value: Extranodal


title: Fosl2 rep 2, Vg6+ gd T

description: Library name: Fosl2_rep2

value: mesenteric lymph node


title: TMA DLBCL F2 [FVP21]


title: C_t2_3


title: E16.5 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK53
10x Genomics scATAC-Seq

value: Wild Type

value: pooled male and female


title: E18.5 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK79
10x Genomics scATAC-Seq


title: C_t2_1


title: C_t3_2


title: E13.5 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK95
10x Genomics scATAC-Seq


title: JunB rep 1, Vg6+ gd T

description: Library name: JunB_rep1

value: Vg6+ZS+gdT (CD3+CD4-CD8-gdTCR+ZS+Vg4-)

value: IL-17A-cre Rosa26-lox-Stop-lox-ZsGreen


title: C_t3_1


title: OE_t3_3


title: TMA DLBCL F2 [FVP20]


title: OE_t3_2


title: E16.5 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK54
10x Genomics scATAC-Seq


title: OE_t3_1


title: C_t1_3


title: E14.5 Wild Type scATAC-Seq Replicate 3

description:
Library name: TKC4
10x Genomics scATAC-Seq


title: E12.5 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK47
10x Genomics scATAC-Seq


title: TMA DLBCL F2 [FVP27]


title: TMA DLBCL F1 [FVP06]

description:
F1_6_exprMat_file.csv
F1_6_fov_positions_file.csv
F1_6_metadata_file.csv
F1_6_tx_file.csv
F1_6-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.

value: Spleen


title: OE_t2_3


title: E12.5 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK43
10x Genomics scATAC-Seq


title: E13.5 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK73
10x Genomics scATAC-Seq


title: E18.5 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK78
10x Genomics scATAC-Seq


title: OE_t2_1


title: TMA DLBCL F2 [FVP19]

description:
F2_1_exprMat_file.csv
F2_1_fov_positions_file.csv
F2_1_metadata_file.csv
F2_1_tx_file.csv
F2_1-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.

value: Nodal


title: C_t1_2


title: E11.5 Wild Type scATAC-Seq Replicate 2

description:
Library name: TK91
10x Genomics scATAC-Seq


title: TMA DLBCL F1 [FVP11]


title: C_t1_1


title: OE_t1_3


title: TMA DLBCL F1 [FVP13]

source_name: EBV+ DLBCL, NOS

value: Positive


title: C_t2_2


title: OE_2

growth_protocol: DMS53 cells were grown in RPMI-1640 media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA was subjected to quantity and quality control using Qubit HS RNA Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity RNA ScreenTape (Agilent Technologies). All RNA samples were high-quality, with RIN values higher than 7. Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction. Briefly,the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with AMPure XP beads (Beckman Coulter), adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). RNAseq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: Lentiviral particles were generated by cotransfection of the pCMV-Delta-8.2 packaging plasmid, the pCMV-VSVG plasmid and the OC2 overexpression or empty plasmid (Origene) into HEK-293 cells. DMS53 cells were subsequently transduced and selected with puromycin.

value: OC2 enforced expression


title: P21 Foxd1-Cre/+ ; Dlx1/2-flox/flox snRNA-Seq Replicate 3

description:
Library name: TKF4
10x Genomics snRNA-Seq

source_name: Zona Incerta/Thalamic Reticular Nucleus/Thalamus

value: snRNA-Seq

value: CD1 & C57BL6

value: Foxd1-Cre/+ ; Dlx1/2-flox/flox


title: TMA DLBCL F2 [FVP18]


title: TMA DLBCL F2 [FVP24]


title: C_2

value: control


title: OE_3


title: C_1


title: P21 Foxd1-Cre/+ ; Dlx1/2-flox/flox snRNA-Seq Replicate 2

description:
Library name: TKF3
10x Genomics snRNA-Seq

value: Zona Incerta/Thalamic Reticular Nucleus/Thalamus


title: TMA DLBCL F1 [FVP17]

value: Negative


title: TMA DLBCL F1 [FVP07]


title: OE_t1_2

value: induction/off-phase/induction of OC2 expression


title: OE_t2_2


title: OE_t1_1


title: TMA DLBCL F1 [FVP01]

value: Extranodal


title: OE_1


title: TMA DLBCL F1 [FVP16]


title: E11.5 Wild Type scATAC-Seq Replicate 1

description:
Library name: TK72
10x Genomics scATAC-Seq

value: Hypothalamus and Prethalamus

value: scATAC-Seq


title: APB5_Mino_2_C57BL6/J_Retina

city: Cologne

first: Urbanus

last: Kinuthia

state: North Rhine Westafalen

address: Kerpener str. 62

department: Ophthalmology

country: Germany

institute: University of Cologne

description:
Library name: Sample11
column name in raw_counts_all samples.csv: APBMino2

data_processing:
Libararies were purifies with KAPA library quantification kit
Libraries were sequenced using Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.4.1.397
The Real-Time Analysis Software (RTA) v3.9.25 was used for image analysis and base calling, and the resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software
Illumina BaseSpace Sequence Hub  was used to process Fastq files and BAM files
The mouse mm39 reference genome (.fasta file) and corresponding reference annotation file (.gtf file) were acquired from NCBI and uploaded onto BaseSpace Hub to build a custom genome using the Reference Builder application (Illumina®). The DRAGEN RNA Pipeline (Illumina®) on BaseSpace Hub was used to align all the .fastq files against the custom genome and generate BAM files. The DRAGEN differential expression tool was used to analyze the BAM files and identify differentially expressed genes and gene counts
Assembly: mm39
Supplementary files format and content: tab-delimited csv file contains raw counts for each sample
Supplementary files format and content: tab-delimited csv file contains transcripts for each sample

source_name: Retina

extract_protocol:
Total RNA was extracted using Rneasy micro kit (Qiagen)
RNAseq libraries were prepared as described in the Illumina “Stranded mRNA Prep Ligation” Reference Guide, the Illumina NextSeq 2000 Sequencing System

treatment_protocol: WT C57BL6/J WT P1 pups were innjected with either 30µg of IgG isotype or a rat anti-mouse PDGFRB monoclonal antibody (clone APB5). At P5, pups were treated with minocycline via daily intraperitoneal injections upto P27 before tissue extraction and processsing at P28

value: Retina

value: WT


title: APB5_Mino_3_C57BL6/J_Retina

description:
Library name: Sample12
column name in raw_counts_all samples.csv: APBMino3


title: P21 Foxd1-Cre/+ ; Dlx1/2-flox/flox snRNA-Seq Replicate 1

description:
Library name: TKD8
10x Genomics snRNA-Seq

value: pooled male and female


title: P21 Foxd1-Cre/+ ; Dlx1/2-flox/+ snRNA-Seq Replicate 2

description:
Library name: TKF2
10x Genomics snRNA-Seq

value: Foxd1-Cre/+ ; Dlx1/2-flox/+


title: APB5_Mino_1_C57BL6/J_Retina

description:
Library name: Sample10
column name in raw_counts_all samples.csv: APBMino1


title: P21 Foxd1-Cre/+ ; Dlx1/2-flox/+ snRNA-Seq Replicate 1

description:
Library name: TKD7
10x Genomics snRNA-Seq


title: TMA DLBCL F1 [FVP15]


title: APB5_3_C57BL6/J_Retina

description:
Library name: Sample9
column name in raw_counts_all samples.csv: APB3


title: APB5_1_C57BL6/J_Retina

description:
Library name: Sample7
column name in raw_counts_all samples.csv: APB1


title: C_3


title: P8 Foxd1-Cre/+ ; Dlx1/2-flox/flox scRNA-Seq Replicate 3

description:
Library name: TKC9
10x Genomics scRNA-Seq

value: scRNA-Seq


title: IgG_Mino_2_C57BL6/J_Retina

description:
Library name: Sample5
column name in raw_counts_all samples.csv: IgGMino2


title: IgG_Mino_1_C57BL6/J_Retina

description:
Library name: Sample4
column name in raw_counts_all samples.csv: IgGMino1


title: P8 Foxd1-Cre/+ ; Dlx1/2-flox/flox scRNA-Seq Replicate 2

description:
Library name: TKC8
10x Genomics scRNA-Seq


title: TMA DLBCL F1 [FVP04]

description:
F1_6_exprMat_file.csv
F1_6_fov_positions_file.csv
F1_6_metadata_file.csv
F1_6_tx_file.csv
F1_6-polygons.csv
The RNA is targeted using ISH probe which is composed of the target-binding and readout domains, the former being a 35–50-nt DNA sequence that hybridizes with target RNA and the latter a 60–80-nt DNA sequence containing four consecutive 10–20-nt reporter-landing domains, where each landing domain can be hybridized with a unique reporter.  The reporter is a single-color branched structure assembled with oligos conjugated with one of four fluorophores and is detected as one of four colors (blue, green, yellow, or red) in SMI images.


title: IgG_Mino_3_C57BL6/J_Retina

description:
Library name: Sample6
column name in raw_counts_all samples.csv: IgGMino3


title: TMA DLBCL F1 [FVP08]


title: IgG_Ctrl_2_C57BL6/J_Retina

description:
Library name: Sample2
column name in raw_counts_all samples.csv: IgGCtrl2


title: IgG_Ctrl_3_C57BL6/J_Retina

description:
Library name: Sample3
column name in raw_counts_all samples.csv: IgGCtrl3


title: P8 Foxd1-Cre/+ ; Dlx1/2-flox/flox scRNA-Seq Replicate 1

description:
Library name: TKC7
10x Genomics scRNA-Seq


title: IgG_Ctrl_1_C57BL6/J_Retina

description:
Library name: Sample1
column name in raw_counts_all samples.csv: IgGCtrl1


title: GEX from CD8 T cell PDAC

city: Chapel Hill

first: Justin

last: Milner

address: 450 West Drive, Lineberger Comprehensive Cancer Center Rm 11-117

institute: University of North Carolina at Chapel Hill

description:
Library name: GEX_CD8_KPC
Single cell GEX library from KPC single cell CD45+CD3+CD8+ T cells at day 15 post tumor implant. Data included are raw sequencing files as well as processed CellRanger outputs as a single output and with oligohashtagged demultiplexing. Additionally, processed Seurat object is provided as this was used for downstream analysis and plots.

data_processing:
Pooled libraries were sequenced on a NextSeq 2000 P3 flow cell (Illumina) in paired end format to a read depth of 1 billion read pairs. Demultiplexing and analysis followed Cell Ranger 7.1.0 with default settings.
Read1: 28 cycles, i7 index: 10 cycles, i5 Index: 10 cycles, Read 2: 90 cycles)
Assembly: mm10
Supplementary files format and content: Filtered Cell Ranger outs for demultiplexed files for each condition include: barcodes, features, and matrix. Clonotype from scVDJseq are provided as csv files.

source_name: tumor

extract_protocol:
Tumors were excised and placed in cold RPMI-1640 media supplemented with 5% FBS (RP5). Cell suspensions were generated by finely mincing tumor samples into 1mm by 1mm pieces using razor blades and samples were digested for 30 minutes at 37degress as previously described (PMID 32024640). Samples were stained with olgio-hashtag antibodies and viable CD45+CD3+CD8+ single cells were sorted from orthotopic KPC-4662 mice. Single cell prepration was performed using 10X Genomics Chromium Controller and the 5' GEM, Library & Gel Bead Kit v2 (PN-1000263). Barcoded products were purified and double-sided size selected with magnetic beads to isolate cDNA and hashtag DNA products following manufacturer's recommendation.
10x Genomics Chromium Controller and Chromium Single Cell 5' GEM, Library, and Gel bead kit v2 was used following manufacturers protocols.

value: tumor

value: CD8 T cells

value: Female


title: E12.5 Foxd1-Cre/+ ; Lhx1-flox/flox scRNA-Seq Replicate 2

last: Kim

description:
Library name: TK62
10x Genomics scRNA-Seq

value: CD1 & C57BL6

value: Foxd1-Cre/+ ; Lhx1-flox/flox


title: APB5_2_C57BL6/J_Retina

description:
Library name: Sample8
column name in raw_counts_all samples.csv: APB2


title: CSP from CD8 T cell PDAC

description:
Library name: CSP_CD8_KPC
Oligo hashtagged cell barcodes from KPC_1, KPC_2, and KPC_3 mice.

library_source: other

molecule: protein


title: TCR from CD8 T cell PDAC

description:
Library name: TCR_CD8_KPC
Single cell VDJ library from KPC single cell CD45+CD3+CD8+ T cells at day 15 post tumor implant.


title: ATAC from P14 CD8 T cell naive

description: 10X Genomics GEX+ATAC

data_processing:
ATAC and Gene expression libraries were sequenced separately. Sequencing followed manufacturers protocols. Sequencing lanes were merged and demultiplexing was performed using cellranger-arc v2.0.0 (batch1) or v2.0.2 (batch2) with default settings.
ATAC (Read1: 50 cycles, i7 index: 8 cycles, i5 Index: 24 cycles, Read 2: 50 cycles)
GEX (Read1: 28 cycles, i7 index: 10 cycles, i5 index: 10 cycles, Read 2: 90 cycles)
Assembly: mm10
Supplementary files format and content: Filtered Cell Ranger Arc outs for demultiplexed files for each condition include: barcodes, features, matrix, and atac fragments.
Library strategy: Multiome

source_name: spleen

extract_protocol:
Nuclei were isolated from viable sorted cells using 10x Genomics Low Cell Input Nuceli isolation protocol per manufacturer's recommendation.
10x Genomics Chromium Controller and Chromium Next GEM Single Cell Multiome ATAC+Gene Expression Reagent Bundle per manufacturer's recommendation.

value: spleen

tag: condition

value: Naïve

value: P14 CD8 T cells

tag: disease


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 48h, replicate 4

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description:
Library name: Sample 95
C96

data_processing:
Raw RNA-Seq reads were trimmed for low-quality bases (Phred quality score < 20) and Illumina sequencing adapters using Cutadapt (v4.4). Reads shorter than 60 bases post-trimming were discarded.
Alignment of the trimmed sequencing reads to the Genome Reference Consortium Human Build (GRCh38) Ensembl version 110 was performed using HISAT2 (v2.2.1) with default settings.
Bam files were filtered for uniquely mapped reads (as flagged by "NH:i:1") and sorted by coordinates using Samtools (v1.18).
Read summarisation was conducted with the featureCounts function from the Rsubread package (v2.16.1) against the Ensembl GTF file version 110
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the bleomycin experiment
Supplementary files format and content: tab-delimited text file contains raw counts for each sample of the TGF-beta experiment

source_name: HUVEC

growth_protocol: Human umbilical cord blood vein cells (HUVEC) were cultured in Endothelial Cell Growth Medium- 2 (EGM-2, Promocell #C-22011) at +37°C, and 5% CO2. Prior to the experiment, cells were expanded in T-75 flasks for 1-2 passages. For the experiments, passages 6-8 were used and cells were plated on 12-well plates with a density of 40 000 cells/cm2. Cells were settled for 24h prior to experimentation.

extract_protocol:
RNA was extracted from cells after 24h, 48h, and 72h of exposure using the RNeasy Mini kit (Qiagen). DNase 1 (Thermo Scientific, EN0521) treatment was used prior to downstream analyses.
RNA-Seq libraries were prepared using the Novogene NGS RNA Library Prep Set (PT042) including polyA-tailed mRNA enrichment. RNA-Seq was performed in two batches i.e., the two exposure experiments of bleomycin and TGF-beta, respectively.

treatment_protocol: Cells were exposed to concentrations of 7, 14, and 21 µg/ml bleomycin or to concentrations of  5, 10, 20 ng/ml TGF-beta. Samples were taken 24h, 48h, and 72h after the start of exposure and from unexposed cells. The two different exposures, bleomycin and TGF-beta, were performed in two different experiments with each having their own controls (unexposed cells).

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype

value: 20 ng/ml TGF-beta

tag: time


title: E12.5 Foxd1-Cre/+ ; Lhx1-flox/flox scRNA-Seq Replicate 1

description:
Library name: TK61
10x Genomics scRNA-Seq

value: Hypothalamus and Prethalamus


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 48h, replicate 4

description:
Library name: Sample 96
C97

value: 5 ng/ml TGF-beta


title: ATAC from P14 CD8 T cell day 7 mWnt-GP

description: 10X Genomics GEX+ATAC

value: mWnt-GP

value: cancer


title: ATAC from P14 CD8 T cell day 42 LCMV CL13 spleen

description: 10X Genomics GEX+ATAC

value: LCMV Clone13

value: chronic infection


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/flox scRNA-Seq Replicate 3

description:
Library name: TK41
10x Genomics scRNA-Seq

value: scRNA-Seq

value: Foxd1-Cre/+ ; Isl1-flox/flox

value: pooled male and female


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 48h, replicate 4

description:
Library name: Sample 94
C93

value: 10 ng/ml TGF-beta


title: TMA DLBCL F1 [FVP10]

value: Extranodal


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 48h, replicate 3

description:
Library name: Sample 93
C91


title: ATAC from P14 CD8 T cell day 42 LCMV Arm IEL

description: 10X Genomics GEX+ATAC

source_name: small intestine intraepithelial lymphocytes

value: LCMV Armstrong

value: acute infection


title: ATAC from P14 CD8 T cell day 7 B-ALL-GP

description: 10X Genomics GEX+ATAC

value: spleen

value: B-ALL-GP

value: P14 CD8 T cells


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 48h, replicate 4

description:
Library name: Sample 91
C88

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype

value: 0 ng/ml TGF-beta


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/flox scRNA-Seq Replicate 1

description:
Library name: TK37
10x Genomics scRNA-Seq

value: Hypothalamus and Prethalamus

value: CD1 & C57BL6


title: GEX from P14 CD8 T cell naive

description: 10X Genomics GEX+ATAC

value: Naïve


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/+ scRNA-Seq Replicate 2

description:
Library name: TK36
10x Genomics scRNA-Seq

value: scRNA-Seq

value: Foxd1-Cre/+ ; Isl1-flox/+


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 24h, replicate 4

description:
Library name: Sample 92
C8


title: GEX from P14 CD8 T cell day 7 mWnt-GP

description: 10X Genomics GEX+ATAC

value: tumor

value: mWnt-GP

value: cancer


title: GEX from P14 CD8 T cell day 42 LCMV Arm spleen

description: 10X Genomics GEX+ATAC

value: LCMV Armstrong


title: GEX from P14 CD8 T cell day 42 LCMV Arm IEL

description: 10X Genomics GEX+ATAC

value: small intestine intraepithelial lymphocytes

value: acute infection


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/+ scRNA-Seq Replicate 1

description:
Library name: TK35
10x Genomics scRNA-Seq

value: pooled male and female


title: GEX from P14 CD8 T cell day 42 LCMV CL13 spleen

description: 10X Genomics GEX+ATAC

value: spleen

value: LCMV Clone13

value: P14 CD8 T cells

value: chronic infection


title: GEX from P14 CD8 T cell day 7 B-ALL-GP

description: 10X Genomics GEX+ATAC

value: B-ALL-GP


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 48h, replicate 2

description:
Library name: Sample 89
C84

value: HUVEC

value: umbilical vein endothelial cells

value: wildtype

value: 20 ng/ml TGF-beta


title: CD4_SNA_low4

city: Toronto

first: Haissi

last: Cui

address: 80 St George St

department: Chemistry

country: Canada

institute: University of Toronto

data_processing:
Resulting reads were trimmed with Trimgalore,10 aligned to Mm39 with Star,11 and differentially expressed genes were identified with DESeq2,12 version 1.38.3.
Assembly: Mm39
Supplementary files format and content: .xlsx file with differential expression changes and padj value

source_name: Spleen

growth_protocol: Splenocytes from four 1 year 1 month old female mice were used for sequencing.

extract_protocol:
Cells were immediately lysed with NEBNext cell lysis buffer with murine RNAse inhibitor from the NEBNext Single Cell/
Low Input RNA Library prep kit for Illumina (cat no. E6420S) and stored at −80°C until cDNA library preparation and sequencing at the Donnelly Sequencing Centre (University of Toronto).

treatment_protocol: 100 SNAHigh and SNALow cells per mouse from CD4+ and CD8+ TEM (CD44+ CD62L−), respectively, were sorted into a 96-well PCR plate.

value: Spleen

value: T cells

value: wt C57Bl6/J


title: P8 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK90
10x Genomics scRNA-Seq

value: Hypothalamus and Prethalamus

value: scRNA-Seq

value: Wild Type


title: CD4_SNA_low3


title: CD4_SNA_low1


title: E12.5 Foxd1-Cre/+ ; Isl1-flox/flox scRNA-Seq Replicate 2

description:
Library name: TK39
10x Genomics scRNA-Seq

value: CD1 & C57BL6

value: Foxd1-Cre/+ ; Isl1-flox/flox


title: ATAC from P14 CD8 T cell day 42 LCMV Arm spleen

description: 10X Genomics GEX+ATAC

value: spleen

value: LCMV Armstrong

value: acute infection


title: CD4_SNA_low2


title: P8 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK85
10x Genomics scRNA-Seq

value: pooled male and female


title: P4 Wild Type scRNA-Seq Replicate 3

description:
Library name: TK84
10x Genomics scRNA-Seq


title: CD8_SNA_high4


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 24h, replicate 3

description:
Library name: Sample 86
C7

value: 0 ng/ml TGF-beta


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 48h, replicate 3

description:
Library name: Sample 88
C83

value: HUVEC

value: 10 ng/ml TGF-beta


title: P4 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK83
10x Genomics scRNA-Seq


title: CD8_SNA_high3


title: CD8_SNA_high1


title: CD8_SNA_high2


title: HUVEC cells exposed to 20 ng/ml TGF-beta for 48h, replicate 3

description:
Library name: Sample 90
C85

value: umbilical vein endothelial cells

value: wildtype


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 48h, replicate 2

description:
Library name: Sample 85
C79


title: CD8_SNA_low4

value: Spleen


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 48h, replicate 2

description:
Library name: Sample 84
C77

value: 5 ng/ml TGF-beta


title: P4 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK82
10x Genomics scRNA-Seq


title: CD8_SNA_low2

value: T cells

value: wt C57Bl6/J


title: CD8_SNA_low3


title: CD8_SNA_low1


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 48h, replicate 2

description:
Library name: Sample 83
C75


title: CD4_SNA_high4


title: HUVEC cells exposed to 0 ng/ml TGF-beta for 48h, replicate 3

description:
Library name: Sample 87
C80


title: E18.5 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK69
10x Genomics scRNA-Seq

value: Hypothalamus and Prethalamus

value: scRNA-Seq


title: nanopore_ribo_minus_SA_rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
First, we used Pychopper (v2.5.0, obtained from GitHub repository at https://github.com/epi2me-labs/pychopper) with parameters -Q 7 -z 50 to identify, orient and trim full-length nanopore cDNA reads. After the Pychopper step, the trimmed full-length reads from each sample were aligned to the CHM13 T2T human reference genome (V2.0, downloaded from GitHub repository at https://github.com/marbl/CHM13 in 2022.08) by using Minimap2 (v2.11). Next, we chose the FLAIR pipeline (v1.7.0) to identify specific transcripts from uniquely-mapped reads. Finally, the quantify module of FLAIR was applied to quantitate SatIII RNA expression in each sample.
Assembly: CHM13 T2T v2.0
Supplementary files format and content: text files include raw counts  in each sample for poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include raw counts  in each sample for ribo- nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from  poly(A)+ nanopore  RNA-seq.
Supplementary files format and content: text files include transcripts information identified  from ribo- nanopore  RNA-seq.
Library strategy: Ribo-Seq

source_name: HeLa

extract_protocol:
For polyadenylated nanopore RNA-seq, HeLa cells were plated onto 6-well plates. The next day, cells were performed SA, HS or control treatment Cells were washed in DPBS and prepared for RNA extraction according to the RNeasy protocol (Qiagen). For rRNA-depleted (ribo-) nanopore RNA-seq, HeLa cells were plated onto 6-well plates. The next day, cells were performed SA, HS or control treatment. Total RNAs were subjected to rRNA removal using the Ribo-off rRNA Depletion Kit.
For polyadenylated nanopore RNA-seq, the preparation of long-read cDNA library was followed the strand-switching protocol from Oxford Nanopore Technologies. Briefly, the cDNA-PCR Sequencing kit by Oxford Nanopore (SQK-PCS109) was used to prepare full-length cDNA libraries from the polyadenylated RNAs. Then the cDNA was amplified by PCR for 13–14 cycles with specific barcoded adapters from the Oxford Nanopore PCR Barcoding kit (SQKPBK004). Finally, the 1D sequencing adapter was ligated to the cDNA prior to loading onto a R9.4.1 FLO PRO002 flow cell for sequencing on a PromethION platform. Base calling of 1D PromethION reads was done with guppy v5.0.16 with the default options. For rRNA-depleted (ribo-) nanopore RNA-seq, adapters were ligated to the 3' ends of the rRNA-depleted RNAs using a ligase enzyme, then the ligation products were purified with RNA Clean beads (Vazyme). Subsequently, reverse transcription primers were annealed to the 3' end adapters of the RNAs, and TSO (Template Switching Oligo) sequences and reverse transcriptase were added to the annealed products to generate full-length cDNA. Following this, barcoded adapters from the Oxford Nanopore PCR Barcoding kit (SQKPBK004) were used for PCR amplification and labeling of different cDNA products, with 13-14 amplification cycles. The amplified products were processed for library construction according to the Oxford Nanopore Ligation Sequencing kit (SQK-LSK110). Finally, the final library was loaded onto an R9.4.1 FLO PRO002 flow cell and sequenced on a PromethION platform.

value: HeLa

value: SA stressed


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 48h, replicate 1

description:
Library name: Sample 82
C73


title: CD4_SNA_high3


title: E16.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK50
10x Genomics scRNA-Seq

value: Wild Type


title: CD4_SNA_high2


title: nanopore_ribo_minus_SA_rep1


title: HUVEC cells exposed to 5 ng/ml TGF-beta for 24h, replicate 4

description:
Library name: Sample 81
C5


title: nanopore_ribo_minus_HS_rep2

value: HS stressed


title: CD4_SNA_high1


title: E16.5 Wild Type scRNA-Seq Replicate 1

description:
Library name: TK49
10x Genomics scRNA-Seq


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 24h, replicate 3

description:
Library name: Sample 80
C3


title: E15.5 Wild Type scRNA-Seq Replicate 2

description:
Library name: TK68
10x Genomics scRNA-Seq


title: HUVEC cells exposed to 10 ng/ml TGF-beta for 24h, replicate 2

description:
Library name: Sample 79
C31