title: 201813A_MSC_ITGB3

city: Shijiazhuang

first: Haijuan

last: Hu

address: Heping West Road

institute: The Second Hospital of Hebei Medical University

library_source: transcriptomic single cell

data_processing:
bcl2fastq tools for base calling
CellRanger software for single cell identifying
PCA and UMAP/TSNE for dimensionality reduction
Seurat for finding clusters
Assembly: mm10
Supplementary files format and content: Gene expression text files with tab-delimited

source_name: Aortic cell

extract_protocol:
The totla cDNA was extracted  for libraries construction by Chromium  GEM Single Cell 3ʹ Reagent Kits v3 according the standard protocol
Libraries were prepared for sequencing using standard Illumina protocols
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end  constructs which begin with P5 and end with P7. 16  bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the sample index read.

value: Aorta

tag: ages

value: ApoE-/-


title: T1_z1812

status: Public on Jul 11 2026

type: SRA

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
Samples were processed using the nf-core/rnaseq v3.22.2 pipeline with nextflow v25.04.6
Briefly, raw reads were trimmed using Trim Galore! v0.6.10 to remove low-quality bases and adapters. Trimmed reads were aligned to the human reference genome, hg38 with STAR v2.7.11b aligner
Finally, salmon Quant v1.10.3 is utilized for assigning reads.
Assembly: hg38
Supplementary files format and content: Tab delimited file with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Homo sapiens

source_name: pancreatic neuroendocrine tumour

extract_protocol:
RNA extraction was done using the Nucleospin RNA extraction column.
RNA libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (reverse stranded) as per manufacturer's instructions

tag: tissue

value: pancreatic neuroendocrine tumour

tag: genotype


title: 201813A_HFD

country: China

molecule: total RNA

organism: Mus musculus

tag: strain


title: U251 cells, shControl-1

city: Shanghai

first: Tingrong

last: Ren

address: 131 Dong'an Road, Xuhui District, Shanghai, China

institute: fudan university

description: Library name: sh-scramble

data_processing:
The integrity of RNA was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent, USA).
Paired-end clean reads were aligned to the hg38 reference genome using HISAT2 (v2.0.5).
Differential expression analysis of the two conditions was performed using the edgeR R package (3.22.5).
rMATS (4.1.0) software was used to analyze the alternative splicing events.
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts and fpkm for each sample
Supplementary files format and content: Excel file includes differentially expressed gene
Supplementary files format and content: Excel file includes raw SE events
Supplementary files format and content: Excel file includes raw RI events
Supplementary files format and content: Excel file includes raw A3SS events
Supplementary files format and content: Excel file includes raw A5SS events
Supplementary files format and content: Excel file includes raw MXE events

source_name: U251 cells

growth_protocol: U251 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and 100 U/mL of penicillin and 100 μg/mL of streptomycin, and the cells were cultured in a humidified incubator at 37°C in the presence of 5% CO2

extract_protocol:
TRIzol reagent (Invitrogen) was used for total RNA extraction according to the manufacturer’s instructions
RNA-seq library was loaded on an Illumina NovaSeq 6000 instrument for sequencing using a 2×150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: U251 cells were infected with lentivirus encoding control shRNA (shCtrl) or shRNA targeting NCDN (shNCDN). 72h after infection, cells were harvested for RNA extraction

tag: cell line

value: U251 cells

tag: cell type

value: glioblastoma cell line

value: WT


title: B18F-P1

status: Public on Jul 10 2026

city: Beijing

first: Yongge

last: Li

state: Haidian

address: FIT 1-108, Tsinghua University, Haidian District

institute: Tsinghua University

description: Positive control

library_source: genomic

data_processing:
The adaptor were removed by trim_galore version 0.6.4, with parameter as -q 20 --stringency 3 --length 20 --nextera -e 0.1
The reads were mapped to reference mouse genome assembly mm10 using Bowtie 2.3.5 with parameters as  -p 10 -5 15.
Successfully mapped reads were then filtered to remove duplicates with the MarkDuplicates function of the Picard tool.
The allelic-specific reads were separated using SNPs of paternal (CAST) and maternal (J129) downloaded from dbSNP (v132) database.
Run Sequential-GAM code to generate capturing summary txt.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include z axis values of each window for each chromosome for paternal. Each line of this file is the z-axis coordinate of the slice in each cell where a locus was captured (with one end of the cell as the axis origin).
Supplementary files format and content: Tab-delimited text files include z axis values of each window for each chromosome for maternal. Each line of this file is the z-axis coordinate of the slice in each cell where a locus was captured (with one end of the cell as the axis origin).
Library strategy: Sequential-GAM

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: mESC cells were cultured at medium with LIF supplement on feeder MEF cells. Before using cells, cultured cells on MEF-free plate twice to remove MEF cells.

extract_protocol:
The DNA in each nuclear profile (NP) is amplified though whole genome amplification.
The amplified DNA were constructed as libraries according to Vazyme's instructions accompanying the DNA Sample Kit. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

treatment_protocol: no

value: CAST x 129

value: embryonic stem cell


title: B18F-P2

description: Positive control


title: B16F-P2

description: Positive control


title: B16F-P1

description: Positive control


title: B16F-N2

description: Negative control


title: Viral IgG PhIP-Seq for participant 29, timepoint Pre, replicate 2

city: Boston

first: Stephen

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description: Library name: Sample_1_206

library_source: other

data_processing:
Seuqencing reads were aligned to library reference files by bowtie.
Read counts were obtained using samtools.
Read counts from multiple samples were merged to generate the read count files.
Assembly: custom peptidome library
Supplementary files format and content: IDs ranging from 1 to 128287 (but 115,753 unique reference sequences reported) vir3_metadata_geo.csv, read counts

molecule: other

source_name: blood

extract_protocol:
Phage display libraries were mixed with human sera to allow antibodies from sera to bind to displayed peptides. These complexes were then immunoprecipitated using Dynabeads coated either with protein A/G (for IgG) or strepavidin conjugated to biotinylated anti-IgA antibody (for IgA). Phage were then lysed and the contained DNA coding for the displayed peptides were amplified and barcoded by PCR, pooled, gel extracted, and prepared for Illumina sequencing.
Peptide libraries tiling across the proteins from viruses that infect humans (VirScan) and the human proteome were packaged in T7 bacteriophage and expanded as described in Xu et al (DOI:10.1126/science.aaa0698) and Larman et al (DOI: 10.1038/nbt.1856).

value: blood

tag: phip isotype

value: IgG

tag: participant id

tag: time point

value: Pre

tag: replicate

tag: run id

value: IgG Vir YL2

tag: outcome

value: birth

tag: series


title: Viral IgG PhIP-Seq for participant 28, timepoint w20, replicate 2

description: Library name: Sample_1_203


title: Viral IgG PhIP-Seq for participant 27, timepoint w4, replicate 2

description: Library name: Sample_1_193


title: Viral IgG PhIP-Seq for participant 28, timepoint Pre, replicate 2

description: Library name: Sample_1_198


title: Viral IgG PhIP-Seq for participant 27, timepoint Post, replicate 2

description: Library name: Sample_1_196

value: Post


title: B18F-NP65

description:
Cell39
gam_seq_mapped_414_Cell39_zlocation_0.csv
gam_seq_mapped_414_Cell39_zlocation_1.csv


title: B18F-NP106


title: B18F-NP103


title: B18F-NP102


title: B18F-NP101


title: B18F-NP98


title: B18F-NP97


title: B18F-NP99


title: B18F-NP75


title: B18F-NP100


title: B18F-NP2

description:
Cell38
gam_seq_mapped_414_Cell38_zlocation_0.csv
gam_seq_mapped_414_Cell38_zlocation_1.csv


title: B18F-NP96


title: B18F-NP4


title: B18F-NP14


title: B18F-NP16


title: B18F-NP12


title: B18F-NP10


title: B18F-NP24


title: B18F-NP26


title: B18F-NP61

description:
Cell28
gam_seq_mapped_414_Cell28_zlocation_0.csv
gam_seq_mapped_414_Cell28_zlocation_1.csv


title: B18F-NP22


title: B18F-NP18


title: B18F-NP54


title: B18F-NP110


title: B18F-NP56


title: B18F-NP58


title: B18F-NP104


title: B18F-NP112


title: B18F-NP127

description:
Cell27
gam_seq_mapped_414_Cell27_zlocation_0.csv
gam_seq_mapped_414_Cell27_zlocation_1.csv


title: B18F-NP116


title: B18F-NP126


title: B18F-NP125


title: B18F-NP124


title: B18F-NP105


title: B18F-NP51


title: B18F-NP107


title: B18F-NP108


title: B18F-NP52

description:
Cell26
gam_seq_mapped_414_Cell26_zlocation_0.csv
gam_seq_mapped_414_Cell26_zlocation_1.csv


title: B18F-NP57


title: B18F-NP55


title: B18F-NP113


title: Viral IgG PhIP-Seq for participant 27, timepoint Pre, replicate 2

description: Library name: Sample_1_191


title: B18F-NP109


title: B18F-NP63

description:
Cell25
gam_seq_mapped_414_Cell25_zlocation_0.csv
gam_seq_mapped_414_Cell25_zlocation_1.csv


title: B18F-NP64


title: B18F-NP115


title: B18F-NP66


title: B18F-NP111


title: B18F-NP68


title: B18F-NP69


title: A673_gMEN1_5_2_tumor_rep3

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

description:
Library name: KO_5F
Raw counts for samples in batch 1,2 and 4

data_processing:
The quality of the sequencing data was analyzed with FastQC.
Adaptor fragments, low quality ends and short sequences were removed with Trim Galore.
Trimmed sequences were aligned to the reference genome, GRCh38, and gene counts generated with STAR (Batches 1-2, 4) or Salmon (Batch 3).
Additional quality control was performed with MultiQC.
Differentially expressed genes were identified with DESeq2
Assembly: GRCh38
Supplementary files format and content: Tab delimited raw count files using STAR for read counts for batches 1,2 and 4
Supplementary files format and content: Tab delimited raw count files using Salmon for read counts for batch 3

source_name: tumor

growth_protocol:
All cell lines were grown in RPMI1640 + 10% FBS + 2 mM L-glutamine.
1e6 A673 MEN1-KO (A673 gMEN1 1-3, A673 gMEN1 5-1, gMEN1 5-2) or A673 control (A673 gControl 1) cells were injected subcutaneously in NSG mice and tumors were collected 28 days later and flash frozen.

extract_protocol:
Total RNA was collected using a Qiagen RNeasy kit
The polyA enrichment library was prepared using NEBNext Ultra II RNA Library Prep kit and sequencing with the Illumina Novaseq6000 or NovaSeq X Plus sequencer utilizing a paired-end 150 bp (PE150) sequencing strategy

treatment_protocol:
A673 and TC32 cells were treated with 10 µM VTP50469 or 0.1% DMSO (control) for 72 hours.
5e4 A673 and TC32 cells were injected into the tail vein of NSG mice and treated for 5 or 6 weeks respectively with 0.1% VTP50469 mouse chow compared to control mouse chow and liver tumors were flash frozen.

value: tumor

value: Ewing sarcoma cell line

tag: batch


title: B18F-NP70


title: A673_gMEN1_5_2_tumor_rep2

description:
Library name: KO_5E
Raw counts for samples in batch 1,2 and 4


title: B18F-NP72


title: B18F-NP76


title: A673_gMEN1_5_1_tumor_rep3

description:
Library name: KO_5C
Raw counts for samples in batch 1,2 and 4


title: A673_gMEN1_5_2_tumor_rep1

description:
Library name: KO_5D
Raw counts for samples in batch 1,2 and 4


title: B18F-NP77


title: A673_gMEN1_5_1_tumor_rep2

description:
Library name: KO_5B
Raw counts for samples in batch 1,2 and 4


title: B18F-NP78


title: A673_gMEN1_5_1_tumor_rep1

description:
Library name: KO_5A
Raw counts for samples in batch 1,2 and 4


title: B18F-NP79


title: A673_gMEN1_1_3_tumor_rep3

description:
Library name: KO_1C
Raw counts for samples in batch 1,2 and 4


title: B18F-NP80


title: A673_gMEN1_1_3_tumor_rep2

description:
Library name: KO_1B
Raw counts for samples in batch 1,2 and 4


title: A673_gMEN1_1_3_tumor_rep1

description:
Library name: KO_1A
Raw counts for samples in batch 1,2 and 4


title: B18F-NP81


title: B18F-NP82


title: A673_gControl1_tumor_rep3

description:
Library name: WT_C
Raw counts for samples in batch 1,2 and 4

value: A673 gControl 1


title: B18F-NP119


title: A673_gControl1_tumor_rep2

description:
Library name: WT_B
Raw counts for samples in batch 1,2 and 4


title: B16F-NP661

description:
Cell20
gam_seq_mapped_219_Cell20_zlocation_0.csv
gam_seq_mapped_219_Cell20_zlocation_1.csv


title: B16F-NP662


title: A673_gControl1_tumor_rep1

description:
Library name: WT_A
Raw counts for samples in batch 1,2 and 4


title: B16F-NP663


title: TC32_gControl3_cells_rep3

description:
Library name: KB35
Raw counts for samples in batch 1,2 and 4

source_name: cell line

value: cell line

value: TC32 gControl 3


title: TC32_gMEN1_5_5_cells_rep3

description:
Library name: KB36
Raw counts for samples in batch 1,2 and 4

value: TC32 gMEN1 5-5


title: B16F-NP664


title: B16F-NP665


title: TC32_VTP50469_cells_rep3

description:
Library name: KB32
Raw counts for samples in batch 1,2 and 4

tag: treatment


title: B16F-NP667


title: B16F-NP668


title: TC32_gMEN1_5_5_cells_rep2

description:
Library name: KB30
Raw counts for samples in batch 1,2 and 4


title: B16F-NP669


title: B16F-NP670


title: TC32_gControl3_cells_rep2

description:
Library name: KB29
Raw counts for samples in batch 1,2 and 4


title: A673_gMEN1_5_1_cells_rep2

description:
Library name: KB28
Raw counts for samples in batch 1,2 and 4


title: A673_gControl1_cells_rep2

description:
Library name: KB27
Raw counts for samples in batch 1,2 and 4


title: B16F-NP672


title: TC32_VTP50469_cells_rep2

description:
Library name: KB26
Raw counts for samples in batch 1,2 and 4


title: B16F-NP643

description:
Cell19
gam_seq_mapped_219_Cell19_zlocation_0.csv
gam_seq_mapped_219_Cell19_zlocation_1.csv


title: TC32_control_cells_rep2

description:
Library name: KB25
Raw counts for samples in batch 1,2 and 4

value: vehicle


title: B16F-NP644


title: TC32_gMEN1_5_5_cells_rep1

description:
Library name: KB24
Raw counts for samples in batch 1,2 and 4


title: B16F-NP645


title: B16F-NP646


title: TC32_gControl3_cells_rep1

description:
Library name: KB23
Raw counts for samples in batch 1,2 and 4


title: B16F-NP648


title: A673_gControl1_cells_rep1

description:
Library name: KB21
Raw counts for samples in batch 1,2 and 4


title: B16F-NP650


title: TC32_VTP50469_cells_rep1

description:
Library name: KB20
Raw counts for samples in batch 1,2 and 4


title: TC32_control_cells_rep1

description:
Library name: KB19
Raw counts for samples in batch 1,2 and 4


title: B16F-NP651


title: B16F-NP652


title: A673_VTP50469_cells_rep3

description:
Library name: KB15
Raw counts for samples in batch 1,2 and 4


title: B16F-NP654


title: B16F-NP655


title: A673_control_cells_rep2

description:
Library name: KB7
Raw counts for samples in batch 1,2 and 4


title: B16F-NP656


title: A673_control_cells_rep3

description:
Library name: KB13
Raw counts for samples in batch 1,2 and 4


title: B16F-NP636

description:
Cell18
gam_seq_mapped_219_Cell18_zlocation_0.csv
gam_seq_mapped_219_Cell18_zlocation_1.csv


title: DLD1 CRISPRi pilot, SAM24471612_1, GEX

city: South San Francisco

first: Jake

last: Yeung

email: yeungj3@gene.com, jakeyeung@gmail.com

state: CA

address: 1 DNA Way

department: Genentech Research & Early Development

institute: Genentech Inc.

description:
Library name: LIB6251428_SAM24471612
10x Chromium Single Cell 3' v4 GEX library. Six MOI conditions (0.1, 0.2, 0.5, 1.0, 3.0, 5.0) multiplexed per channel via MULTI-seq CMO hashing.

data_processing:
Raw sequencing reads were demultiplexed and aligned to the GRCh38-2020-A reference genome using Cell Ranger v9.0.1 (10x Genomics) with intron counting enabled.
Hashtag demultiplexing was performed using MULTI-seq CMO counts to assign cells to MOI conditions.
Guide RNA assignments were determined from the sgRNA capture library counts.
Quality control filtering included nuclear fraction estimation (DropletQC) and removal of low-quality cells.
Differential expression analysis was performed using limma-voom on pseudobulk counts aggregated per perturbation target, with perturbation-matched control cells (perturbmatch). MENG guides were excluded. Outputs are genes x perturbations matrices of log-fold-change (lfc), standard error (se), z-score (lfc/se), and pairwise cosine similarity between perturbation z-score profiles.
Assembly: GRCh38-2020-A (10x Genomics pre-built reference)
Supplementary files format and content: HDF5 files containing filtered and raw feature-barcode count matrices (Cell Ranger output). Each .h5 file contains barcodes, gene features, and UMI count data.
Supplementary files format and content: Processed SCE objects: assays.h5 files contain HDF5-serialized count matrices from SingleCellExperiment objects (genes x cells) after QC, hashtag demultiplexing, and guide assignment. se.rds files contain the full R SummarizedExperiment with cell-level metadata (colData) and gene annotations (rowData). Pilot objects are split by MOI condition (MOI_0.1 through MOI_5.0). SubLib2 objects are split by MOI level (Low, Med, High).
Supplementary files format and content: DE result matrices: gzipped CSV files (csv.gz) containing differential expression results from limma-voom weighted GLM with perturbation-matched controls. Four matrix types per condition: lfc_matrix (log-fold-change, genes x perturbations), se_matrix (standard error), zscore_matrix (lfc/se), and cosine_sim (pairwise cosine similarity between perturbation z-score profiles, perturbations x perturbations).
Supplementary files format and content: Hashing UMI-corrected count matrices: HDF5 files (.hashing.umi_correct.h5) containing MULTI-seq CMO hashtag barcode counts per cell, used for sample demultiplexing. sgRNA capture UMI-corrected count matrices: HDF5 files (.crispr.umi_correct.h5) containing guide RNA barcode counts per cell, used for perturbation assignment.

growth_protocol: DLD-1 cells stably expressing TET-DD-inducible Zim3-dCas9 were maintained in standard culture conditions.

extract_protocol:
After 5 days of doxycycline and Shield-1 induction, cells from each MOI condition were harvested, labeled with MULTI-seq CMO hashtag barcodes, pooled, and sorted by FACS. Sorted cells were resuspended and loaded onto 10x Genomics Chromium GEM-X chips targeting ~50,000 cells per channel.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3' GEM-X v4 kit according to the manufacturer's instructions. Three libraries were constructed per 10x channel: gene expression (GEX), sgRNA capture, and MULTI-seq CMO (cell multiplexing oligo) hashing. For the scaled experiment (sub-library 2), 44 10x channels were used (Low MOI: 24, Medium MOI: 12, High MOI: 8). For the pilot experiment, 4 10x channels were used.

treatment_protocol: Cells were transduced with lentiviral CRISPRi guide RNA libraries at specified MOI levels. For the pilot experiment, a 94-guide library was used at MOI 0.1, 0.2, 0.5, 1.0, 3.0, and 5.0. For the scaled experiment, a 6,455-guide CRISPRi sub-library 2 was used at MOI ~0.3 (Low), ~3 (Medium), and ~10 (High), with 5% non-targeting control (NTC) guides spiked in. Cells were treated with 250 ng/mL doxycycline and Shield-1 ligand (1:500) to induce Zim3-dCas9 expression for 5 days. Cells from each MOI pool were labeled with MULTI-seq cell multiplexing oligo (CMO) barcodes, pooled, and sorted by FACS.

value: colorectal adenocarcinoma

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 94-guide pilot library; MOI 0.1-5.0 multiplexed via MULTI-seq CMO hashing


title: B16F-NP638

value: CAST x 129


title: B16F-NP634

value: embryonic stem cell


title: B16F-NP653


title: DLD1 CRISPRi pilot, SAM24471609_1, GEX

description:
Library name: LIB6251425_SAM24471609
10x Chromium Single Cell 3' v4 GEX library. Six MOI conditions (0.1, 0.2, 0.5, 1.0, 3.0, 5.0) multiplexed per channel via MULTI-seq CMO hashing.


title: B16F-NP628


title: NUBF05

first: Junlin

last: Zhou

state: Chaoyang

address: 8 Gongti South Road

institute: Beijing Chaoyang hospital

description:
Library name: sample 8
10x Genomics

data_processing:
Raw sequencing data were processed with fastp to remove primer sequences and low-quality bases.
Assembly: GRCh38
Supplementary files format and content: Per-sample Matrix Market count matrices: matrix.mtx.gz files contain raw gene-by-cell UMI count matrices; features.tsv.gz files contain gene/feature annotations; barcodes.tsv.gz files contain cell barcodes generated by Seeksoul tools.

source_name: fractured bone

extract_protocol:
Fresh tissues were washed in ice-cold PBS and dissociated using the SeekMate Tissue Dissociation Reagent Kit A Pro according to the manufacturer's instructions. DNase I was added when required according to homogenate viscosity. Erythrocytes were removed using red blood cell lysis reagent. Cell number and viability were assessed using a SeekMate Tinitan Fluorescence Cell Counter with AO/PI reagent. Debris and dead-cell removal was performed when required using Miltenyi kits. Cells were washed twice with RPMI-1640 medium and resuspended at 1 x 10^6 cells/mL in RPMI-1640 supplemented with 2% FBS.
Single-cell RNA-seq libraries were prepared using the SeekOne Digital Droplet Single Cell 3-prime library preparation kit. Cells were mixed with reverse-transcription reagents and loaded into a SeekOne chip S3 with barcoded hydrogel beads and partitioning oil to generate emulsion droplets. Reverse transcription was performed at 42 degrees C for 90 min and inactivated at 85 degrees C for 5 min. cDNA was recovered from broken droplets, amplified by PCR, fragmented, end-repaired, A-tailed, adaptor-ligated, indexed by PCR, purified using VAHTS DNA Clean Beads, quantified using Qubit, assessed using a Bio-Fragment Analyzer, and sequenced as paired-end 150-bp reads on a SURFSeq 5000 platform.

value: fractured bone

value: non-union


title: B16F-NP626


title: A673_VTP5046_cells_rep2

description:
Library name: KB9
Raw counts for samples in batch 1,2 and 4


title: NUBF04

description:
Library name: sample 7
10x Genomics


title: NUBF03

description:
Library name: sample 6
10x Genomics


title: B16F-NP624


title: B16F-NP612


title: NUBF02

description:
Library name: sample 5
10x Genomics


title: B16F-NP610


title: NUBF01

description:
Library name: sample 4
10x Genomics


title: B16F-NP607


title: A673_gMEN1_5_1_cells_rep3

description:
Library name: KB34
Raw counts for samples in batch 1,2 and 4


title: B16F-NP666

description:
Cell20
gam_seq_mapped_219_Cell20_zlocation_0.csv
gam_seq_mapped_219_Cell20_zlocation_1.csv


title: TC32_control_cells_rep3

description:
Library name: KB31
Raw counts for samples in batch 1,2 and 4


title: A673_gControl1_cells_rep3

description:
Library name: KB33
Raw counts for samples in batch 1,2 and 4


title: G0607

description:
Library name: sample 3
10x Genomics

value: control


title: B16F-NP605


title: G0601

description:
Library name: sample 2
10x Genomics


title: G0531

description:
Library name: sample 1
10x Genomics


title: B16F-NP603


title: B16F-NP671


title: Patient #4, refractory

first: Qingyu

last: Luo

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: P4_Fefractory

data_processing:
IDSEQ DNBseq platform
Assembly: hg38
Supplementary files format and content: txt file includes tpm for each sample

source_name: Bone marrow

extract_protocol:
Rneasy Plus Mini Kit
Low input poly ASMART V4 RNA

value: Bone marrow

tag: sample group

value: refractory


title: B16F-NP617


title: B16F-NP601


title: B16F-NP619


title: Patient #4, pretreatment

description: Library name: P4_Pretreatment

value: pretreatment


title: Patient #3, refractory

description: Library name: P3_Fefractory


title: A673_MEN1_KO_5_1_cells_rep1

description:
Library name: KB22
Raw counts for samples in batch 1,2 and 4


title: B16F-NP642

description:
Cell17
gam_seq_mapped_219_Cell17_zlocation_0.csv
gam_seq_mapped_219_Cell17_zlocation_1.csv


title: B16F-NP641


title: Patient #2, residual

description: Library name: P2_Residual

value: residual


title: Patient #3, pretreatment

description: Library name: P3_Pretreatment


title: B16F-NP640


title: B16F-NP639


title: Patient #2, pretreatment

description: Library name: P2_Pretreatment


title: Patient #1, residual

description: Library name: P1_Residual


title: B16F-NP637


title: Patient #1, pretreatment

description: Library name: P1_Pretreatment


title: B16F-NP635


title: UPN011, post-ACT lesion (biopsy 1), CD3+ T cells (scRNA-seq + scTCR-seq)

city: Basel

first: Michael

middle: Thomas

last: Sandholzer

address: Hebelstrasse 20

department: Department for Biomedicine

country: Switzerland

institute: University Hospital Basel

description: Library name: UPN011_postACT1

data_processing:
FASTQ generation and demultiplexing (Genomics Facility Basel).
GEX and V(D)J reads aligned/quantified with CellRanger v7.1 (GEX: GRCh38-2020-A; V(D)J: GRCh38 ensembl-7.1.0).
Count matrices processed in R v4.3.0 / Seurat v5.1.0; cells filtered (nFeature>650, nCount>1250, %mito<15, %ribo>5, %hemoglobin<10); TCR-based doublets removed; counts normalized and regressed for cell cycle, %mito and IFN-response genes.
Per-cell TCR contigs integrated using scRepertoire v1.7.2.
Raw UMI counts, cell metadata and per-cell TCR annotation combined into a Seurat v5 object (.rds).
Assembly: GEX: GRCh38 (10x refdata-gex-GRCh38-2020-A); TCR V(D)J: GRCh38 ensembl-7.1.0 (CellRanger v7.1).
Supplementary files format and content: Seurat v5 object (.rds) containing the raw (unnormalized) RNA UMI count matrix, cell-level metadata (patient, timepoint, sex, clinical response, QC metrics, cell-type/cluster annotation) and per-cell TCR alpha/beta clonotype annotation (CDR3, V/D/J genes).

source_name: Melanoma metastasis, post-treatment lesion

extract_protocol:
Resected tumor lesions were mechanically dissociated and enzymatically digested (accutase, collagenase IV, hyaluronidase, DNase I), filtered and cryopreserved. Cells were thawed, Fc-blocked, surface-stained and FACS-sorted for viable CD3+ T cells prior to 10x encapsulation.
Single-cell 5-prime gene expression and TCR V(D)J libraries were prepared with the 10x Genomics Chromium Single Cell V(D)J Reagent Kits v2, loading ~10,000 cells per sample per manufacturer instructions. Libraries sequenced on Illumina NovaSeq 6000 (Genomics Facility Basel).

treatment_protocol: Patients received autologous TIL adoptive cell therapy combined with PD-1 blockade within the phase I BaseTIL trial (NCT04165967).

value: CD3+ T cells (FACS-sorted)

tag: Sex

value: male

tag: clinical response

value: PD

value: post-ACT, post-treatment tumor biopsy 1


title: B16F-NP633


title: UPN011, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN011_PBMC7dpt

source_name: Peripheral blood

tag: tissue

value: Peripheral blood

value: PBMC, 7 days post TIL transfer


title: UPN011, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN011_TILproduct

source_name: Ex vivo expanded tumor-infiltrating lymphocytes

value: final TIL product, after rapid expansion protocol (REP)


title: B16F-NP631


title: B16F-NP629


title: UPN011, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN011_preREP

value: Ex vivo expanded tumor-infiltrating lymphocytes

value: intermediate product, after preREP expansion


title: A673_VTP50469_cells_rep1

description:
Library name: KB3
Raw counts for samples in batch 1,2 and 4

value: cell line

value: Ewing sarcoma cell line

tag: genotype


title: A673_control_cells_rep1

description:
Library name: KB1
Raw counts for samples in batch 1,2 and 4

value: vehicle


title: UPN011, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN011_preACT

source_name: Melanoma metastasis, baseline tumor lesion

value: pre-ACT (before TIL therapy)


title: B16F-NP627

tag: strain

value: CAST x 129

value: embryonic stem cell


title: UPN009, post-ACT lesion (biopsy 2), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_postACT2

value: Melanoma metastasis, post-treatment lesion

value: female

value: SD

value: post-ACT, post-treatment tumor biopsy 2


title: DLD1 CRISPRi pilot, SAM24471611_1, GEX

description:
Library name: LIB6251427_SAM24471611
10x Chromium Single Cell 3' v4 GEX library. Six MOI conditions (0.1, 0.2, 0.5, 1.0, 3.0, 5.0) multiplexed per channel via MULTI-seq CMO hashing.

tag: cell line

value: colorectal adenocarcinoma

value: 250ng/mL doxycycline + Shield-1 (1:500) for 5 days; CRISPRi; 94-guide pilot library; MOI 0.1-5.0 multiplexed via MULTI-seq CMO hashing


title: B16F-NP625

tag: cell type


title: B16F-NP623


title: UPN009, post-ACT lesion (biopsy 1), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_postACT1

value: CD3+ T cells (FACS-sorted)

value: post-ACT, post-treatment tumor biopsy 1


title: B16F-NP632


title: B16F-NP630


title: B16F-NP611


title: DLD1 CRISPRi pilot, SAM24471610_1, GEX

description:
Library name: LIB6251426_SAM24471610
10x Chromium Single Cell 3' v4 GEX library. Six MOI conditions (0.1, 0.2, 0.5, 1.0, 3.0, 5.0) multiplexed per channel via MULTI-seq CMO hashing.


title: UPN009, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_PBMC7dpt

value: Peripheral blood

value: PBMC, 7 days post TIL transfer


title: B16F-NP609


title: UPN009, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_TILproduct

value: Ex vivo expanded tumor-infiltrating lymphocytes

value: final TIL product, after rapid expansion protocol (REP)


title: B16F-NP608


title: UPN009, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_preACT

value: Melanoma metastasis, baseline tumor lesion


title: B16F-NP606


title: UPN009, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN009_preREP

value: intermediate product, after preREP expansion


title: B16F-NP604


title: UPN008, post-ACT lesion (biopsy 2), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_postACT2


title: B16F-NP602


title: UPN008, post-ACT lesion (biopsy 1), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_postACT1


title: B16F-NP600


title: UPN008, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_PBMC7dpt


title: UPN008, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_TILproduct


title: UPN008, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_preACT

value: pre-ACT (before TIL therapy)


title: B16F-NP614

value: CAST x 129


title: UPN008, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN008_preREP


title: B16F-NP616

value: embryonic stem cell


title: UPN006, post-ACT lesion (biopsy 2), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_postACT2

value: Melanoma metastasis, post-treatment lesion

value: male


title: RNA-seq of Mus musculus : old cultured HSCs, rep2

city: Sendai

first: Keiyo

last: Takubo

address: 2-1 Seiryo-machi Aoba-ku

department: Graduate School of Medicine

country: Japan

institute: Tohoku University

description:
Library name: Old_Cultured_HSC_RNAseq_rep2
Old HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to RNA-seq, rep2

data_processing:
STAR (version 2.7.10) was used for mapping to the reference genome (UCSC/mm10). Gene expression levels were quantified using featureCounts. Downstream analyses were performed using R (v4.3.0) programs. Count data were normalized and analyzed using DESeq2 (v1.30.1)
Assembly: mm10
Supplementary files format and content: count.txt provides a tab-deliminated raw count data generated by featureCounts.
Supplementary files format and content: Counts.normalized.txt provieds a tab-deliminated normalized count data noramalized by DESeq2 package, and low expression genes were removed.

extract_protocol:
A total of 3000 cells from either fresh or 26-hour cultured young/old HSCs were lysed with 700 µL of RLT buffer from the RNeasy kit plus 1 v/v% of 2-ME and stored in -80°C until use. Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen).
DNA was synthesized using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, Palo Alto, CA, USA). ds-cDNA was fragmented using a S220 Focused-ultrasonicator (Covaris) and cDNA libraries were generated using a NEBNext Ultra DNA Library Prep Kit (New England BioLabs, Beverly, MA, USA)

treatment_protocol: Each replicate (n = 2 biological replicates per group) consisted of a pool of 12 young mice (14 weeks old) and 2 old mice (25 and 28 months old). In each group, 3,000 CD150+CD48-LSK cells were sorted and either immediately subjected to RNA-seq for the fresh group or cultured for 26 hours under SF-O3 conditions supplemented with 4% BSA, 1 ng/mL SCF, 100 ng/mL TPO, and 1% O₂, followed by RNA-seq for the culture group.

value: Bone marrow

value: Hematopoietic stem cells (CD150+CD48-LSK cells)

value: Wild type

value: Cultured for 26 hr


title: RNA-seq of Mus musculus : old cultured HSCs, rep1

description:
Library name: Old_Cultured_HSC_RNAseq_rep1
Old HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to RNA-seq, rep1


title: UPN006, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_TILproduct

value: CD3+ T cells (FACS-sorted)

value: SD


title: RNA-seq of Mus musculus : old fresh HSCs, rep2

description:
Library name: Old_Fresh_HSC_RNAseq_rep2
Old HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to RNA-seq, rep2

value: Freshly isolated


title: RNA-seq of Mus musculus : old fresh HSCs, rep1

description:
Library name: Old_Fresh_HSC_RNAseq_rep1
Old HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to RNA-seq, rep1


title: UPN006, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_preREP


title: RNA-seq of Mus musculus : young cultured HSCs, rep2

description:
Library name: Young_Cultured_HSC_RNAseq_rep2
Young HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to RNA-seq, rep2


title: UPN006, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_preACT


title: RNA-seq of Mus musculus : young cultured HSCs, rep1

description:
Library name: Young_Cultured_HSC_RNAseq_rep1
Young HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to RNA-seq, rep1


title: UPN003, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN003_TILproduct

value: female

value: PR


title: RNA-seq of Mus musculus : young fresh HSCs, rep1

description:
Library name: Young_Fresh_HSC_RNAseq_rep1
Young HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to RNA-seq, rep1


title: UPN003, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN003_preREP

value: Ex vivo expanded tumor-infiltrating lymphocytes


title: ATAC-seq of Mus musculus : old cultured HSCs, rep2

description:
Library name: Old_Cultured_HSC_ATACseq_rep2
Old HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to ATAC-seq, rep2

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit following removal of peaks with low signal.
Supplementary files format and content: Peaks_noBL_th0.bed is a BED file providing a +/- 125bp around summits detected by MACS3 followed by removal of low signal peaks. Problematic regions ("blacklist") were removed.

extract_protocol:
Cell suspension of 30000 fresh or cultured HSCs was centrifuged at 600 x g for 10 min at 4°C. Cells were resuspended in 50 uL of cold PBS and centrifuged at 600 x g for 5 min. After removal of supernatant, 100 uL/sample of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 2mM MgCl2, 0.1% IGEPAL CA-630) was added, left 5 min on ice, and centrifuged at 600 x g for 10 min to extract nuclei.
Immediately following removal supernatant, nuclei pellet was resupended in 50 uL transposase mix (25 uL 2x TD buffer, 2.5 uL of transposase, 22.5 uL of Water), and incubated for 30 min at 37°C. Each sample was purified with GIAGEN miniElute kit and elute with 14 uL water. Then, tagmented genomic DNA was amplified by PCR using NEB Next High Fidelity 2x PCR mix with primers containing adaptor and index sequences. PCR product was purified using QIAGEN miniElute kit and elute with 30 uL water.

treatment_protocol: Each replicate (n = 2 biological replicates per group) consisted of a pool of 12 young mice (14 weeks old) and 2 old mice (25 and 28 months old). In each group, 30,000 CD150+CD48-LSK cells were sorted and either immediately subjected to ATAC-seq for the fresh group or cultured for 26 hours under SF-O3 conditions supplemented with 4% BSA, 1 ng/mL SCF, 100 ng/mL TPO, and 1% O₂, followed by ATAC-seq for the culture group.


title: UPN002, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN002_PBMC7dpt

value: Peripheral blood

value: PD

value: PBMC, 7 days post TIL transfer


title: ATAC-seq of Mus musculus : old fresh HSCs, rep2

description:
Library name: Old_Fresh_HSC_ATACseq_rep2
Old HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to ATAC-seq, rep2


title: UPN002, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN002_TILproduct

value: final TIL product, after rapid expansion protocol (REP)


title: UPN002, intermediate product (preREP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN002_preREP

value: intermediate product, after preREP expansion


title: UPN002, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN002_preACT

value: Melanoma metastasis, baseline tumor lesion

value: pre-ACT (before TIL therapy)


title: ATAC-seq of Mus musculus : young cultured HSCs, rep1

description:
Library name: Young_Cultured_HSC_ATACseq_rep1
Young HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to ATAC-seq, rep1

value: Bone marrow


title: ATAC-seq of Mus musculus : young fresh HSCs, rep2

description:
Library name: Young_Fresh_HSC_ATACseq_rep2
Young HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to ATAC-seq, rep2

value: Hematopoietic stem cells (CD150+CD48-LSK cells)


title: UPN001, post-ACT lesion (biopsy 1), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN001_postACT1

value: Melanoma metastasis, post-treatment lesion

value: male

value: post-ACT, post-treatment tumor biopsy 1


title: ATAC-seq of Mus musculus : young fresh HSCs, rep1

description:
Library name: Young_Fresh_HSC_ATACseq_rep1
Young HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to ATAC-seq, rep1

value: Wild type


title: UPN001, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN001_PBMC7dpt

value: CD3+ T cells (FACS-sorted)


title: UPN001, TIL product (post-REP), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN001_TILproduct


title: IL-1a TNFa C1q EV+MAPS

city: Hangzhou

first: Mengying

last: An

state: Zhejiang

address: 西湖区浙大路38号

institute: Zhejiang University

description:
Library name: SAMPLES3
Single-cell transcriptomic profiling of dissociated cells isolated from the ipsilateral hemisphere at 14 days after ischemic stroke following implantation of IL-1a TNFa C1q EV+MAPS at day 5 post-stroke.

data_processing:
Raw BCL files were converted to FASTQ format using bcl2fastq (v5.0.1).
FASTQ files were processed using Cell Ranger (v7.0.0) for read alignment, barcode assignment, UMI counting, and generation of gene-cell count matrices.
Gene expression matrices were imported into Seurat (v4.1.0) for quality control. Cells expressing fewer than 500 genes or containing more than 25% mitochondrial transcripts were excluded.
Expression data were normalized using LogNormalize. Highly variable genes were selected for dimensionality reduction and clustering. PCA was performed and the top 20 principal components were used for graph-based clustering and UMAP visualization.
Cell-type annotation was performed using marker genes and reference databases including SingleR, scCATCH, and LC-Marker. Functional enrichment, AUCell scoring, and cell-cell communication analyses were subsequently conducted.
Assembly: GRCm39
Supplementary files format and content: Processed data include filtered gene-cell UMI count matrices generated by Cell Ranger and used for downstream analyses.

source_name: ipsilateral brain hemisphere

extract_protocol:
Brain tissues were immediately collected and washed twice with cold RNase-free PBS. Samples were minced and enzymatically dissociated in digestion buffer containing Collagenase IV, Papain, and DNase I for 20 min at 37 °C. Enzymatic digestion was terminated with PBS supplemented with 10% FBS, followed by mechanical trituration. Cell suspensions were filtered through 70 µm and 30 µm strainers. Red blood cells and dead cells were removed using erythrocyte lysis buffer and Dead Cell Removal MicroBeads (MACS), respectively. Live cells were washed and resuspended in PBS containing 0.04% BSA. Only cell suspensions with viability greater than 85% were used for downstream library preparation.
Single-cell suspensions were loaded onto Chromium Single Cell 3′ Chips (10x Genomics, v3) targeting approximately 8,000 cells per sample. Single-cell barcoding, reverse transcription, cDNA amplification, and library construction were performed according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp sequencing.

treatment_protocol: Mice subjected to ischemic stroke received implantation of different hydrogel microsphere formulations into the infarct cavity at 5 days post-stroke. At day 14 after stroke, ipsilateral hemispheres were harvested for single-cell RNA sequencing analysis. Healthy control mice received no treatment.

value: ipsilateral brain hemisphere

value: Stroke+IL-1a TNFa C1q EV+MAPS


title: UT EV+MAPS

description:
Library name: SAMPLES2
Single-cell transcriptomic profiling of dissociated cells isolated from the ipsilateral hemisphere at 14 days after ischemic stroke following implantation of UT_EV+MAPS at day 5 post-stroke.


title: UPN001, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN001_preACT

value: PR


title: UPN000, control PBMC, CD3+ T cells (scRNA-seq + scTCR-seq)

description:
Library name: UPN000_PBMCctrl
sex: NA (control donor)

value: Peripheral blood

value: control PBMC (reference donor)


title: MAPS

description:
Library name: SAMPLES1
Single-cell transcriptomic profiling of dissociated cells isolated from the ipsilateral hemisphere at 14 days after ischemic stroke following implantation of MAPS at day 5 post-stroke.

value: Stroke+MAPS


title: OTM Day 6 PDL

first: Fumitoshi

last: Ohori

address: 4-1 Seiryo-machi, Aoba-ku

department: Graduate School of Dentistry

description:
Library name: OTMday6
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger pipeline (v7.0.1). Reads were aligned to the mouse reference genome (mm10) to generate filtered gene-barcode matrices.
Downstream analysis was performed using the Seurat R package for quality control, normalization, and clustering.
Intercellular communication analysis was conducted using CellChat, and developmental trajectories of neutrophils were analyzed using Monocle3 (pseudotime analysis).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Sparse matrix files (matrix.mtx.gz), barcode files (barcodes.tsv.gz), and feature/gene files (features.tsv.gz).
Supplementary files format and content: The matrix files contain UMI counts, and the tsv files provide corresponding cell barcodes and gene identifiers.

source_name: Periodontal ligament

extract_protocol:
Tissues adhering to extracted tooth roots and extraction sockets were collected and pooled (n=5 per group). Cells were isolated via a two-step enzymatic digestion: (1) 2 mg/mL collagenase for 30 min at 37°C, (2) 0.25% trypsin for 30 min at 37°C. Cell suspensions were filtered through 70 μm and 30 μm strainers and washed with DMEM supplemented with 10% FBS.
Single-cell libraries were prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics). Approximately 5,000 cells per sample were targeted for recovery. GEMs were generated using the Chromium Controller, followed by reverse transcription to produce barcoded full-length cDNA.

treatment_protocol: Orthodontic tooth movement induced by a 10-g mesial force for 6 days.

value: Periodontal ligament

tag: age

value: 8 weeks old


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), RNA-seq, R3

city: Bethesda

first: Astrid

middle: D

last: Haase

state: MD

address: 50 South Dr

department: LCDB

institute: NIDDK

description:
Library name: RNAseq VT+ xrTestes R3
raw_gene_counts.xlsx

data_processing:
RNA-seq reads were mapped to the human T2T-CHM13v2 reference genome using STAR v2.7.10b with up to 100 alignments per read and a maximum mismatch ratio of 0.05. Gene-level counts were obtained using featureCounts (v2.20.0).
For small RNA-seq reads, the 3′ adapter sequence (see 'description column' for 3' adapter sequences of sample) was trimmed, and reads were collapsed by sequence to remove PCR duplicates. Unique molecular identifiers (UMIs, 8 nt at the 5’ end and 2 nt at the 3’ end) were then excised. Adapter, UMIs, and artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC; present only in iPSC R1/R2, PGCLC R1/R2, and VT xrTestes R1) were removed using Cutadapt v4.4. Reads shorter than 20 nt were discarded. Structural RNAs were removed. Remaining reads were mapped to the human genome (T2T-CHM13v2) with splicing disabled, allowing up to 100 alignments per read and a maximum of one mismatch per alignment, using STAR v2.7.10b. FASTQ quality was assessed with FastQC v0.11.9. BAM files were sorted and indexed using Samtools v1.17. Reads overlapping snRNA and tRNA loci (RepeatMasker-derived annotations, extended ±10 bp) were additionally removed.
Assembly: Human T2T-CHM13v2
Supplementary files format and content: Raw gene counts for total RNA-seq, normalized read length distributions file, format: .xlsx

source_name: xenogeneic reconstituted testes-derived VT+ germ cells

extract_protocol:
Total RNA-seq and small RNA-seq libraries were generated for induced Pluripotent Stem Cells (iPSCs), primordial germ cell-like cells (PGCLCs), FACS-sorted VT+ xrTestes (VT+ xrTestes) and xrTestes (total), with three biological replicates per sample. RNA was isolated using the PureLink miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The long RNA fraction (>200 nt) was retained and further purified with TRIzol. Small RNAs were extracted using the same kit in combination with TRIzol, following the manufacturer’s protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library Prep kit with rRNA depletion following the manufacturer's instructions. Small RNAs for small RNA-seq were prepared for sequencing as described in Konstantinidou et al. (2024).


title: Control PDL

description:
Library name: Contorl
10x Genomics


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), RNA-seq, R2

description:
Library name: RNAseq VT+ xrTestes R2
raw_gene_counts.xlsx

value: xenogeneic reconstituted testes-derived VT+ germ cells


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), RNA-seq, R1

description:
Library name: RNAseq VT+ xrTestes R1
raw_gene_counts.xlsx


title: Salivary_Gland_tumor_1

city: Genova

first: Chiara

last: Pedicone

address: Largo Rosanna Benzi, 10

department: Neuroscienze Sperimentali

country: Italy

institute: IRCCS Azienda Ospedaliera Metropolitana Policlinico San Martino

description:
Library name: G8022
Salivary gland tumor from CD4CreSHIP1flox/flox  mouse G8022

data_processing:
Reads were aligned to the GRCm38 reference genome using STAR v2.5 with mismatch =2. Transcript abundance was estimated with HTSeq v0.6.1 with -m union parameter.
Assembly: GRCm38
Supplementary files format and content: Comma separated value file of Fragments Per Kilobase of transcript per Million mapped fragments

source_name: Salivary Gland

extract_protocol:
Qiagen RNAeasy Mini extraction of total RNA
poly-A selection and sequencing 150bp 40 mil reads/sample.

value: Salivary Gland tumor

tag: status

value: tumor

value: Salivary Gland


title: Peyer_Patch_2

description:
Library name: P8004
Healthy Peyer's Patch from CD4CreSHIP1flox/flox  mouse P8004

source_name: Peyer Patch

value: Peyer's Patch

value: control

value: Peyer Patch


title: Peyer_Patch_1

description:
Library name: P8002
Healthy Peyer's patch from CD4CreSHIP1flox/flox  mouse P8002


title: primordial germ cell-like cells (PGCLC), RNA-seq, R1

description:
Library name: RNAseq PGCLC R1
raw_gene_counts.xlsx

source_name: primordial germ cell-like cells

extract_protocol:
Total RNA-seq and small RNA-seq libraries were generated for induced Pluripotent Stem Cells (iPSCs), primordial germ cell-like cells (PGCLCs), xrSpermatogonia (xrSpgn) and xrTestes (total), with three biological replicates per sample. RNA was isolated using the PureLink miRNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. The long RNA fraction (>200 nt) was retained and further purified with TRIzol. Small RNAs were extracted using the same kit in combination with TRIzol, following the manufacturer’s protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II directional RNA library Prep kit with rRNA depletion following the manufacturer's instructions. Small RNAs for small RNA-seq were prepared for sequencing as described in Konstantinidou et al. (2024).

value: primordial germ cell-like cells


title: Peyer_Patch_tumor_2

description:
Library name: P7983
Peyer's patch tumor from CD4CreSHIP1flox/flox  mouse P7983

value: Peyer's Patch tumor


title: primordial germ cell-like cells (PGCLC), RNA-seq, R2

description:
Library name: RNAseq PGCLC R2
raw_gene_counts.xlsx


title: Peyer_Patch_tumor_1

description:
Library name: P8051
Peyer's patch tumor from CD4CreSHIP1flox/flox  mouse P8051


title: RNA-seq of Mus musculus : young fresh HSCs, rep2

description:
Library name: Young_Fresh_HSC_RNAseq_rep2
Young HSCs were freshly isolated and directly lysed in RLT buffer, then subjected to RNA-seq, rep2

value: Bone marrow

value: Hematopoietic stem cells (CD150+CD48-LSK cells)

value: Wild type

value: Freshly isolated


title: induced Pluripotent Stem Cells (iPSC), RNA-seq, R3

description:
Library name: RNA-seq iPSC R3
raw_gene_counts.xlsx

source_name: induced Pluripotent Stem Cells

value: induced Pluripotent Stem Cells


title: Mesenteric_Lymph_Node_tumor_3

description:
Library name: M6102
Mesenteric lymph node tumor from CD4CreSHIP1flox/flox  mouse M6102

source_name: Lymph Node

value: Mesenteric Lymph Node Tumor

value: Lymph Node


title: Viral IgG PhIP-Seq for participant 33, timepoint Post, replicate 1

description: Library name: Sample_1_53

source_name: blood

value: blood

tag: phip isotype

value: IgG

tag: participant id

tag: time point

value: Post

value: IgG Vir YL1

value: birth


title: Mesenteric_Lymph_Node_tumor_2

description:
Library name: M8051
Mesenteric lymph node tumor from CD4CreSHIP1flox/flox  mouse M8051

value: tumor


title: induced Pluripotent Stem Cells (iPSC), RNA-seq, R1

description:
Library name: RNA-seq iPSC R1
raw_gene_counts.xlsx


title: Mesenteric_Lymph_Node_tumor_1

description:
Library name: M8022
Mesenteric lymph node tumor from CD4CreSHIP1flox/flox  mouse M8022


title: xenogeneic reconstituted testes (xrTestes), small RNA-seq, R3

description:
Library name: smallRNAseq xrTestes R3
3' adapter: (NN)ACGACTTGGAATTCTCGGGTGCCAAGG
piRNA_lengths_xr_vs_juvenile.xlsx

source_name: xenogeneic reconstituted testes

value: xenogeneic reconstituted testes


title: xenogeneic reconstituted testes (xrTestes), small RNA-seq, R2

description:
Library name: smallRNAseq xrTestes R2
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG
piRNA_lengths_xr_vs_juvenile.xlsx


title: Spleen_tumor_3

description:
Library name: S6102
Spleen tumor from CD4CreSHIP1flox/flox  mouse S6102

source_name: spleen

value: Spleen Tumor

value: spleen


title: xenogeneic reconstituted testes (xrTestes), small RNA-seq, R1

description:
Library name: smallRNAseq xrTestes R1
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG
piRNA_lengths_xr_vs_juvenile.xlsx


title: Spleen_tumor_2

description:
Library name: S8021
Spleen tumor from CD4CreSHIP1flox/flox  mouse S8021


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), small RNA-seq, R3

description:
Library name: smallRNAseq VT+ xrTestes R3
3' adapter: (NN)ACGACTTGGAATTCTCGGGTGCCAAGG
reads_length_distribution_miR_normalized.xlsx

value: xenogeneic reconstituted testes-derived VT+ germ cells


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), small RNA-seq, R2

description:
Library name: smallRNAseq VT+ xrTestes R2
3' adapter: (NN)ACGACTTGGAATTCTCGGGTGCCAAGG
reads_length_distribution_miR_normalized.xlsx


title: Viral IgG PhIP-Seq for participant 32, timepoint Post, replicate 1

description: Library name: Sample_1_45

tag: replicate

tag: run id

tag: outcome


title: cbfs_input_pC

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

description: Library name: cbfs_input_pC

data_processing:
The Novoseq PE150 was used for high-throughput sequencing of the ChIP-seq libraries. The raw sequence data were processed using the GAPipeline Illumina sequence data analysis pipeline.
Assembly: Bowtie2 was then employed to map the reads to the Arabidopsis genome (TAIR10). The mapped reads were retained for further analysis.
Supplementary files format and content: The alignments were first converted to Wiggle (WIG) files using deepTools. The data were then imported into the Integrated Genome Viewer (IGV) (Thorvaldsdottir et al., 2013) for visualization. The H3Ac peaks were analyzed by MACS2 (Zhang et al., 2008).

organism: Arabidopsis thaliana

source_name: aerial parts

growth_protocol: Arabidopsis (Arabidopsis thaliana) plants were germinated on MS medium and grown at 22℃ under short day (8 h light /16 h dark cycle) condition for 14 days.

extract_protocol:
Chromatin extracts were prepared from seedlings treated with 1% formaldehyde. The chromatin was sheared to the mean length of 500 bp by sonication, and proteins and DNA fragments were immunoprecipitated using antibodies against anti-GFP (Abcam, catalog no. ab290). The DNA cross-linked to immunoprecipitated proteins was reversed
2 ng of DNA from ChIP was used to ensure enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries. End repair, adaptor ligation, and amplification were carried out using the KAPA DNA Library Prep kit (cat no. E7645) according to the manufacturer's protocol.

treatment_protocol: For the prolonged cold treatment, 14-day-old Arabidopsis plants were transferred to 4℃ and grown under short day condition for 6 weeks. The hag1 mutant (SALK_048427, hag1–5) was a previously reported T-DNA insertion mutant (Kornet and Scheres, 2009; Chen et al., 2017). The CRISPER-Cas9 generated cbf1/2/3 triple mutants (cbf1/2/3-97 and cbf1/2/3-93) were also reported previously (Xie et al., 2021). All mutants used in this study were in the Col-0 background.

value: aerial parts

tag: ecotype

value: col


title: Retina-RPE male 1.5 months biol rep 1

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

description:
Library name: BC1
Male retina-RPE collected from a 1.5-month-old fish. Biological replicate 1.

data_processing:
Base calling, demultiplexing, and FASTQ file generation were performed by GENEWIZ/Azenta.
Raw sequencing reads were analyzed using the MKMC software package.
K-mer counting was performed directly from FASTQ files to generate multi-sample k-mer count matrices.
K-mer count matrices were normalized prior to downstream analyses.
Principal component analysis, UMAP dimensionality reduction, and differential abundance analyses were performed using MKMC as described in the accompanying manuscript.
Assembly: Not applicable (alignment-free k-mer analysis)
Supplementary files format and content: Tab-delimited text files containing normalized k-mer abundance matrices generated by MKMC and used for downstream analyses.
Supplementary files format and content: Tab-delimited text files containing normalized k-mer abundance matrices generated by MKMC and gene-level count matrices used for downstream analyses.

organism: Nothobranchius furzeri

source_name: retina-RPE

growth_protocol: Nothobranchius furzeri animals were raised as described in the accompanying manuscript. All animals used in this study were male fish derived from a mutant line that had been backcrossed for multiple generations onto the GRZ strain. Retina-retinal pigment epithelium (retina-RPE) tissue was collected from fish at 1.5, 3.0, 4.5, and 6.0 months of age.

extract_protocol:
Adult male fish were euthanized using an ice-water slurry. Retina-retinal pigment epithelium (retina-RPE) tissue was dissected by removing the cornea, lens, iris, sclera, and choroid while keeping the retinal pigment epithelium attached to the retina. Samples were washed in ice-cold 1× PBS, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted using the QIAGEN RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to the manufacturer's instructions and eluted in a final volume of 13 μL.
RNA sequencing libraries were prepared and sequenced by GENEWIZ/Azenta (South Plainfield, NJ, USA) using the Illumina Nextera XT DNA Library Preparation Kit (FC-131-1024). Libraries were sequenced on one lane of an Illumina NovaSeq S4. Base calling, demultiplexing, and FASTQ file generation were performed by GENEWIZ/Azenta.

treatment_protocol: No experimental treatment was applied. Samples were collected from untreated animals at four different ages.

value: retina-RPE

value: male

value: 1.5 months

value: GRZ backcross mutant line


title: Retina-RPE male 1.5 months biol rep 2

description:
Library name: BC2
Male retina-RPE collected from a 1.5-month-old fish. Biological replicate 2.


title: Viral IgG PhIP-Seq for participant 33, timepoint Pre, replicate 1

description: Library name: Sample_1_47

value: Pre

tag: series


title: FACS-sorted VT+ xrTestes (VT+ xrTestes), small RNA-seq, R1

description:
Library name: smallRNAseq VT+ xrTestes R1
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG; artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC
reads_length_distribution_miR_normalized.xlsx


title: mBMEC CCM3KO rapamycin biological replicate 2

city: Santiago de Compostela

first: Juan

last: Zalvide

state: A Coruña

address: CIMUS, Avda de Barcelona s/n

department: Physiology

country: Spain

institute: Universidad de Santiago de Compostela

description:
Library name: Sample 15
Unstranded RNA-seq

data_processing:
Sequenced reads were cleaned for adaptor sequence by Novogene. Samples were aligned to the Genome Reference Consortium Human (GRCh) Build 39 with Ensembl annotation 104 using STAR (v.0.6.7) . Quality reads with >Q30 were kept previously to the alignment with Trimgalore (v.0.6.7). Gene quantification was computed using htseq (v.0.13.5) and normalization  was performed using DESeq2 (v.1.34.0, performed in an R environment (v.4.2.2))
In addition, a full selective alignment with a decoy-aware transcriptome was performed using Salmon (v. 1.5.2). This decoy-aware transcriptome was generated concatenating the Genome Reference Consortium Mouse (GRCm) Build 39 with GENCODE Annotation Release M27 to the end of the transcript sequences from the same release. The set of parameters used to get the quantification were --gcBias, --validateMappings and --numBootstraps 30.
Assembly: GRCm39
Supplementary files format and content: Salmon quantification files: plain-text, tab-separated files.
Supplementary files format and content: DESeq2 normalized counts: xlsx file.

source_name: Brain

growth_protocol: Brain microvascular endothelial cells (mBMEC) were isolated from adult 8–10-week Cdh5 (PAC)-CreERT2/PDCD10fl/fl mice. cells were seeded onto plates coated with collagen I in DMEM-Hi glucose supplemented 15% v/v fetal bovine serum, 1% v/v de Penicillin/Streptomycin/L-Glutamine, 100 μg/mL heparin and 50 μg/ml endothelial cell growth supplement.

extract_protocol:
Total RNAs were extracted using the Trizol reagent (life Technologies), according to according to the manufacturer’s protocol.
RNA was sent for RNAseq analysis to Novogene, where messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.

treatment_protocol: mBMEC were left untreated or treated for 24 hours with either propranolol 10 µM or rapamycin 100 nM

value: Brain

value: Brain microvascular endothelial cells

tag: treatment

value: 100 nM rapamycin 24 h


title: primordial germ cell-like cells (PGCLC), small RNA-seq, R2

description:
Library name: smallRNAseq PGCLC R2
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG; artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC
reads_length_distribution_miR_normalized.xlsx

value: primordial germ cell-like cells


title: primordial germ cell-like cells (PGCLC), small RNA-seq, R1

description:
Library name: smallRNAseq PGCLC R1
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG; artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC
reads_length_distribution_miR_normalized.xlsx


title: mBMEC CCM3KO propranolol biological replicate 3

description:
Library name: Sample 13
Unstranded RNA-seq

value: 10 µM propranolol 24 h


title: mBMEC CCM3KO propranolol biological replicate 2

description:
Library name: Sample 12
Unstranded RNA-seq


title: mBMEC CCM3KO rapamycin biological replicate 1

description:
Library name: Sample 14
Unstranded RNA-seq


title: induced Pluripotent Stem Cells (iPSC), small RNA-seq, R3

description:
Library name: smallRNAseq iPSC R3
3' adapter: (NN)ACGACTTGGAATTCTCGGGTGCCAAGG
reads_length_distribution_miR_normalized.xlsx

value: induced Pluripotent Stem Cells


title: Spleen_tumor_1

description:
Library name: S8924
Spleen tumor from CD4CreSHIP1flox/flox  mouse S8924

value: tumor


title: mBMEC CCM3KO propranolol biological replicate 1

description:
Library name: Sample 11
Unstranded RNA-seq


title: induced Pluripotent Stem Cells (iPSC), small RNA-seq, R1

description:
Library name: smallRNAseq iPSC R1
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG; artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC
reads_length_distribution_miR_normalized.xlsx


title: induced Pluripotent Stem Cells (iPSC), small RNA-seq, R2

description:
Library name: smallRNAseq iPSC R2
3' adapter: (NN)TGACTGTGGAATTCTCGGGTGCCAAGG; artificial calibrator sequences (CUCAUGGUUGUAAGUCCCGGUAAUCU, UCAUGGUUGUAAGUCCCGGUAAUCUA, AUGGUUGUAAGUCCCGGUAAUCUACG, and GGUUGUAAGUCCCGGUAAUCUACGUC
reads_length_distribution_miR_normalized.xlsx


title: mBMEC CCM3KO untreated biological replicate 2

description:
Library name: Sample 9
Unstranded RNA-seq

value: Untreated


title: mBMEC CCM3KO untreated biological replicate 3

description:
Library name: Sample 10
Unstranded RNA-seq


title: mBMEC CCM3KO untreated biological replicate 1

description:
Library name: Sample 8
Unstranded RNA-seq


title: Liver biopsies, capture area A1

city: Manchester

first: Karen

last: Piper Hanley

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description: Library name: EJ1-2JR6DFV-A1

data_processing:
FASTQ files were processed using 10x Genomics Space Ranger (3.1.3) using standard parameters
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5 : filtered feature-barcode matrices at 2micron binning
Supplementary files format and content: tissue_positions.parquet : spatial coordinates of barcodes
Supplementary files format and content: cytassist_image.tiff : sample cytassist image
Supplementary files format and content: tissue_hires_image.png : high resolution sample image
Supplementary files format and content: full_res_image.tif : full resolution sample image
Supplementary files format and content: tissue_lowres_image.png : low resolution sample image
Library strategy: Spatial Transcriptomics

source_name: Liver biopsy

extract_protocol:
FFPE embedded biopsies were sectioned at 5um thickness and processed according to the 10x Genomics Visium HD Spatial Gene Expression Reagent Kits User Guide (GC000685) using Visium Human Transcriptome Probe Set v2.0
Libraries were constructed according to the 10x Genomics Visium HD Spatial Gene Expression Reagent Kits User Guide (GC000685)

value: Liver biopsy


title: mBMEC CCM3WT rapamycin biological replicate 1

description:
Library name: Sample 6
Unstranded RNA-seq


title: ATAC_BC1042

city: Stanford

first: Laura

last: Amaya

address: 269 Campus Drive

institute: Stanford University

description: Library name: ATAC_BC10242

library_source: genomic single cell

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics) was employed for sample demultiplexing, alignment, filtering, and UMI counting for RNA-seq libraries, using the human GRCh38 genome assembly and RefSeq gene model. For V(D)J libraries, the Cell Ranger Single-Cell Software (10X Genomics) was used for sample demultiplexing, de novo assembly, alignment, annotation against germline segment V(D)J reference sequences and clonotype grouping.
Assembly: GRCh38
Supplementary files format and content: fragments.tsv for scATAC, filtered_feature_matrix.h5 for scRNA and contig_annotations.csv for scTCR.

source_name: Blood

extract_protocol: Live singlet CD3+CD4+ T cells from T-allo10 cell products were purified by FACS, counted, and their cell concentration adjusted in PBS with 0.04% BSA to allow capture up to 10,000 cells per well of the Chromium Next GEM chip, which was then loaded onto a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA). RNA-seq and V(D)J libraries were prepared using the Chromium Single Cell 5′ Library, Gel Beads, & Multiplex Kit according to manufacturer’s instructions.

value: Blood

value: CD4 T cells

tag: disease state

value: Healthy

tag: time

value: TimeNA

value: No treatment


title: mBMEC CCM3WT propranolol biological replicate 2

description:
Library name: Sample 5
Unstranded RNA-seq

tag: tissue

tag: genotype


title: GE_BC1042

description: Library name: GE_BC10242

tag: cell line


title: GE_Day9_d2

description: Library name: GE_Day9_d2

value: Invitro culture day9


title: mBMEC CCM3WT propranolol biological replicate 1

description:
Library name: Sample 4
Unstranded RNA-seq

tag: cell type


title: Spleen_tumor_4

description:
Library name: S8922
Spleen tumor from CD4CreSHIP1flox/flox  mouse S8922

value: Spleen Tumor

value: spleen


title: GE_Day9_d1

description: Library name: GE_Day9_d1


title: mBMEC CCM3WT untreated biological replicate 3

description:
Library name: Sample 3
Unstranded RNA-seq

value: Brain


title: GE_Day6_d2

description: Library name: GE_Day6_d2

value: Invitro culture day6


title: mBMEC CCM3WT untreated biological replicate 2

description:
Library name: Sample 2
Unstranded RNA-seq

value: Brain microvascular endothelial cells


title: GE_Day6_d1

description: Library name: GE_Day6_d1


title: mBMEC CCM3WT untreated biological replicate 1

description:
Library name: Sample 1
Unstranded RNA-seq


title: GE_Day3_d2

description: Library name: GE_Day3_d2

value: Invitro culture day3


title: Old_Pbx1OE_RNAseq_D3_rep3

description:
Library name: Old_Pbx1OE_RNAseq_D3_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep3

data_processing:
STAR (version 2.7.10) was used for mapping to the reference genome (UCSC/mm10). Gene expression levels were quantified using featureCounts.Downstream analyses were performed using R (v4.3.0) programs. Count data were normalized and analyzed using DESeq2 (v1.30.1)
Assembly: mm10
Supplementary files format and content: count.txt provides a tab-deliminated raw count data generated by featureCounts.
Supplementary files format and content: Counts.normalized.txt provieds a tab-deliminated normalized count data noramalized by DESeq2 package, and low expression genes were removed.

source_name: Bone marrow

extract_protocol:
RNA was extracted using RNeasy-micro kit (QIAGEN).
RNA from a total of 5000 cells from either Mock- or Pbx1-transduced GFP+ cells were subjected to cDNA synthesis using a SMART-Seq HT Kit (Clontech, Palo Alto, CA, USA). Library was prepared using Nextera XT DNA Library Prep Kit with Nextera XT index Kit v2 primers.  Sequencing was performed using NovaSeq6000 (Illumina) with a paired-end sequencing length of 150bp.

treatment_protocol: Either CD150+CD48-CD41-CD34- LSK cells from 4 young (2.5mo) mice per sample, or CD150+CD48- CD34- LSK cells from 1 old (18mo) mouse per sample was isolated. Each experimental sample comprised cells from four young mice or one old mouse per sample. All isolated cells underwent retroviral transduction with mock or Pbx1-expressing vectors, after which 5,000 GFP+ cells for RNA-seq and 50,000 GFP+ cells for ATAC-seq were selected.

value: Bone marrow

value: Old HSC

value: Wild type


title: GE_Day3_d1

description: Library name: GE_Day3_d1


title: mBMEC CCM3KO rapamycin biological replicate 3

description:
Library name: Sample 16
Unstranded RNA-seq

value: 100 nM rapamycin 24 h


title: GE_Day0_d2

description: Library name: GE_Day0_d2

value: Invitro culture day0


title: Old_Pbx1OE_RNAseq_D3_rep1

description:
Library name: Old_Pbx1OE_RNAseq_D3_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep1


title: GE_Day0_d1

description: Library name: GE_Day0_d1

value: Blood


title: Old_Mock_RNAseq_D3_rep3

description:
Library name: Old_Mock_RNAseq_D3_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep3

value: Mock-transduced


title: primordial germ cell-like cells (PGCLC), small RNA-seq, R3

description:
Library name: smallRNAseq PGCLC R3
3' adapter: (NN)ACGACTTGGAATTCTCGGGTGCCAAGG
reads_length_distribution_miR_normalized.xlsx

value: primordial germ cell-like cells


title: ATAC_Day9_d2

description: Library name: ATAC_Day9_d2

value: CD4 T cells

value: Healthy


title: ATAC_Day9_d1

description: Library name: ATAC_Day9_d1

value: Invitro culture day9

value: No treatment


title: Old_Mock_RNAseq_D3_rep2

description:
Library name: Old_Mock_RNAseq_D3_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep2


title: Old_Mock_RNAseq_D3_rep1

description:
Library name: Old_Mock_RNAseq_D3_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep1


title: ATAC_Day6_d2

description: Library name: ATAC_Day6_d2


title: B16F-NP613

first: Yongge

last: Li

address: FIT 1-108, Tsinghua University, Haidian District

description:
Cell17
gam_seq_mapped_219_Cell17_zlocation_0.csv
gam_seq_mapped_219_Cell17_zlocation_1.csv

data_processing:
The adaptor were removed by trim_galore version 0.6.4, with parameter as -q 20 --stringency 3 --length 20 --nextera -e 0.1
The reads were mapped to reference mouse genome assembly mm10 using Bowtie 2.3.5 with parameters as  -p 10 -5 15.
Successfully mapped reads were then filtered to remove duplicates with the MarkDuplicates function of the Picard tool.
The allelic-specific reads were separated using SNPs of paternal (CAST) and maternal (J129) downloaded from dbSNP (v132) database.
Run Sequential-GAM code to generate capturing summary txt.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include z axis values of each window for each chromosome for paternal. Each line of this file is the z-axis coordinate of the slice in each cell where a locus was captured (with one end of the cell as the axis origin).
Supplementary files format and content: Tab-delimited text files include z axis values of each window for each chromosome for maternal. Each line of this file is the z-axis coordinate of the slice in each cell where a locus was captured (with one end of the cell as the axis origin).
Library strategy: Sequential-GAM

source_name: embryonic stem cell

extract_protocol:
The DNA in each nuclear profile (NP) is amplified though whole genome amplification.
The amplified DNA were constructed as libraries according to Vazyme's instructions accompanying the DNA Sample Kit. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

tag: strain

value: CAST x 129

value: embryonic stem cell


title: B16F-NP618


title: ATAC_Day6_d1

description: Library name: ATAC_Day6_d1

value: Invitro culture day6


title: Young_Pbx1OE_RNAseq_D3_rep3

description:
Library name: Young_Pbx1OE_RNAseq_D3_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep3

value: Young HSC


title: UPN006, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_PBMC7dpt

source_name: Peripheral blood

value: Peripheral blood

value: CD3+ T cells (FACS-sorted)

tag: Sex

value: male

tag: clinical response

value: SD

value: PBMC, 7 days post TIL transfer

tag: batch


title: UPN006, post-ACT lesion (biopsy 1), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN006_postACT1

source_name: Melanoma metastasis, post-treatment lesion

value: post-ACT, post-treatment tumor biopsy 1


title: Young_Pbx1OE_RNAseq_D3_rep2

description:
Library name: Young_Pbx1OE_RNAseq_D3_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep2

value: Bone marrow

value: Wild type


title: Old_Pbx1OE_RNAseq_D3_rep2

description:
Library name: Old_Pbx1OE_RNAseq_D3_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep2

value: Old HSC


title: ATAC_Day3_d2

description: Library name: ATAC_Day3_d2

value: Blood

value: CD4 T cells

value: Invitro culture day3


title: Young_Pbx1OE_RNAseq_D3_rep1

description:
Library name: Young_Pbx1OE_RNAseq_D3_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to RNA-seq on day 3, rep1


title: ATAC_Day3_d1

description: Library name: ATAC_Day3_d1

value: Healthy

value: No treatment


title: ATAC_Day0_d2

description: Library name: ATAC_Day0_d2

value: Invitro culture day0


title: Young_Mock_RNAseq_D3_rep3

description:
Library name: Young_Mock_RNAseq_D3_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep3

value: Mock-transduced


title: ATAC_Day0_d1

description: Library name: ATAC_Day0_d1


title: Young_Mock_RNAseq_D3_rep2

description:
Library name: Young_Mock_RNAseq_D3_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep2

value: Young HSC


title: Liver biopsies, capture area D1

description: Library name: EJ2-2JR6DFV-D1

value: Liver biopsy


title: UPN003, PBMC 7 days post transfer, CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN003_PBMC7dpt

value: Peripheral blood

value: CD3+ T cells (FACS-sorted)

value: female

value: PR


title: Young_Mock_RNAseq_D3_rep1

description:
Library name: Young_Mock_RNAseq_D3_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to RNA-seq on day 3, rep1


title: UPN003, pre-ACT (baseline tumor), CD3+ T cells (scRNA-seq + scTCR-seq)

description: Library name: UPN003_preACT

source_name: Melanoma metastasis, baseline tumor lesion

value: pre-ACT (before TIL therapy)


title: ATAC-seq of Mus musculus : old cultured HSCs, rep1

description:
Library name: Old_Cultured_HSC_ATACseq_rep1
Old HSCs were cultured for 26 hours in SCF1 ng/mL and TPO100 ng/mL conditions, then subjected to ATAC-seq, rep1

value: Bone marrow

value: Hematopoietic stem cells (CD150+CD48-LSK cells)

value: Cultured for 26 hr


title: Old_Pbx1_CutTag_rep3

description:
Library name: Old_Pbx1_CutTag_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep3

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit.
Supplementary files format and content: Peak_250bp_noBL.bed is a BED file providing a +/- 125bp around summits detected by MACS3. Problematic regions ("blacklist") were removed.
Supplementary files format and content: Peaks_gene10kb.bed is a BED file defining regions spanning +/- 10 kb around gene bodies, based on annotations from mm10 RefSeq genes.
Supplementary files format and content: PeakCounts_gene10kb.txt is a tab-delimited file containing raw read count data for the regions specified in Peaks_gene10kb.bed.
Library strategy: CUT&TAG

extract_protocol:
A tatoal of 50000 Mock- or Pbx1-transduced HSCs were subjected to the CUT&Tag assay, utilizing the CUT&Tag Assay Kit (Cell Signaling Technology) according to the manufacturer's instructions with minor modifications.
For the detection of di-methyl H3K9 (H3K9me2), 2 uL of Rabbit anti-H3K9me2 monoclonal antibody (Cell Signaling Technology) per sample was bound to activated concanavalin A beads and incubated with the cell suspension overnight at 4°C. Subsequently, 1 uL of goat anti-rabbit IgG (H+L) antibody was used as the secondary antibody and was bound for 30 minutes at room temperature. pAG-Tn5 was then bound to the secondary antibody for tagmentation for 1 hour at room temperature. Following this, the fragmented DNA was released, purified using a spin column, and amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS) to incorporate the Nextera XT Index Kit v2. Each sample was prepared using 25 uL of 2X KAPA HiFi HS RM, 5 uL each of index 1 and index 2 primers, and 15 μL of the tagmented library. The thermal cycler conditions were set as follows: 72°C for 5 min, 98°C for 30 s, and 13 cycles of 98°C for 10 s followed by 60°C for 11 s. The residual PCR products were further elongated at 72°C for 1 min and maintained at 4°C. The library was purified using AMPure XP beads and sequenced on the NovaSeq 6000 platform with a paired-end read length of 150 bp.

treatment_protocol: Either CD150+CD48-CD41-CD34- LSK cells from 4 young (2.5mo) mice per sample, or CD150+CD48- CD34- LSK cells from 1 old (18mo) mouse per sample was isolated. Each experimental sample comprised cells from four young mice or one old mouse per sample. All isolated cells underwent retroviral transduction with mock or Pbx1-expressing vectors, after which 50,000 GFP+ cells for Cut&Tag were selected.

tag: chip antibody

value: anti-H3K9me2 (Cell Signaling Technology)

value: Old HSC

value: Wild type


title: mBMEC CCM3WT rapamycin biological replicate 2

description:
Library name: Sample 7
Unstranded RNA-seq

value: Brain

value: Brain microvascular endothelial cells

value: 100 nM rapamycin 24 h


title: VDJ_SampleC

description: Library name: VDJ_SampleC

value: Blood

value: CD4 T cells

value: Healthy

value: TimeNA

value: No treatment


title: GE_SampleC

description: Library name: GE_SampleC


title: Old_Pbx1_CutTag_rep2

description:
Library name: Old_Pbx1_CutTag_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep2


title: GE_SampleB

description: Library name: GE_SampleB


title: Old_Mock_CutTag_rep3

description:
Library name: Old_Mock_CutTag_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep3

value: Mock-transduced


title: Old_Mock_CutTag_rep2

description:
Library name: Old_Mock_CutTag_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep2


title: Young_Pbx1_CutTag_rep3

description:
Library name: Young_Pbx1_CutTag_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep3

value: Young HSC


title: IMR32_KO_rescue2_Rep2

city: Segrate

first: Simona

last: Di Lascio

address: Via Fratelli Cervi 93

institute: University of Milan

description:
Library name: Sample 11
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue2_Rep2

data_processing:
Base calling, demultiplexing and adapter masking were performed using Illumina BCL Convert v3.9.3
Sequence reads were trimmed for adaptor sequence/low-quality bases using ERNE software
Reads were aligned on hg38-iGenomes genome with STAR (default parameters),
Assembling and quantitation of full-length transcripts for each gene locus were performed by Stringtie (default parameters).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: The human neuroblastoma cell line IMR32 was grown in RPMI 1640 medium, supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 mg/mL streptomycin, 2 mM L-glutamine. The IMR32 PHOX2B KO stable clone was maintained under selection with 0.150 mg/mL Puromycin dihydrochloride. The IMR32 KO clones re-expressing PHOX2B (rescue_1 and rescue_2) were maintained under selection by adding Puromycin dihydrochloride and Geneticin (G-161 418 Sulphate) at 0.150 mg/mL and 0.170 mg/mL final concentration, respectively. All cell lines grow in adhesion at 37°C in a humified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
VAHTS Universal v10 RNA-Seq kit (Vazyme, Nanjing, PRC) has been used for library preparation following the manufacturer’s instructions (library type: fr-firststrand).

value: Neuroblastoma

value: PHOX2B Knockdown + PHOX2B re-expression


title: IMR32_KO_rescue2_Rep3

description:
Library name: Sample 12
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue2_Rep3


title: IMR32_KO_rescue2_Rep1

description:
Library name: Sample 10
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue2_Rep1


title: IMR32_scramble

description:
Library name: Sample 13
Column name in  raw_counts_All_Samples.txt : IMR32_scramble

value: WT


title: Young_Pbx1_CutTag_rep1

description:
Library name: Young_Pbx1_CutTag_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep1

value: Bone marrow


title: Young_Mock_CutTag_rep3

description:
Library name: Young_Mock_CutTag_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep3

value: anti-H3K9me2 (Cell Signaling Technology)


title: IMR32_KO_rescue1_Rep1

description:
Library name: Sample 7
Column name in  raw_counts_All_Samples.txt : IMR32_KO_rescue1_Rep1


title: Young_Pbx1_CutTag_rep2

description:
Library name: Young_Pbx1_CutTag_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep2


title: Young_Mock_CutTag_rep2

description:
Library name: Young_Mock_CutTag_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 on day 3, rep2


title: IMR32_KO_Rep3

description:
Library name: Sample 6
Column name in  raw_counts_All_Samples.txt : IMR32_KO_Rep3

value: PHOX2B Knockdown


title: Young_Mock_CutTag_rep1

description:
Library name: Young_Mock_CutTag_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to Cut&Tag for H3K9me2 for H3K9me2 on day 3, rep1

value: Wild type


title: Old_Pbx1_ATAC-seq_rep2

description:
Library name: Old_Pbx1_ATAC-seq_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep2

data_processing:
Fastq files were trimmed using Trim Galore and aligned to the reference mouse genome (mm10) using bowtie2 with a --very-sensitive and single-read mode. Mitochondrial genome, Y chromosome, and scaffold chromosomes were removed using samtools, and duplicate reads were removed using picard MarkDuplicates. Peak calling was performed using MACS3 for each group with -q = 0.05, --extsize =100, and --shift = 50 with narrow peak mode. All peaks called in each group were merged, and peaks overlapping with blacklist region were excluded, and peaks within a distance smaller than 50bp considered as an identical peak. After further removing peaks with average of log CPM < -1, peak count around +/- 125bp of each summit was performed using csaw package of R.
Assembly: mm10
Supplementary files format and content: BigWig files were generated using Deeptools from BAM files removing duplicated reads after normalized to peak counts, and biological replicates were merged with DeepTools.
Supplementary files format and content: PeakCounts_th0.txt provides a tab-deliminated raw count data, counting reads 250bp around each summit following removal of peaks with low signal.
Supplementary files format and content: Peak_250bp_noBL.bed is a BED file providing a +/- 125bp around summits detected by MACS3. Problematic regions ("blacklist") were removed.

extract_protocol:
A total of 50000 Mock- or Pbx1 transduced young or old HSCs were sorted into 1.5-mL tubes containing 500 uL of SF-O3 medium and pelleted by centrifugation for 5 minutes at 700g. The cells were then incubated with ATAC-S buffer 25uL and ATAC-lysis buffer 25uL of Zymo-Seq ATAC Library Kit (Zymo Research) for 3 minutes on ice. Then 1 mL of ATAC-wash buffer was added and centrifuged at 1000 x g for 10 minutes to collect nuclei.
Extracted nuclei were treated with Tn5 transposase bound with adaptor sequences for 30 minutes at 37°C with gentle shaking, followed by amplification with PCR. Sequencing was performed using NovaSeq6000 with a paired-end sequencing length of 150bp.

value: Old HSC


title: IMR32_CTRL_Rep3

description:
Library name: Sample 3
Column name in  raw_counts_All_Samples.txt : IMR32_CTRL_Rep3


title: IMR32_KO_Rep1

description:
Library name: Sample 4
Column name in  raw_counts_All_Samples.txt : IMR32_KO_Rep1


title: IMR32_KO_Rep2

description:
Library name: Sample 5
Column name in  raw_counts_All_Samples.txt : IMR32_KO_Rep2


title: Old_Pbx1_ATAC-seq_rep1

description:
Library name: Old_Pbx1_ATAC-seq_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep1


title: IMR32_CTRL_Rep1

description:
Library name: Sample 1
Column name in  raw_counts_All_Samples.txt : IMR32_CTRL_Rep1


title: Old_Mock_ATAC-seq_rep3

description:
Library name: Old_Mock_ATAC-seq_rep3
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep3


title: Old_Mock_ATAC-seq_rep2

description:
Library name: Old_Mock_ATAC-seq_rep2
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep2


title: Old_Mock_ATAC-seq_rep1

description:
Library name: Old_Mock_ATAC-seq_rep1
Old hematopoietic stem cells (CD150+CD48-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep1


title: ATAC-seq, hPIB-142_d9_G_DP_2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: hPIB-142_d9_G_DP_2

data_processing:
In order to pre-process the FASTQ files of ATAC-Seq experiments, we used the nf-core ATAC-seq pipeline version 1.2.2 with default parameters. Technical replicates were merged together.
Reads were mapped to the GRCh38 reference genome using BWA. Peak calling was performed with MACS2 separately for each sample. A combined peak list for all samples was obtained using BEDTools. Finally, read counts on a combined peak list were calculated using featureCounts.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

source_name: skin

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
5000-10000 cells were sorted intro PBS with 2 % FBS and processed according to the procedure described by Buenrostro et al. (2015).
ATAC-seq primers were prepared according to the procedure described by Buenrostro et al. (2015), with 96-plex indexing primers.

treatment_protocol: HDFs were transduced on day -1 with lentiviral vectors encoding for PIB and with lentiviral vectors encoding for miRNA hairpins. Cells were sorted on day 3, 6 or 9. Human dendritic cells were enriched from peripheral blood and sorted for subtype-specific markers.

value: skin

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+ HLA-DR+

tag: technical replicates


title: ATAC-seq, hPIB-142_d9_S_DP_2

description: Library name: hPIB-142_d9_S_DP_2


title: Young_Pbx1_ATAC-seq_rep2

description:
Library name: Young_Pbx1_ATAC-seq_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep2


title: Young_Pbx1_ATAC-seq_rep1

description:
Library name: Young_Pbx1_ATAC-seq_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep1


title: Young_Pbx1_ATAC-seq_rep3

description:
Library name: Young_Pbx1_ATAC-seq_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with Pbx1-IRES-GFP and subjected to ATAC-seq on day 3, rep3


title: Young_Mock_ATAC-seq_rep3

description:
Library name: Young_Mock_ATAC-seq_rep3
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep3


title: ATAC-seq, hPIB-124_d9_G_DP_2

description: Library name: hPIB-124_d9_G_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-124 on day -1 of reprogramming.


title: ATAC-seq, hPIB-124_d9_S_DP_2

description: Library name: hPIB-124_d9_S_DP_2


title: ATAC-seq, hPIB-SCR_d9_L_DP_2

description: Library name: hPIB-SCR_d9_L_DP_2

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for a scrambled control hairpin on day -1 of reprogramming.


title: Young_Mock_ATAC-seq_rep2

description:
Library name: Young_Mock_ATAC-seq_rep2
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep2

value: Mock-transduced


title: Young_Mock_ATAC-seq_rep1

description:
Library name: Young_Mock_ATAC-seq_rep1
Young hematopoietic stem cells (CD150+CD48-CD41-CD34-LSK) were retrovirally transduced with pMYs-IRES-GFP and subjected to ATAC-seq on day 3, rep1

value: Young HSC


title: ATAC-seq, hPIB-SCR_d9_G_DP_2

description: Library name: hPIB-SCR_d9_G_DP_2


title: ATAC-seq, hPIB-SCR_d9_S_DP_2

description: Library name: hPIB-SCR_d9_S_DP_2


title: ATAC-seq, hPIB-142_d9_L_CD45_2

description: Library name: hPIB-142_d9_L_CD45_2

value: live (DAPI-) and CD45+ HLA-DR-