title: 1_1.5h_WT_IntS11_ChIPseq_replicate_2

description: Library name: 1_1.5h_WT_IntS11_ChIPseq_replicate_2


title: 2.5_3h_WT_IntS11_ChIPseq_replicate_1

status: Public on Mar 31 2026

type: SRA

city: Kunming

first: Liangliang

last: Wang

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

country: China

institute: Yunnan University

description: Library name: 2.5_3h_WT_IntS11_ChIPseq_replicate_1

library_source: genomic

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2).Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Peaks were calculated using macs2 (v2.2.7.1)
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
The embryos of indicated genotypes were harvested and subjected to cross-linking by fixation buffer (50 mM HEPES, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl and 1.8% formaldehyde).  They were cross-linked for 20 minutes and then quenched with 125 mM glycine (final concentration) for 5 minutes at room temperature.  Chromatin immunoprecipitation (ChIP) reactions were carried out in duplicate using the Pierce Magnetic ChIP Kit.
Sequencing libraries were generated using the VAHTS Universal DNA Library Prep Kit for MGI.

tag: tissue

value: embryo


title: Streptomyces cells, co-culture, Hour12

city: Turku

first: Mikko

last: Metsä-Ketelä

address: Tykistökatu 6A

department: Department of Life Technologies

country: Finland

institute: University of Turku

library_source: transcriptomic

data_processing:
Chipster (CSC)
Reads were trimmed using TRIMMOMATIC (default parameters)
Trimmed reads were mapped using BowTie2 (default parameters)
Mapped reads were counted using HTSeq
Differential expression was done using edgeR
Assembly: Streptomyces lavendulae genome (GCA_008016805.1) / Saccharomyces cerevisiae genome (GCA_000146045.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Streptomyces lavendulae

source_name: bacterial cells

growth_protocol: Cells were grown in SC medium (Samples 17-20 contained autoclaved yeast 26 g/l)

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Illumina PCR-free library

treatment_protocol: Co-cultures with live or dead yeast

tag: cell type

value: bacterial cells

tag: strain

tag: genotype

value: WT

tag: treatment

value: co-culture

tag: time

value: Hour 12


title: Streptomyces cells, co-culture, Hour24

value: Hour 24


title: Streptomyces cells, control, Day7

value: axenic culture

value: Day 7


title: Streptomyces and yeast cells, co-culture, Day1

organism:
Streptomyces lavendulae
Saccharomyces cerevisiae

source_name: bacterial and yeast cells

value: bacterial and yeast cells

value: YAKB-15 and BY25610

value: WT and ::mCherry

value: Day 1


title: Streptomyces cells, control, Hour6

value: Hour 6


title: Streptomyces cells, control, Hour48

value: Hour 48


title: Streptomyces cells, control, Hour24


title: Streptomyces cells, control, Day3

value: Day 3


title: Streptomyces cells, control, Day5

value: Day 5


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_ATACseq_replicate_2

data_processing:
Paired-end reads were trimmed by trimmomatic (v0.39).
Clean reads were mapped to mapped to Drosophila melanogaster (dm6) using bowtie2 (v2.2.5).
PCR duplicates were marked using sambamba (v0.8.2).Non-uniquely mapped reads, low-quality reads (quality scores less than 30) were removed using samtools (v1.18).
Peaks were calculated using macs2 (v2.2.7.1)
Bigwig files were generated from resulting deduplicated and filtered bam files using deeptools (v3.5.1).
Assembly: dm6
Supplementary files format and content: BigWig, narrowPeak

extract_protocol:
The embryos of indicated genotypes were harvested and dechorionated in 50% commercial bleach solution.  Subsequently, the embryos were resuspended with ATAC-lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) and homogenized with a loose stroke 50 times, followed by centrifugation at 500 g for 5 minutes to pellet the nuclei at 4℃.
The ATAC-seq libraries of embryos were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina.


description: Library name: 2.5_3h_Mutant_IntS11_mislocalized_ATACseq_replicate_1


description: Library name: 2.5_3h_WT_IntS11_mislocalized_ATACseq_replicate_2


description: Library name: 2.5_3h_WT_IntS11_mislocalized_ATACseq_replicate_1


title: Streptomyces cells, control, Day1


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_ATACseq_replicate_2


title: Myc_OFF_12hrs_#1

city: London

first: Roderik

last: Kortlever

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: Myc4W_12hrsOff_E5
10X Genomics

library_source: transcriptomic single cell

data_processing:
Read processing was performed using the 10X Genomics workflow. Briefly, the Cell Ranger Single-Cell Software Suite (6.1.1) was used for demultiplexing, barcode assignment and UMI quantification. The reads were aligned to the pre-built mm10 reference genome provided by 10x Genomics.
Assembly: Mouse mm10
Supplementary files format and content: Cellranger output files

organism: Mus musculus

source_name: Lung

growth_protocol: Mice were allowed to grow KrasG12D-induced lung tumours under normal housing conditions after AdenoCRE infection.

extract_protocol:
Lungs were isolated from KM mice, placed into MACS tissue storage solution (130-100-008, Miltenyi) on ice and processed to single cell suspension on a gentleMACS Octo Dissociator with Heaters (130-096-427, Miltenyi) according to manufacturers’ instructions.  In brief, after manually dissecting the lungs in ~1mm2 pieces, they were further processed into a single cell suspension using the mouse tumour dissociation kit (130-096-730, Miltenyi) in gentleMACS C tubes (130-096-334, Miltenyi). After dissociation the cell suspension was incubated with Red Blood Lysis Solution (130-094-183, Miltenyi) to remove red blood cells. Subsequently the cell suspension was filtered through 70µm MACS SmartStrainers (130-098-462) before being counted. 6000 cells per sample were offered for single cell sequencing.
Library preparation of murine samples was performed according to instruction in the 10X Chromium single cell kit 3’ v3.

treatment_protocol: Mice were treated with Tamoxifen to activate MycER (Myc ON). After 4 weeks (Myc4W) cohorts were taken off tamoxifen food for 2, 4, 8, 12 or 24 hours (Myc4W_2hrsOFF,  Myc4W_4hrsOFF, Myc4W_8hrsOFF, Myc4W_12hrsOFF, Myc4W_24hrsOFF) and euthanised. Whole lungs (including tumours) were isolated at endpoints, snapfrozen and ground to a powder while frozen (under liquid nitrogen-assisted conditions).

value: Lung

tag: cell line

value: Tissue

value: Lung cells

value: Tamoxifen 4wks then no Tamoxifen for 12hrs

tag: batch


title: Myc_OFF_8hrs_#2

description:
Library name: Myc4W_8hrsOff_B1
10X Genomics

value: Tamoxifen 4wks then no Tamoxifen for 8hrs


title: Myc_OFF_4hrs_#2

description:
Library name: Myc4W_4hrsOff_F1
10X Genomics

value: Tamoxifen 4wks then no Tamoxifen for 4hrs


description: Library name: 1_1.5h_Mutant_IntS11_mislocalized_ATACseq_replicate_1

value: embryo


title: Myc_OFF_12hrs_#2

description:
Library name: Myc4W_12hrsOff_F5
10X Genomics


title: Myc_OFF_24hrs_#3

description:
Library name: Myc4W_24hrsOff_G5
10X Genomics

value: Tamoxifen 4wks then no Tamoxifen for 24hrs


title: Myc_OFF_4hrs_#6

description:
Library name: Myc4W_4hrsOff_H1
10X Genomics


title: Myc_OFF_24hrs_#2

description:
Library name: Myc4W_24hrsOff_F1
10X Genomics


title: Myc_OFF_8hrs_#4

description:
Library name: Myc4W_8hrsOff_D5
10X Genomics


description: Library name: 1_1.5h_WT_IntS11_mislocalized_ATACseq_replicate_1


title: Myc_OFF_12hrs_#3

description:
Library name: Myc4W_12hrsOff_G1
10X Genomics


description: Library name: 1_1.5h_WT_IntS11_mislocalized_ATACseq_replicate_2


title: Myc_OFF_4hrs_#4

description:
Library name: Myc4W_4hrsOff_G1
10X Genomics


title: Myc_OFF_12hrs_#4

description:
Library name: Myc4W_12hrsOff_H1
10X Genomics


title: Myc_OFF_8hrs_#3

description:
Library name: Myc4W_8hrsOff_C5
10X Genomics


title: Myc_OFF_24hrs_#4

description:
Library name: Myc4W_24hrsOff_H5
10X Genomics


title: Myc_OFF_4hrs_#3

description:
Library name: Myc4W_4hrsOff_G11
10X Genomics


title: Myc_OFF_8hrs_#1

description:
Library name: Myc4W_8hrsOff_A1
10X Genomics


title: Myc_OFF_4hrs_#1

description:
Library name: Myc4W_4hrsOff_F11
10X Genomics


title: Myc_OFF_24hrs_#1

description:
Library name: Myc4W_24hrsOff_E1
10X Genomics


title: Myc_OFF_4hrs_#5

description:
Library name: Myc4W_4hrsOff_H11
10X Genomics


title: Myc_OFF_2hrs_#4

description:
Library name: Myc4W_2hrsOff_D1
10X Genomics

value: Tamoxifen 4wks then no Tamoxifen for 2hrs


title: Myc_OFF_2hrs_#6

description:
Library name: Myc4W_2hrsOff_E1
10X Genomics


title: Myc_OFF_2hrs_#2

description:
Library name: Myc4W_2hrsOff_C1
10X Genomics


title: Myc_OFF_2hrs_#5

description:
Library name: Myc4W_2hrsOff_E11
10X Genomics


title: Myc_ON_#7

description:
Library name: Myc4W_C1
10X Genomics

value: Tamoxifen 4 weeks


title: Myc_OFF_2hrs_#3

description:
Library name: Myc4W_2hrsOff_D11
10X Genomics


title: Myc_ON_#3

description:
Library name: Myc4W_A5
10X Genomics


title: Myc_ON_#8

description:
Library name: Myc4W_D1
10X Genomics


title: Myc_ON_#2

description:
Library name: Myc4W_A1
10X Genomics


title: Myc_OFF_2hrs_#1

description:
Library name: Myc4W_2hrsOff_C11
10X Genomics


title: Myc_ON_#6

description:
Library name: Myc4W_B5
10X Genomics


title: MycON_8hrs_2

description:
Library name: SIGAD5
10X Genomics

data_processing:
Read processing was performed using the 10X Genomics workflow. Briefly, the Cell Ranger Single-Cell Software Suite (6.1.1) was used for demultiplexing, barcode assignment and UMI quantification. The reads were aligned to the pre-built mm10 reference genome provided by 10x Genomics.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Tissue

treatment_protocol: Mice were untreated (KrasG12D-only) or treated with Tamoxifen to activate MycER (Myc ON) fro 8 or 24 hours or 7 days. Whole lungs (including tumours) were isolated at endpoints, snapfrozen and ground to a powder while frozen (under liquid nitrogen-assisted conditions).

value: Tamoxifen for 8 hours


title: Myc_ON_#4

description:
Library name: Myc4W_B11
10X Genomics


title: Myc_ON_#1

description:
Library name: Myc4W_A11
10X Genomics


title: MycON_7d_4

description:
Library name: SIGAH4
10X Genomics

value: Tamoxifen for 7 days


title: MycON_7d_3

description:
Library name: SIGAG4
10X Genomics


title: MycON_7d_1

description:
Library name: SIGAE4
10X Genomics


title: MycON_8hrs_3

description:
Library name: SIGAE5
10X Genomics


title: KRasG12D_only_6

description:
Library name: SIGAD4
10X Genomics

value: No Tamoxifen


title: MycON_24hrs_2

description:
Library name: SIGAG5
10X Genomics

value: Tamoxifen for 24 hours


title: KRasG12D_only_1

description:
Library name: SIGAA5
10X Genomics


title: MycON_7d_2

description:
Library name: SIGAF4
10X Genomics


title: MycON_24hrs_3

description:
Library name: SIGAH5
10X Genomics


title: MycON_24hrs_1

description:
Library name: SIGAF5
10X Genomics


title: KRasG12D_only_3

description:
Library name: SIGAA4
10X Genomics


title: MycON_8hrs_1

description:
Library name: SIGAC5
10X Genomics


title: Myc_ON_#5

description:
Library name: Myc4W_B1
10X Genomics


title: KRasG12D_only_4

description:
Library name: SIGAB4
10X Genomics


title: KRasG12D_only_5

description:
Library name: SIGAC4
10X Genomics


title: KRasG12D_only_2

description:
Library name: SIGAB5
10X Genomics


title: Day 5, no intravenous injection, experimental repeat 2, hashtags (HTO)

status: Public on Mar 30 2026

city: Denver

first: Richard

middle: Lee

last: Reinhardt

state: Colorado

address: 1400 Jackson Street, K817A

department: Biomedical Research

country: USA

institute: National Jewish Health

description:
Library name: No_TVI_B_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_B_h1.h5
AK46_NoTVI_B_h2.h5

library_source: other

data_processing:
Reads were aligned to the refdata-gex-GRCm39-2024-A reference transcriptome using cellranger v9.0.0, cellranger multi command.
Downstream analysis was done using Seurat v4.0.2.
Individual biological samples were filtered to retain cells with at least 3000 total transcripts (nCount_RNA > 3000) and at least 2000 unique transcripts (nFeature_RNA > 2000). Cells with either metric above the 98th percentile for that metric were also filtered out. Further, cells with more than 1000 reads on PE were also filtered out. Raw PE-CITE-seq reads were then used to determine vascular/parenchymal classification. Cells with greater than 100 PE reads were classified as vascularly labelled, while cells with 100 PE reads or less were classified as parenchymal. In sum, individual samples were assigned metadata for the following: vascular/parenchymal, timepoint, replicate, treatment. Initial PCA-and-UMAP based clustering was examined to determine that biological replicates had good overlap and there was no batch effect, providing justification for merging data for downstream analysis. Quality-controlled and metadata-assigned samples were merged across all intravenously injected biological samples (Day 5 with intravenous injection cohort and the Day 7 with intravenous injection cohort) using the Seurat merge function. This combined Seurat object was then log-normalized for RNA, following which variable features were identified (FindVariableFeatures) and data scaled for all genes. PCA was performed on this post-processed RNA data and dimensions for final clustering determined by titration along the inflection points on the resultant elbow-plot. UMAP and clustering were then calculated using default Seurat settings (UMAP using normalized Laplacian + noise and nearest neighbor graph using SNN, Modularity Optimizer version 1.3.0 and Louvain algorithm). ADT data was normalized using center log ratio and normalizing per feature across cells [NormalizeData with assay = “ADTsubset” (excluding PE), method = “CLR”, margin = “2”]. These data were then scaled, to enable visualization on heatmaps. Anti-PE, already used to determine vascular/non-vascular, was excluded from this post-processing.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: RDS file of final post-processed Seurat-object used for analyses and figure generation in accompanying manuscript.
Supplementary files format and content: individual sample h5
Library strategy: CITE-seq

molecule: protein

source_name: lung

extract_protocol:
ILC2s were sorted into complete media, spun down, and resuspended in 1x PBS + 0.4% BSA. Samples were then counted and loaded for emulsion droplet construction on a 10X Genomic IX controller.
Gene Expression and ADT/HTO library preparation was performed by combining the instructions in the TotalSeq A Dual Index Protocol and 10X Genomics Chromium Single Cell 3′ Reagent Kits V3.1. One quarter of the cDNA was used to build the gene expression libraries, and indexed using the 10X, Set TT A index plate. Gene Expression libraries were pooled based off the projected number of cells captured and sequenced using an Ilumina NextSeq 2000, aiming for 20,000 reads per cell. For the ADT/HTO libraries, one quarter of the cDNA generated was used to build the ADT/HTO libraries and indexed using the TotalSeq A indexes listed in the protocol. ADT/HTO libraries were pooled based on the number of cells captured and sequenced using an Illumina NextSeq 2000, aiming for 5,500 reads/cell. All libraries were sequenced together in a single sequencing run.

value: lung

value: Arg1-YFP reporter

tag: library type

value: HTO


title: Day 5, no intravenous injection, experimental repeat 1, hashtags (HTO)

description:
Library name: No_TVI_A_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_A_h1.h5
AK46_NoTVI_A_h2.h5


title: Day 5, no intravenous injection, experimental repeat 1, mRNA (GEX)

description:
Library name: No_TVI_A_S1
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_A_h1.h5
AK46_NoTVI_A_h2.h5

data_processing:
Reads were aligned to the refdata-gex-GRCm39-2024-A reference transcriptome using cellranger v9.0.0, cellranger multi command.
Downstream analysis was done using Seurat v4.0.2.
Individual biological samples were filtered to retain cells with at least 3000 total transcripts (nCount_RNA > 3000) and at least 2000 unique transcripts (nFeature_RNA > 2000). Cells with either metric above the 98th percentile for that metric were also filtered out. Further, cells with more than 1000 reads on PE were also filtered out. Raw PE-CITE-seq reads were then used to determine vascular/parenchymal classification. Cells with greater than 100 PE reads were classified as vascularly labelled, while cells with 100 PE reads or less were classified as parenchymal. In sum, individual samples were assigned metadata for the following: vascular/parenchymal, timepoint, replicate, treatment. Initial PCA-and-UMAP based clustering was examined to determine that biological replicates had good overlap and there was no batch effect, providing justification for merging data for downstream analysis. Quality-controlled and metadata-assigned samples were merged across all intravenously injected biological samples (Day 5 with intravenous injection cohort and the Day 7 with intravenous injection cohort) using the Seurat merge function. This combined Seurat object was then log-normalized for RNA, following which variable features were identified (FindVariableFeatures) and data scaled for all genes. PCA was performed on this post-processed RNA data and dimensions for final clustering determined by titration along the inflection points on the resultant elbow-plot. UMAP and clustering were then calculated using default Seurat settings (UMAP using normalized Laplacian + noise and nearest neighbor graph using SNN, Modularity Optimizer version 1.3.0 and Louvain algorithm). ADT data was normalized using center log ratio and normalizing per feature across cells [NormalizeData with assay = “ADTsubset” (excluding PE), method = “CLR”, margin = “2”]. These data were then scaled, to enable visualization on heatmaps. Anti-PE, already used to determine vascular/non-vascular, was excluded from this post-processing.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: RDS file of final post-processed Seurat-object used for analyses and figure generation in accompanying manuscript.
Supplementary files format and content: individual sample h5

molecule: polyA RNA

value: mRNA


title: Day 5, no intravenous injection, experimental repeat 2, CITE-seq (ADT)

description:
Library name: No_TVI_B_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_B_h1.h5
AK46_NoTVI_B_h2.h5

value: ADT


title: Day 5, no intravenous injection, experimental repeat 2, mRNA (GEX)

description:
Library name: No_TVI_B_S4
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_B_h1.h5
AK46_NoTVI_B_h2.h5


title: IFNa or PBS  treated lung with MMTV tumour cells biol

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

description:
Library name: VB1
Cancer cells (1), Immune cells (3), Epithelial cells (3), Mesenchymal cells (3)

data_processing:
CellRanger (version7.2.0) was used with the "multi"  option to demultiplex four samples from FASTQ files.
Probe barcodes for demultiplexing : PBS1 = BC001; PBS2 = BC002 ;  IFNa1 = BC003; IFNa2 = BC004
Assembly: mm10-2020
Supplementary files format and content: CellRanger multi outputs files. Zipped csv files.

extract_protocol:
Samples were stained for FACS before being fixed with x10 fixation kit and stored.
Chromium Fixed RNA Kit, Mouse Transcriptome, 4 rxns x 4

value: multiple (multiplexed sample)


title: Day 7, intravenous injection, experimental repeat 2, mRNA (GEX)

description:
Library name: D7_B_S6
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_B_h1.h5
AK46_D7_B_h2.h5


title: Day 7, intravenous injection, experimental repeat 1, mRNA (GEX)

description:
Library name: D7_A_S3
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_A_h1.h5
AK46_D7_A_h2.h5


title: Day 7, intravenous injection, experimental repeat 2, hashtags (HTO)

description:
Library name: D7_B_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_B_h1.h5
AK46_D7_B_h2.h5


title: Day 7, intravenous injection, experimental repeat 1, hashtags (HTO)

description:
Library name: D7_A_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_A_h1.h5
AK46_D7_A_h2.h5


title: Day 5, intravenous injection, experimental repeat 2, hashtags (HTO)

description:
Library name: D5_B_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_B_h1.h5
AK46_D5_B_h2.h5


title: Day 5, intravenous injection, experimental repeat 2, mRNA (GEX)

description:
Library name: D5_B_S5
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_B_h1.h5
AK46_D5_B_h2.h5


title: Day 7, intravenous injection, experimental repeat 2, CITE-seq (ADT)

description:
Library name: D7_B_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_B_h1.h5
AK46_D7_B_h2.h5


title: Day 5, no intravenous injection, experimental repeat 1, CITE-seq (ADT)

description:
Library name: No_TVI_A_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_NoTVI_A_h1.h5
AK46_NoTVI_A_h2.h5


title: Day 5, intravenous injection, experimental repeat 1, mRNA (GEX)

description:
Library name: D5_A_S2
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_A_h1.h5
AK46_D5_A_h2.h5


title: lung, uninfected, experimental repeat 2, hashtags (HTO)

description:
Library name: UF_2_HTO
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_B_h1.h5
AK54_Uninfected_B_h2.h5

data_processing:
Reads were aligned to the refdata-gex-GRCm39-2024-A reference transcriptome using cellranger v9.0.0, cellranger multi command.
Downstream analysis was done using Seurat v4.0.2.
Individual biological samples were filtered to retain cells with at least 2500 total transcripts (nCount_RNA > 2500) and at least 1500 unique transcripts (nFeature_RNA > 1500). Cells with either metric above the 98th percentile for that metric were also filtered out. Further, cells with more than 150 reads on PE were also filtered out. Raw PE-CITE-seq reads were then used to determine donor/endogenous cell classification for recipient samples. Cells with greater than 15 PE reads were classified as donor cells, while cells with 15 PE reads or less were classified as endogenous host cells. In sum, individual samples were assigned metadata for the following: donor/endogenous, timepoint, replicate, treatment. Initial PCA-and-UMAP based clustering was examined to determine that biological replicates had good overlap and there was no batch effect, providing justification for merging data for downstream analysis. Quality-controlled and metadata-assigned samples were merged across all cohorts using the Seurat merge function. This combined Seurat object was then log-normalized for RNA, following which variable features were identified (FindVariableFeatures) and data scaled for all genes. PCA was performed on this post-processed RNA data and dimensions for final clustering determined by titration along the inflection points on the resultant elbow-plot. UMAP and clustering were then calculated using default Seurat settings (UMAP using normalized Laplacian + noise and nearest neighbor graph using SNN, Modularity Optimizer version 1.3.0 and Louvain algorithm). ADT data was normalized using center log ratio and normalizing per feature across cells [NormalizeData with assay = “ADTsubset” (excluding PE), method = “CLR”, margin = “2”]. These data were then scaled, to enable visualization on heatmaps. Anti-PE, already used to determine congenic/endogenous, was excluded from this post-processing.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: RDS file of final post-processed Seurat-object used for analyses and figure generation in accompanying manuscript
Supplementary files format and content: individual sample h5
Library strategy: CITE-seq

extract_protocol:
ILC2s were sorted into complete media, spun down, and resuspended in 1x PBS + 0.4% BSA. Samples were then counted and loaded for emulsion droplet construction on a 10X Genomic IX controller.
Gene Expression and ADT/HTO library preparation was performed by combining the instructions in the TotalSeq A Dual Index Protocol and 10X Genomics Chromium Single Cell 3′ Reagent Kits V4. One quarter of the cDNA was used to build the gene expression libraries, and indexed using the 10X, Set TT A index plate. Gene Expression libraries were pooled based off the projected number of cells captured and sequenced using an Ilumina NextSeq 2000, aiming for 20,000 reads per cell. For the ADT/HTO libraries, one quarter of the cDNA generated was used to build the ADT/HTO libraries and indexed using the TotalSeq A indexes listed in the protocol. ADT/HTO libraries were pooled based on the number of cells captured and sequenced using an Illumina NextSeq, aiming for 5,500 reads/cell. All libraries for a single experiment (both experimental days) were sequenced together in a single sequencing run.

value: no infection, no cell transfer


title: Day 7, intravenous injection, experimental repeat 1, CITE-seq (ADT)

description:
Library name: D7_A_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D7_A_h1.h5
AK46_D7_A_h2.h5


title: Day 5, intravenous injection, experimental repeat 1, CITE-seq (ADT)

description:
Library name: D5_A_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_A_h1.h5
AK46_D5_A_h2.h5


title: lung, uninfected, experimental repeat 2, CITE-seq (ADT)

description:
Library name: UF_2_ADT
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_B_h1.h5
AK54_Uninfected_B_h2.h5


title: lung, uninfected, experimental repeat 2, mRNA (GEX)

description:
Library name: UF_2_GEX
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_B_h1.h5
AK54_Uninfected_B_h2.h5

data_processing:
Reads were aligned to the refdata-gex-GRCm39-2024-A reference transcriptome using cellranger v9.0.0, cellranger multi command.
Downstream analysis was done using Seurat v4.0.2.
Individual biological samples were filtered to retain cells with at least 2500 total transcripts (nCount_RNA > 2500) and at least 1500 unique transcripts (nFeature_RNA > 1500). Cells with either metric above the 98th percentile for that metric were also filtered out. Further, cells with more than 150 reads on PE were also filtered out. Raw PE-CITE-seq reads were then used to determine donor/endogenous cell classification for recipient samples. Cells with greater than 15 PE reads were classified as donor cells, while cells with 15 PE reads or less were classified as endogenous host cells. In sum, individual samples were assigned metadata for the following: donor/endogenous, timepoint, replicate, treatment. Initial PCA-and-UMAP based clustering was examined to determine that biological replicates had good overlap and there was no batch effect, providing justification for merging data for downstream analysis. Quality-controlled and metadata-assigned samples were merged across all cohorts using the Seurat merge function. This combined Seurat object was then log-normalized for RNA, following which variable features were identified (FindVariableFeatures) and data scaled for all genes. PCA was performed on this post-processed RNA data and dimensions for final clustering determined by titration along the inflection points on the resultant elbow-plot. UMAP and clustering were then calculated using default Seurat settings (UMAP using normalized Laplacian + noise and nearest neighbor graph using SNN, Modularity Optimizer version 1.3.0 and Louvain algorithm). ADT data was normalized using center log ratio and normalizing per feature across cells [NormalizeData with assay = “ADTsubset” (excluding PE), method = “CLR”, margin = “2”]. These data were then scaled, to enable visualization on heatmaps. Anti-PE, already used to determine congenic/endogenous, was excluded from this post-processing.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: RDS file of final post-processed Seurat-object used for analyses and figure generation in accompanying manuscript
Supplementary files format and content: individual sample h5


title: lung, uninfected, experimental repeat 1, hashtags (HTO)

description:
Library name: UF_1_HTO
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_A_h1.h5
AK54_Uninfected_A_h2.h5


title: Day 5, intravenous injection, experimental repeat 1, hashtags (HTO)

description:
Library name: D5_A_HTO
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_A_h1.h5
AK46_D5_A_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 2, hashtags (HTO)

description:
Library name: Transfer_2_HTO
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_B_h1.h5
AK54_Transfer_B_h2.h5

value: received Arg1-YFP reporter CD45.2 iILC2s (pooled lung and lymph node) on Day 3 of infection


title: lung, uninfected, experimental repeat 1, mRNA (GEX)

description:
Library name: UF_1_GEX
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_A_h1.h5
AK54_Uninfected_A_h2.h5


title: lung, uninfected, experimental repeat 1, CITE-seq (ADT)

description:
Library name: UF_1_ADT
B6 CD45.1 mouse, naïve to all treatments
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Uninfected_A_h1.h5
AK54_Uninfected_A_h2.h5


title: Day 5, intravenous injection, experimental repeat 2, CITE-seq (ADT)

description:
Library name: D5_B_ADT
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK46_D5_B_h1.h5
AK46_D5_B_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 2, mRNA (GEX)

description:
Library name: Transfer_2_GEX
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_B_h1.h5
AK54_Transfer_B_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 2, CITE-seq (ADT)

description:
Library name: Transfer_2_ADT
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_B_h1.h5
AK54_Transfer_B_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 1, hashtags (HTO)

description:
Library name: Transfer_1_HTO
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_A_h1.h5
AK54_Transfer_A_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 1, mRNA (GEX)

description:
Library name: Transfer_1_GEX
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_A_h1.h5
AK54_Transfer_A_h2.h5


title: lung, IL-25-treated, experimental repeat 2, hashtags (HTO)

description:
Library name: Lung_2_HTO
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_B_h1.h5
AK54_Lung_B_h2.h5


title: lung, IL-25-treated, experimental repeat 2, mRNA (GEX)

description:
Library name: Lung_2_GEX
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_B_h1.h5
AK54_Lung_B_h2.h5


title: lung, infected, received donor iILC2s, experimental repeat 1, CITE-seq (ADT)

description:
Library name: Transfer_1_ADT
B6 CD45.1 mouse infected with Nippostrongylus brasiliensis and intravenously injected on day 3 of infection with donor Arg1-YFP reporter CD45.2 iILC2s (pooled lung and mesenteric lymph node). Lung harvested and total ILC2 sorted for sequencing on day 13 of infection.
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Transfer_A_h1.h5
AK54_Transfer_A_h2.h5


title: lung, IL-25-treated, experimental repeat 1, mRNA (GEX)

description:
Library name: Lung_1_GEX
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_A_h1.h5
AK54_Lung_A_h2.h5


title: lung, IL-25-treated, experimental repeat 2, CITE-seq (ADT)

description:
Library name: Lung_2_ADT
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_B_h1.h5
AK54_Lung_B_h2.h5


title: lung, IL-25-treated, experimental repeat 1, CITE-seq (ADT)

description:
Library name: Lung_1_ADT
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_A_h1.h5
AK54_Lung_A_h2.h5


title: mesenteric lymph node, IL-25-treated, experimental repeat 1, mRNA (GEX)

description:
Library name: LN_1_GEX
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_A_h1.h5
AK54_mesLN_A_h2.h5

source_name: mesenteric lymph node

value: mesenteric lymph node


title: mesenteric lymph node, IL-25-treated, experimental repeat 2, mRNA (GEX)

description:
Library name: LN_2_GEX
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_B_h1.h5
AK54_mesLN_B_h2.h5


title: Rhesus Macaque, Putamen, rep 7

status: Public on Mar 27 2026

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

description: Library name: Macaque_put_7

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v6.0.0)
Gene annotation files of non-human primates were generated using Liftoff tool (v1) using the human gene annotation file as reference. Then the genome files were generated using "CellRanger mkref" using the genome fasta files given below with the newly generated gene anniotation files for these species.
The “mkfastq” command was used to generate FASTQ files and the "CellRanger count" command was used to generate raw gene-cell expression matrices.
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Data were filtered, normalized, integrated, clustered, annotated, and visualized using a Seurat v3 pipeline
Assembly: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10), Marmoset: calJac3, Bat:GCF_004126475.2_mPhyDis1.pri.v3, Mouse: mm10, Ferret: GCF_011764305.1_ASM1176430v1.1
Supplementary files format and content: barcodes.tsv.gz' contains cell barcodes, 'features.tsv.gz' containts gene symbols, 'matrix.mtx.gz' contains raw counts. 'meta.tsv.gz' contains the meta data.
Supplementary files format and content: In addition to raw data generated in-house, publicly available raw data for mouse and ferrets from publications were used to process the data for this project. Processed data is also included with this dataset.

molecule: nuclear RNA

organism: Macaca mulatta

source_name: Putamen

extract_protocol:
Nuclei for snRNA-seq were isolated from bat putamen and caudate brain tissue. Briefly, the tissue was homogenized in 500 µL of ice-cold Nuclei EZ lysis buffer (EZ PREP NUC-101, Sigma) using a pre-chilled glass Dounce homogenizer. Debris was removed via density gradient centrifugation using Nuclei PURE 2 M sucrose cushion solution and Nuclei PURE sucrose cushion buffer (Nuclei PURE prep isolation kit, no. NUC201-1KT, Sigma Aldrich). These two solutions were mixed in a 9:1 ratio, and 500 µL of the sucrose solution was added to a 2-ml Eppendorf tube. The homogenized nuclei suspension was mixed with 900 µL of sucrose cushion solution by pipetting 10 times, resulting in a 1,400 µL volume, which was carefully layered over the sucrose buffer without mixing. The samples were centrifuged at 13,000 x g for 45 min at 4 °C, and all but 100 µL of supernatant was discarded. Nuclei were resuspended in 300 µL of nucleus suspension buffer (NSB), consisting of 1× PBS, 2% BSA (no. AM2618, Thermo Fisher Scientific), and 0.4 U µL −1 RNAse inhibitor (no. AM2694, Thermo Fisher Scientific). Samples were then centrifuged at 550 x g for 5 min at 4 °C, and all but 50 µL of supernatant was discarded. The nuclear pellet was resuspended in NSB and filtered through a 40-μm Flowmi cell strainer (Bel-Art Products, #H13680-0040) into a new tube. The nuclei concentration was measured using Hoechst and decreased to 1,000 nuclei per µL with NSB if necessary. Cellular nuclei for snRNA-seq were isolated from the putamen and caudate nuclei of human, chimpanzee, and rhesus macaque tissues. Briefly, the tissue was homogenized in 750 µL of ice-cold NP40 lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Nonidet P40 Substitute, 1 mM DTT, 0.2 U/µL RNAse inhibitor) using a pre-chilled glass Dounce homogenizer. An additional 750 µL of ice-cold NP40 lysis buffer was added, and the mixture was pipette-mixed during a 5-minute incubation on ice. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, resuspended in 1 mL of ice-cold lysis buffer, and incubated on ice for 5 minutes with gentle pipette mixing throughout. The nuclei were then centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. Next, 500 µL of nucleus suspension buffer (NSB) containing 1× PBS, 1% Ultrapure BSA (no. AM2618, Thermo Fisher Scientific), and 0.2 U/µL RNAse inhibitor (no. AM2694, Thermo Fisher Scientific) was added, and the sample was incubated for 5 minutes on ice without mixing. The pellet was resuspended, centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. The nuclei were then resuspended in 500 µL of NSB and filtered through a 70-μm Flowmi cell strainer (no. H13680-0070, Bel-Art) into a 1.5 mL tube.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 (10x Genomics) kit, following the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: sample id

tag: age

tag: Sex

value: female

value: Putamen


title: Rhesus Macaque, Putamen, rep 4

description: Library name: Macaque_put_4

value: male


title: Jurkat, BCL11B-dTAG, dTAGV-1, rep1, ATAC

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Library name: ATAC_Jurkat_BCL11BdTAG_dTAG_rep1

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values

organism: Homo sapiens

source_name: Jurkat

growth_protocol: CD34+ HSPCs were expanded in Stemspan media supplemented with 1X penicillin-streptomycin-glutamine, 100ng/mL SCF, TPO, IL-6 and FLT3-L, and 1 µM stemregenin-1. Jurkat cells were cultured in RPMI-1640 supplemented with 1X penicillin-streptomycin-glutamine and 10% FBS.

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

treatment_protocol: Cells were treated with 500nM dTAGV-1 or an equivalent volume of DMSO(1ul/mL media) for 6 hours and then immediately harvested for downstream processing.

value: Jurkat

value: T cell acute lymphoblastic leukemia

tag: genetic modifiction

value: BCL11B-dTAG (CRISPR knockin)


title: mesenteric lymph node, IL-25-treated, experimental repeat 1, CITE-seq (ADT)

description:
Library name: LN_1_ADT
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_A_h1.h5
AK54_mesLN_A_h2.h5


title: Jurkat, BCL11B-dTAG, DMSO, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_DMSO_rep1

value: DMSO


title: mesenteric lymph node, IL-25-treated, experimental repeat 2, hashtags (HTO)

description:
Library name: LN_2_HTO
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_B_h1.h5
AK54_mesLN_B_h2.h5


title: Rhesus Macaque, Putamen, rep 5

description: Library name: Macaque_put_5


title: Jurkat, BCL11B-dTAG, DMSO, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_DMSO_rep2


title: Jurkat, BCL11B-dTAG, dTAGV-1, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_dTAG_rep2


title: Rhesus Macaque, Putamen, rep 6

description: Library name: Macaque_put_6


title: Rhesus Macaque, Putamen, rep 2

description: Library name: Macaque_put_2


title: Rhesus Macaque, Putamen, rep 3

description: Library name: Macaque_put_3


title: mesenteric lymph node, IL-25-treated, experimental repeat 2, CITE-seq (ADT)

description:
Library name: LN_2_ADT
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_B_h1.h5
AK54_mesLN_B_h2.h5


title: Jurkat, BCL11B-WT, dTAGV-1, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_dTAG_rep2

value: WT


title: Rhesus Macaque, Putamen, rep 1

description: Library name: Macaque_put_1


title: Jurkat, BCL11B-WT, dTAGV-1, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_dTAG_rep1


title: Jurkat, BCL11B-WT, DMSO, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_DMSO_rep2


title: Rhesus Macaque, Caudate Nucleus, rep 3

description: Library name: Macaque_caud_3

source_name: Caudate Nucleus

value: Caudate Nucleus


title: Jurkat, BCL11B-WT, DMSO, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_DMSO_rep1


title: CD34, BCL11B-dTAG, dTAGV-1, rep1, ATAC

description: Library name: CD34_BCL11BdTAG_dTAG_rep1

source_name: Cord Blood

value: Cord Blood

value: CD34+ HSPC


title: CD34, BCL11B-dTAG, dTAGV-1, rep2, ATAC

description: Library name: CD34_BCL11BdTAG_dTAG_rep2


title: Rhesus Macaque, Caudate Nucleus, rep 2

description: Library name: Macaque_caud_2


title: Rhesus Macaque, Caudate Nucleus, rep 1

description: Library name: Macaque_caud_1


title: lung, IL-25-treated, experimental repeat 1, hashtags (HTO)

description:
Library name: Lung_1_HTO
sorted Yarg-low iILC2s from the lung, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_Lung_A_h1.h5
AK54_Lung_A_h2.h5

value: lung

value: Arg1-YFP reporter

value: HTO


title: mesenteric lymph node, IL-25-treated, experimental repeat 1, hashtags (HTO)

description:
Library name: LN_1_HTO
sorted Yarg-low iILC2s from the mesenteric lymph node, representative of the donor population that was transferred into recipient mice
2 biological samples hashed and pooled. h1 = HTO_A0301 = "hashtag 1"; h2 = HTO_A0302 = "hashtag 2"
AK54_mesLN_A_h1.h5
AK54_mesLN_A_h2.h5


title: CD34, BCL11B-dTAG, DMSO, rep1, ATAC

description: Library name: CD34_BCL11BdTAG_DMSO_rep1


title: CD34, empty vector, DMSO, rep1, ATAC

description: Library name: CD34_Empty_DMSO_rep1

value: Empty vector


title: CD34, empty vector, dTAGV-1, rep2, ATAC

description: Library name: CD34_Empty_dTAG_rep2


title: CD34, BCL11B-dTAG, DMSO, rep2, ATAC

description: Library name: CD34_BCL11BdTAG_DMSO_rep2


title: CD34, BCL11B, rep2, ATAC

description: Library name: CD34_BCL11B_rep2


title: CD34, empty vector, rep2, ATAC

description: Library name: CD34_Empty_rep2


title: CD34, BCL11B-dTAG, RUNX1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_dTAG_rep2

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: CUT&Run

tag: antibody


title: Rhesus Macaque, Caudate Nucleus, rep 4

description: Library name: Macaque_caud_4


title: CD34, empty vector, rep1, ATAC

description: Library name: CD34_Empty_rep1


title: Bat, Putamen, rep 4

description: Library name: Bat_put_4

organism: Phyllostomus discolor


title: CD34, empty vector, dTAGV-1, rep1, ATAC

description: Library name: CD34_Empty_dTAG_rep1


title: CD34, BCL11B-dTAG, RUNX1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_dTAG_rep1


title: CD34-018, empty vector, RUNX1

description:
Library name: CUTRUN_CD34_018_Empty_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: CD34, BCL11B-dTAG, RUNX1, DMSO, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_DMSO_rep2


title: Bat, Putamen, rep 3

description: Library name: Bat_put_3


title: Bat, Putamen, rep 2

description: Library name: Bat_put_2


title: Bat, Caudate Nucleus, rep 4

description: Library name: Bat_caud_4


title: Bat, Putamen, rep 1

description: Library name: Bat_put_1


title: CD34, BCL11B-dTAG, RUNX1, DMSO, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_DMSO_rep1


title: CD34, empty vector, RUNX1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_dTAG_rep2


title: Bat, Caudate Nucleus, rep 3

description: Library name: Bat_caud_3


title: CD34, empty vector, RUNX1, DMSO, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_DMSO_rep2


title: Bat, Caudate Nucleus, rep 1

description: Library name: Bat_caud_1


title: CD34, empty vector, RUNX1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_dTAG_rep1


title: CD34, empty vector, RUNX1, DMSO, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_DMSO_rep1


title: CD34, empty vector, RUNX1, merged

description: Library name: CUTRUN_CD34_Empty_RUNX1_merge


title: CD34, BCL11B-dTAG, RUNX1, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_rep2


title: CD34, BCL11B-dTAG, RUNX1, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_rep1


title: CD34, BCL11B-dTAG, HA, merged

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_merge

value: HA (CST3724S)


title: CD34, BCL11B-dTAG, RUNX1, merged

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_merge


title: CD34, empty vector, RUNX1, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_rep2


title: CD34, BCL11B-dTAG, IgG

description: Library name: CUTRUN_CD34_BCL11BdTAG_IgG

value: IgG (Epicypher)


title: CD34, empty vector, RUNX1, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_rep1


title: Bat, Caudate Nucleus, rep 2

description: Library name: Bat_caud_2


title: CD34, empty vector, HA, merged

description: Library name: CUTRUN_CD34_Empty_HA_merge


title: CD34, empty vector, HA, rep2

description: Library name: CUTRUN_CD34_Empty_HA_rep2


title: CD34, empty vector, HA, rep1

description: Library name: CUTRUN_CD34_Empty_HA_rep1


title: CD34, BCL11B-dTAG, HA, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_rep1


title: CD34, BCL11B-dTAG, HA, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_rep2


title: CD34, BCL11B, rep1, ATAC

description: Library name: CD34_BCL11B_rep1


title: Chimpanzee, Putamen, rep 5

description: Library name: Chimp_put_5

organism: Pan troglodytes

value: female


title: Chimpanzee, Putamen, rep 3

description: Library name: Chimp_put_3

value: Putamen


title: Chimpanzee, Putamen, rep 6

description: Library name: Chimp_put_6

value: male


title: Chimpanzee, Putamen, rep 1

description: Library name: Chimp_put_1


title: CD34, empty vector, IgG

description: Library name: CUTRUN_CD34_Empty_IgG


title: CD34, BCL11B-dTAG, dTAGV-1, rep3, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0249
TPM_CD34_017.txt


title: CD34, BCL11B-dTAG, dTAGV-1, rep1, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0615
TPM_CD34_017.txt


title: Chimpanzee, Putamen, rep 4

description: Library name: Chimp_put_4


title: Chimpanzee, Caudate Nucleus, rep 3

description: Library name: Chimp_caud_3


title: Chimpanzee, Caudate Nucleus, rep 2

description: Library name: Chimp_caud_2


title: Chimpanzee, Putamen, rep 2

description: Library name: Chimp_put_2


title: CD34, empty vector, dTAGV-1, rep3, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0249
TPM_CD34_017.txt


title: CD34, BCL11B-dTAG, DMSO, rep1, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0615
TPM_CD34_017.txt


title: CD34, BCL11B-dTAG, dTAGV-1, rep2, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_dTAG_0205
TPM_CD34_017.txt


title: Chimpanzee, Caudate Nucleus, rep 4

description: Library name: Chimp_caud_4


title: CD34, BCL11B-dTAG, DMSO, rep3, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0249
TPM_CD34_017.txt


title: CD34, BCL11B-dTAG, DMSO, rep2, RNA

description:
Library name: RNAseq_CD34_BCL11BdTAG_DMSO_0205
TPM_CD34_017.txt


title: CD34, empty vector, DMSO, rep2, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0205
TPM_CD34_017.txt


title: CD34, empty vector, dTAGV-1, rep2, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0205
TPM_CD34_017.txt


title: CD34, empty vector, DMSO, rep3, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0249
TPM_CD34_017.txt


title: CD34, empty vector, dTAGV-1, rep1, RNA

description:
Library name: RNAseq_CD34_Empty_dTAG_0615
TPM_CD34_017.txt


title: Chimpanzee, Caudate Nucleus, rep 1

description: Library name: Chimp_caud_1


title: CD34, empty vector, DMSO, rep1, RNA

description:
Library name: RNAseq_CD34_Empty_DMSO_0615
TPM_CD34_017.txt


title: Jurkat, BCL11B-dTAG, HA

description: Library name: CUTRUN_Jurkat_BCL11BdTAG_HA

value: Jurkat


title: Jurkat, BCL11B-dTAG, IgG

description: Library name: CUTRUN_Jurkat_BCL11BdTAG_IgG

value: T cell acute lymphoblastic leukemia


title: CD34-016, empty vector, BRG1, DMSO, rep1

description: Library name: CUTRUN_CD34_016_Empty_DMSO_BRG1_rep1

value: BRG1 (CSTD1Q7F)


title: CD34-016, BCL11B-dTAG, BRG1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_dTAG_BRG1_rep1


title: CD34-016, BCL11B-dTAG, BRG1, DMSO, rep1

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_DMSO_BRG1_rep1

value: DMSO


title: CD34-016, empty vector, BRG1, DMSO, rep2

description: Library name: CUTRUN_CD34_016_Empty_DMSO_BRG1_rep2


title: CD34-016, BCL11B-dTAG, BRG1, DMSO, rep2

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_DMSO_BRG1_rep2


title: CD34-018, BCL11B-dTAG, RUNX1

description:
Library name: CUTRUN_CD34_018_BCL11BdTAG_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: CD34-016, empty vector, BRG1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_016_Empty_dTAG_BRG1_rep1


title: CD34-016, BCL11B-dTAG, IgG

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_IgG


title: CD34-016, empty vector, IgG

description: Library name: CUTRUN_CD34_016_Empty_IgG


title: CD34-016, BCL11B-dTAG, BRG1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_016_BCL11BdTAG_dTAG_BRG1_rep2


title: CD34-018, BCL11B-dTAG, IgG

description:
Library name: CUTRUN_CD34_018_BCL11BdTAG_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: CD34-016, empty vector, BRG1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_016_Empty_dTAG_BRG1_rep2


title: CD34-018, empty vector, IgG

description:
Library name: CUTRUN_CD34_018_Empty_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: CD34-018, BCL11B, IgG

description:
Library name: CUTRUN_CD34_018_BCL11B_IgG.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: Human, Putamen, rep 7

description: Library name: Human_put_7


title: CD34-018, BCL11B, RUNX1

description:
Library name: CUTRUN_CD34_018_BCL11B_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG


title: Human, Putamen, rep 5

description: Library name: Human_put_5


title: Human, Putamen, rep 4

description: Library name: Human_put_4


title: Human, Caudate Nucleus, rep 6

description: Library name: Human_caud_6


title: Human, Putamen, rep 2

description: Library name: Human_put_2


title: Human, Putamen, rep 1

description: Library name: Human_put_1


title: CD34, empty vector, DMSO, rep2, ATAC

description: Library name: CD34_Empty_DMSO_rep2


title: Human, Putamen, rep 6

description: Library name: Human_put_6


title: Human, Putamen, rep 3

description: Library name: Human_put_3


title: Human, Caudate Nucleus, rep 4

description: Library name: Human_caud_4


title: Human, Caudate Nucleus, rep 5

description: Library name: Human_caud_5


title: Human, Caudate Nucleus, rep 2

description: Library name: Human_caud_2


title: Jurkat, BCL11BdTAG, dTAGV-1, rep1, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_dTAGV-1_rep1

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: BRU-Seq

value: BCL11B-dTAG (CRISPR knockin)


title: 23366-64_ATAC

status: Public on Mar 26 2026

city: Ames

first: Roger

last: Wise

state: IA

address: Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, 1344 Advanced Teaching & Research Bldg., 2213 Pammel Dr.

department: CICGRU

institute: USDA/ARS

description:
Library name: 23366-64_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI

data_processing:
The nf-core/atacseq pipeline (https://nf-co.re/atacseq/2.1.2/) was used to process ATAC-Seq data (Ewels et al., 2020). Following the initial analysis with the nf-core/atacseq pipeline, further explorations into the data were carried out using customized bioinformatics tools including differential analysis and motif analysis. First, FastQC (Andrews, 2010) was used to produce quality metrics. Then adapter trimming was performed with Trim Galore, a comprehensive wrapper combining Cutadapt and FastQC, for the refinement of FastQ files (Andrews, 2010; Martin, 2011). We used default settings to identify and remove adapter sequences to streamline preprocessing steps without manual intervention.
Hisat2 was used to align sequencing data (Kim et al., 2015). Trimmed ATAC-Seq reads were aligned against the MorexV3 reference genome with the addition of Bln1 (Bln1 was not annotated in the original MorexV3 release) (Mascher et al., 2021). The output was transmitted into Samtools (Li and Durbin, 2009), which was then converted into a compressed BAM file, filtering out secondary alignments, and leveraging multiple threads for efficiency. After alignment, reads were filtered using a combination of SAMtools, BEDTools, BAMTools, and Pysam (https://github.com/pysam-developers/pysam) to ensure high-quality alignments for downstream analysis (Li and Durbin, 2009; Quinlan and Hall, 2010; Barnett et al., 2011). SAMtools and BEDTools were used to remove reads mapping to blacklisted genomic regions, as well as reads marked as duplicates, non-primary alignments, unmapped reads, and those mapping to multiple genomic locations. BAMTools handled the exclusion of reads with excessive mismatches (more than four), soft-clipped alignments, large insert sizes (>2 kb), and provided additional quality control. Pysam was employed to filter out inter-chromosomal paired-end reads, those with improper FR orientation, and to remove both reads from any pair where a single read failed the criteria.
MACS2 was applied to identify regions with narrow or broad peaks (Zhang et al., 2008). Filtered BAM files were then converted into BigWig format using deepTools (Ramírez et al., 2014), employing Counts Per Million (CPM) as the default normalization method to generate genome wide accessibility profiles suitable for comparative analyses and downstream bioinformatics processing. Peak regions were annotated relative to the MorexV3 reference genome supplemented with the Bln1 sequence (Mascher et al., 2021). Annotation of peak coordinates was performed to enable assignment of genomic features such as promoters, UTRs, exons, introns, and intergenic regions.
After obtaining the count matrix where each row is a consensus peak region and each column is a sample, we implemented a differential analysis to compute statistically significant differential peaks between pairwise comparisons through DESeq2 (Love et al., 2014). A minimal pre-filtering step was performed to keep only rows that had at least 10 reads total. After differential tests were been applied to each peak, p-values were calculated and adjusted to control false positives via  multiple testing. This filtering threshold was automatically determined to maximize detection power (i.e., maximize the number of differential peaks detected) at a specified false discovery rate (FDR). Tables were generated to report the peak annotation, and statistics and p adjusted and fold change for each pairwise comparison.
Assembly: Barley (Mascher 2021) and Blumeria (Ensembl Fungi Assembly EF 2) (Spanu 2018).
Supplementary files format and content: Aligned Next-Generation Sequencing reads in bigWig format
Supplementary files format and content: ATAC-seq peak files provide genomic coordinates where Tn5 transposase inserted adapters into open, accessible chromatin

molecule: other

organism: Hordeum vulgare

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: The wild-type progenitor, CI 16151 (Mla6, Bln1), was developed by the introgression of Mla6 into the Manchuria background (Moseman 1972) [10.2135/cropsci1972.0011183X001200050038x] and maintained by single seed descent. CI 16151 derived mutants [m18982 (mla6, Bln1); m19089 (Mla6, bln1); m19028 (mla6, bln1)] were generated via fast-neutrons (4 Gy Nf) as described in Meng et al. (2009) [10.1104/pp.108.129031] and Xi et al. (2009) [https://doi.org/10.1105/tpc.109.066167] and further characterized by  Chapman et al. 2021 [10.1093/genetics/iyaa026] and Velásquez-Zapata et al. (2024) [https://doi.org/10.1016/j.isci.2024.111013]. Seven-day old barley (Hordeum vulgare) first leaves were grown in 20 × 30-cm trays using sterilized potting mix (Sunshine Mix #1, Sungrow) in a climate-controlled greenhouse (16 h supplemental light, 20-22 C).

extract_protocol:
Nuclei were prepared by REquest Genomics (Athens, GA, USA). Barley tissue was chopped on ice using a razor blade for ~2 minutes in 600 μL of pre-chilled Nuclei Isolation Buffer (NIB) [https://doi.org/10.1186/1746-4811-9-31]. The chopped tissue was filtered through a 40-μm cell strainer and then subjected to centrifugation at 500 rcf for 5 minutes at 4C. The supernatant was removed and the pellet was resuspended in 500 μL of NIB. The sample was filtered again using a 20-μm cell strainer and then loaded onto the surface of 1 mL of a 35% Percoll buffer, prepared by mixing 35% Percoll with 65% NIB wash buffer. The nuclei centrifuged at 500 rcf for 10 minutes at 4C. The supernatant was carefully removed, and the pellets were washed in 100 μL of 1X TAPS buffer (5X TAPS buffer:  50mM TAPS-NaOH, pH8.0; 25mM MgCl2) [https://doi.org/10.1093/nar/gkw1179].
ATAC-seq libraries were prepared by REquest Genomics (Athens, GA, USA). Nuclei were reconstituted in 30 μL of 2.5X TAPS buffer. A total of 5 μL of nuclei were diluted tenfold and stained with DAPI (Sigma Cat. D9542) to evaluate the quality and abundance using a hemocytometer. A total of 50,000 nuclei were use for library preparation. The Tn5 assembly and library preparation procedures were conducted following previously established methods [https://doi.org/10.1093/nar/gkw1179].

treatment_protocol: Trays were blocked by biological replicate and plant genotype with seedling rows randomly assigned to one of four harvest timepoints (0, 16, 20, and 32 HAI). First leaf seedlings were inoculated with Blumeria hordei (Bh) isolate 5874 (AVRa6) and immediately transferred to a growth chamber (16 h light / 8 dark, 18 C). One gram of pooled tissue was collected for each timepoint and flash frozen in liquid nitrogen. Four biological replicates were collected for each genotype / timepoint combination; two replicates on August 25/26, 2023 and two replicates on September 29/30, 2023 and processed for ATAC-Seq protocols.

value: Barley infected first leaf (PO:0007094)

tag: plant genotype

tag: fungal isolate

value: Bh isolate 5874 (AVRa6)

tag: time point

value: 32 HAI

tag: replication

value: Rep # 4


title: Jurkat, BCL11BdTAG, DMSO, rep2, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_DMSO_rep2

tag: cell type


title: Jurkat, BCL11BdTAG, DMSO, rep1, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_DMSO_rep1


title: 23366-61_ATAC

description:
Library name: 23366-61_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

tag: tissue

value: m19089 (resistant bln1 mutant)

value: 16 HAI


title: 23366-62_ATAC

description:
Library name: 23366-62_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI

value: CI 16151 (resistant progenitor)


title: 23366-57_ATAC

description:
Library name: 23366-57_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI

value: m18982 (susceptible mla6 mutant)

value: 0 HAI


title: 23366-63_ATAC

description:
Library name: 23366-63_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI

value: 20 HAI


title: 23366-52_ATAC

description:
Library name: 23366-52_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: 23366-58_ATAC

description:
Library name: 23366-58_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI


title: 23366-59_ATAC

description:
Library name: 23366-59_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI


title: Jurkat, BCL11BdTAG, dTAGV-1, rep2, RNA

description: Library name: BRUseq_Jurkat_BCL11BdTAG_dTAGV-1_rep2

tag: genotype


title: Human, Caudate Nucleus, rep 1

description: Library name: Human_caud_1

value: Caudate Nucleus


title: Human, Caudate Nucleus, rep 3

description: Library name: Human_caud_3

value: male


title: 23366-60_ATAC

description:
Library name: 23366-60_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI


title: 23366-54_ATAC

description:
Library name: 23366-54_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI


title: 23366-56_ATAC

description:
Library name: 23366-56_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: 23366-47_ATAC

description:
Library name: 23366-47_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI

value: Rep # 3


title: 23366-48_ATAC

description:
Library name: 23366-48_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI


title: 23366-53_ATAC

description:
Library name: 23366-53_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI


title: 23366-51_ATAC

description:
Library name: 23366-51_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI


title: 23366-49_ATAC

description:
Library name: 23366-49_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI


title: 23366-55_ATAC

description:
Library name: 23366-55_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI


title: 23366-43_ATAC

description:
Library name: 23366-43_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI


title: 23366-40_ATAC

description:
Library name: 23366-40_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: 23366-46_ATAC

description:
Library name: 23366-46_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI


title: 23366-45_ATAC

description:
Library name: 23366-45_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI


title: 23366-50_ATAC

description:
Library name: 23366-50_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI


title: 23366-44_ATAC

description:
Library name: 23366-44_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI


title: 23366-34_ATAC

description:
Library name: 23366-34_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI


title: 23366-32_ATAC

description:
Library name: 23366-32_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: Rep # 2


title: 23366-38_ATAC

description:
Library name: 23366-38_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI


title: 23366-28_ATAC

description:
Library name: 23366-28_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: 23366-33_ATAC

description:
Library name: 23366-33_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI


title: 23366-35_ATAC

description:
Library name: 23366-35_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI


title: 23366-42_ATAC

description:
Library name: 23366-42_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI


title: 23366-36_ATAC

description:
Library name: 23366-36_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI


title: 23366-41_ATAC

description:
Library name: 23366-41_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI


title: 23366-31_ATAC

description:
Library name: 23366-31_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI


title: 23366-30_ATAC

description:
Library name: 23366-30_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI


title: 23366-37_ATAC

description:
Library name: 23366-37_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI


title: 23366-25_ATAC

description:
Library name: 23366-25_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI


title: 23366-26_ATAC

description:
Library name: 23366-26_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI


title: 23366-39_ATAC

description:
Library name: 23366-39_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: 23366-21_ATAC

description:
Library name: 23366-21_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI


title: 23366-19_ATAC

description:
Library name: 23366-19_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI


title: 23366-16_ATAC

description:
Library name: 23366-16_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 16 HAI

value: Rep # 1


title: 23366-22_ATAC

description:
Library name: 23366-22_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI


title: 23366-27_ATAC

description:
Library name: 23366-27_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI


title: 23366-29_ATAC

description:
Library name: 23366-29_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: 23366-14_ATAC

description:
Library name: 23366-14_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI


title: 23366-11_ATAC

description:
Library name: 23366-11_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI


title: 23366-24_ATAC

description:
Library name: 23366-24_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI


title: 23366-23_ATAC

description:
Library name: 23366-23_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 20 HAI


title: 23366-13_ATAC

description:
Library name: 23366-13_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI


title: 23366-17_ATAC

description:
Library name: 23366-17_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 0 HAI


title: 23366-15_ATAC

description:
Library name: 23366-15_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 20 HAI


title: 23366-07_ATAC

description:
Library name: 23366-07_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 16 HAI


title: 23366-20_ATAC

description:
Library name: 23366-20_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI


title: 23366-18_ATAC

description:
Library name: 23366-18_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 16 HAI


title: 23366-09_ATAC

description:
Library name: 23366-09_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 32 HAI


title: 23366-10_ATAC

description:
Library name: 23366-10_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 0 HAI


title: 23366-08_ATAC

description:
Library name: 23366-08_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 20 HAI


title: 23366-02_ATAC

description:
Library name: 23366-02_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 16 HAI


title: 23366-03_ATAC

description:
Library name: 23366-03_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 0 HAI


title: 23366-12_ATAC

description:
Library name: 23366-12_ATAC
Barley infected first leaf (PO:0007094) of m19028 (susceptible mla6 + bln1 double mutant) at 32 HAI


title: 23366-06_ATAC

description:
Library name: 23366-06_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 32 HAI


title: 23366-01_ATAC

description:
Library name: 23366-01_ATAC
Barley infected first leaf (PO:0007094) of m18982 (susceptible mla6 mutant) at 20 HAI


title: 23366-04_ATAC

description:
Library name: 23366-04_ATAC
Barley infected first leaf (PO:0007094) of CI 16151 (resistant progenitor) at 32 HAI


title: mCherry+SOCS1-24h-rep2

status: Public on Mar 25 2026

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Science Research

institute: Guangzhou National Laboratory

description: Library name: mChe+SOCS1-24h-rep2

data_processing:
Raw sequencing reads were first subjected to basic quality control including removal of potential sequencing adapters, and poor quality bases or reads using TrimGalore (v0.6.10). Then, clean reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.10b) with default arguments, and only uniquely mapped reads were retained. Reads quantification on the gene level was performed using featureCounts (v2.0.6). Genes with a minimal raw count of 10 and detected in at least three samples were retained. Differentially gene expression analysis was conducted using DESeq2 package (v1.40.2, p < 0.05 and fold change > 1.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: HUVEC

extract_protocol:
HUVECs were collected at 6h and 24h after IVT mRNA transfection. Then, total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
RNA-seq libraries were prepared according to the standard protocol of VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Cat# NR603).

treatment_protocol: We co-transfected 6μg mCherry mRNA with 1.2μg Luc, M, and SOCS1 mRNA into HUVECs, respectively.

value: HUVEC

tag: treatment


title: 23366-05_ATAC

description:
Library name: 23366-05_ATAC
Barley infected first leaf (PO:0007094) of m19089 (resistant bln1 mutant) at 0 HAI


title: mCherry+SOCS1-24h-rep3

description: Library name: mChe+SOCS1-24h-rep3


title: Alpha-beta  neurons,18 hours after pupa formation, rep 3

city: Rehovot

first: Oren

last: Schuldiner

address: 234 Herzl Street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: ab18F_3_S26

data_processing:
Two sequencing runs of RNA were combined, yielding a mean of 22.5 million reads (single-read sequencing) and a minimum of 10 million reads per sample. The reads were aligned with STAR (DOI: 10.1093/bioinformatics/bts635) v2.5.2 to the reference genome of Drosophila melanogaster (DM6, UCSC). Gene annotations were obtained from FlyBase.org (Dmel r6.46). Gene expression levels were quantified using STAR.
Assembly: DM6
Supplementary files format and content: excel file includes read counts and differential gene expression analysis

source_name: Brain

growth_protocol: All fly strains were reared under standard laboratory conditions at 25°C on molasses containing food. Males and females were chosen at random. Developmental stage is referred to in the relevant places while adult refers to 3-5 days post eclosion.

extract_protocol:
Brains were dissected a cold Ringer’s solution, incubated with collagenase/dispase mix at 29ºC, washed in dissociation solution, mechanically dissociated into single cells and transferred via 35um mesh. 1000 GFP+ positive cells were sorted directly into 100μl Pico-Pure RNA isolation kit extraction buffer followed by RNA extraction using the kit or stored in -80 for later use.
Libraries were prepared based on the smart-seq2 protocol (Picelli et al., 2014). Briefly, Reverse transcription was performed using Oligo-dT primers, followed by PCR.The amplified cDNA underwent library generation using Nextera XT (Illumina)

value: Brain

value: Alpha-beta neurons

value: 18 hours after pupa formation


title: Alpha-beta  neurons, 21 hours after pupa formation, rep3

description: Library name: ab21E_3_S27

value: 21 hours after pupa formation


title: Alpha-beta  neurons,27 hours after pupa formation, rep 3

description: Library name: ab27D_3_S29

value: 27 hours after pupa formation


title: Gamma neurons,18 hours after pupa formation,rep5

description: Library name: gamma18F_6_S32

value: Gamma neurons


title: Alpha-beta  neurons,30 hours after pupa formation,rep4

description: Library name: ab30F_6_S30

value: 30 hours after pupa formation


title: Alpha-beta neurons,Adult,rep3

description: Library name: ab_adult_J_3_S25

value: Adult


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 4

description: Library name: ab24F_5_S35

value: 24 hours after pupa formation


title: Alpha-beta  neurons, 24 hours after pupa formation, rep 5

description: Library name: ab24I_6_S28


title: mCherry+SOCS1-24h-rep1

description: Library name: mChe+SOCS1-24h-rep1


title: mCherry+SOCS1-6h-rep1

description: Library name: mChe+SOCS1-6h-rep1


title: mCherry+Mpro-24h-rep1

description: Library name: mChe+M-24h-rep1


title: mCherry+SOCS1-6h-rep2

description: Library name: mChe+SOCS1-6h-rep2


title: mCherry+SOCS1-6h-rep3

description: Library name: mChe+SOCS1-6h-rep3


title: mCherry+Luc-24h-rep2

description: Library name: mChe+Luc-24h-rep2


title: mCherry+Mpro-6h-rep2

description: Library name: mChe+M-6h-rep2


title: mCherry+Mpro-6h-rep1

description: Library name: mChe+M-6h-rep1


title: mCherry+Luc-6h-rep3

description: Library name: mChe+Luc-6h-rep3


title: mCherry+Luc-6h-rep2

description: Library name: mChe+Luc-6h-rep2


title: mCherry+Luc-6h-rep1

description: Library name: mChe+Luc-6h-rep1


title: mCherry+Mpro-24h-rep3

description: Library name: mChe+M-24h-rep3


title: mCherry-24h-rep2

description: Library name: mChe-24h-rep2


title: mCherry+Mpro-6h-rep3

description: Library name: mChe+M-6h-rep3


title: mCherry+Luc-24h-rep3

description: Library name: mChe+Luc-24h-rep3


title: mCherry+Mpro-24h-rep2

description: Library name: mChe+M-24h-rep2


title: mCherry-24h-rep3

description: Library name: mChe-24h-rep3


title: mCherry+Luc-24h-rep1

description: Library name: mChe+Luc-24h-rep1


title: mCherry-6h-rep2

description: Library name: mChe-6h-rep2


title: CT-6h-rep1

description: Library name: CT-6h-rep1


title: CT-6h-rep2

description: Library name: CT-6h-rep2


title: 2B_Donors 289, 292, 310, and 313 with DPI only

status: Public on Mar 18 2026

city: Brest

first: Marie

last: Frutoso

address: 9 rue Félix le Dantec

country: France

institute: LBAI, UMR1227

description: Library name: Cartridge_2_B

data_processing:
Fastq files were processed via the standard Rhapsody analysis pipeline (BD Biosciences) on Seven Bridges (www.sevenbridges.com). In brief, after read filtering, reads are aligned to a reference genome and annotated, barcodes and UMIs are counted, followed by determining putative cells. The final output (molecule per cell count matrix) was analysed in R using Seurat.
Assembly: GRCh38
Supplementary files format and content: A Seurat Object in RDS format combining all donors, tissues and cell types (data.integrated)
Supplementary files format and content: A Seurat Object in RDS format containing only NK cells, without chorioamnionitis donors and without cordblood (data.NK.pure)

source_name: mfPLAC (renamed DPI in the paper)

extract_protocol:
After thawing, cells from maternal blood, cordblood, DPI and decidua were stained with a cytometry panel and one specific Sample-Tag for multiplexing (BD Biosciences SMK).  Live, CD45+ immune cells were sorted (using the BD Symphony S6 cell sorter equipped with a 70um nozzle for batches 1 and 2 and the FACSAria III equiped with a 100um nozzle). For batches 1 and 2, Live CD45+ cells were enriched for ILC (CD45+CD19-CD14-CD3-CD127+CD34-), NK cells (CD45+CD19-CD14-CD3-CD127-NKp46+) and myeloid cells (CD45+CD3-CD19-NKp46-HLA-DR+). For batch 3 CD45+ were sorted without enrichment of specific cell type. After sorting, cells from all donors and tissues were pooled and stained with 56 oligo-proteins. Stained cells were then loaded on the BD Rhapsody cartridges (between 35 - 45,000 cells were loaded per cartridges).
Libraries were performed according to manufacturer's instructions (BD RhapsodyTM System, mRNA WTA, Abseq and Sample Tag library Preparation protocol). In brief, after sorting, single cells were stained with AbSeq antibodies, washed three times, pooled and counted and subsequently loaded onto a nano-well cartridge (BD Rhapsody), lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell Capture Beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent random priming extension and amplification using the human primer xtension mix and via PCR (10–11 cycles). PCR products were purified, and mRNA PCR products were separated from Sample-Tag and AbSeq. PCR products with double-sided size selection using SPRIselect magnetic beads (Beckman Coulter). mRNA and Sample Tag products were further amplified using PCR (10 cycles). PCR products were then purified using SPRIselect magnetic beads.Quality of PCR products was determined by using an Agilent 2200TapeStation with High Sensitivity D5000 ScreenTape (Agilent) in the Fred Hutch Genomics Shared Resource laboratory. The quantity of PCR products was determined by Qubit with Qubit dsDNA HS Assay (Q32851). Whole transcriptome mRNA product was diluted at less than 2 nM (8 pcr cycles), and the Sample Tag and AbSeq PCR products were diluted to 0.25 ng μl−1 to prepare final libraries. Final libraries were indexed using PCR (8 cycles for WTA and 7 cycles for SampleTag and AbSeq libraries). Index PCR products were purified using SPRIselect magnetic beads. Quality of all final libraries was assessed by using Agilent 2200 TapeStation with High Sensitivity D5000 ScreenTape and quantified using a Qubit Fluorometer using the Qubit dsDNA HS Kit (ThermoFisher). Final libraries were diluted to 3 nM and multiplexed for paired-end (100 bp) sequencing on a NovaSeq 6000 (Illumina) using S1 and S2 flow cells. For the gene expression library, we targeted 35,000 reads per cell, for the AbSeq library 22,000 reads per cell, and for the Sample-Tag libraries 2,000 reads per cell.

value: mfPLAC (renamed DPI in the paper)

tag: donor

value: PRI289 PRI313 PRI292 PRI310

tag: group

value: Healthy (PRI289 PRI313) and Chorioamniontis (PRI292 PRI310)

tag: annotation

value: PRI289_mfPLAC; PRI313_mfPLAC; PRI292_mfPLAC; PRI310_mfPLAC

tag: sample tag

value: PRI289_mfPLAC (SMK9); PRI313_mfPLAC (SMK10); PRI292_mfPLAC (SMK11); PRI310_mfPLAC (SMK12)