title: Zebra finch Gonadal culture timecourse, DIV8 replicate 1

description:
Library name: zT8_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 8 days in vitro


title: Zebra finch Gonadal culture timecourse, DIV7 replicate 1

status: Public on Jul 06 2026

type: SRA

city: New York

first: Matthew

middle: T

last: Biegler

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

description:
Library name: zT7_r1
ZF_Gonad_timecourse_fcCounts.csv

library_source: transcriptomic

data_processing:
Quality control analysis was performed using similar approaches in our previous study28. Briefly, raw sequencing data, was aligned to either the zebra finch, chicken, or mouse reference genome (depending on the sample) using CellRanger (v6.0.1). The DIV150 chicken dataset was also aligned to a concatenated chicken and mouse assembly for competitive mapping. Subsequent processing steps (quality controls and barcode trimming) were performed using R (v4.4.1) with soupX (v1.5.2), Seurat (v5.1.0), and DoubletFinder (v2.0.4).
For bulk RNA sequencing data,, gonadal and blood culture samples (see Table S11 from the associated study) were aligned to the bTaegut1.4.pri reference genome using HiSAT2 (v2.2.1) and analyzed with DESeq2 using a standard pipeline.
Assembly: Zebra Finch - bTaeGut1.4.pri: GCF_003957565.2 with custom GTF
Supplementary files format and content: ZF_Gonad_timecourse_fcCounts.csv contains assigned gene counts for all timecourse samples.

molecule: total RNA

organism: Taeniopygia guttata

source_name: primary cell culture

growth_protocol: Gonadal cultures from HH28 zebra finch and chicken embryos were generated as previously described9,27, incubated at 37°C and 5% CO2 in a Heracell VIOS 160i incubator (Thermo Scientific). Cell culture media recipes used are available in Table S16 of the associated manuscript.  For the primary culture pool, forty embryos (unsexed male and female) were pooled and dissociated at 37°C with 0.05% trypsin (zebra finch: 5min; chicken: 15min) and equally split across multiple wells of a 12-well plate (zebra finch = 8 wells; chicken = 12 wells). For the non-adherent fraction, the supernatant was collected from all wells after briefly swirling the plate and pelleted at 300xg for 5min. For the adherent cells, wells were washed twice with HBSS and dissociated with 0.05% trypsin for 5min, neutralized in PGC media, and pelleted at 300xg for 5min. For each fraction, half of the pellets were taken for DIV3 samples, while the remaining cells were resuspended in fresh PGC media and incubated in 4-6 wells until DIV6.

extract_protocol:
RNA was extracted from cell pellets using RNA micro kit (QIAGEN, Cat. # 74034), reverse transcribed using SuperScript Reverse Transcriptase II (Invitrogen, Cat. # 18064014), and PCR amplified for 16 cycles with KAPA Hi-Fi HotStart ReadyMix (KAPA Biosystems, Cat. #KK2601).
Bulk RNA Sequencing libraries were prepared using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, Cat. #E7805S) before being sent to Novogene Corporation, Inc. (Sacramento, CA, USA) for sequencing on an Illumina HiSeq 4000.

treatment_protocol: At designated time points, non-adherent cells were pelleted at 250xg for 3min.

tag: Sex

value: pooled male and female

tag: cell line

value: primary cell culture

tag: days in_vitro

value: 7 days in vitro

tag: cell type

value: embryonic gonadal cell cultures (HH28)

tag: batch

value: C


title: Zebra finch Gonadal culture timecourse, DIV9 replicate 1

description:
Library name: zT9_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 9 days in vitro


title: Zebra finch Gonadal culture timecourse, DIV6 replicate 1

description:
Library name: zT6_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 6 days in vitro


title: Mycosis fungoides patient 12 plaque skin lesion CosMx SMI

status: Public on Jul 07 2026

type: RNA

city: Seoul

first: Myoung Eun

last: Choi

address: Song-pa gu

country: South Korea

institute: Asan medical center

description: CosMx SMI profiling of MF plaque stage skin, patient 12

hyb_protocol: In situ hybridization was performed on FFPE sections according to the NanoString CosMx SMI protocol. Probe hybridization, ligation, and fluorescence imaging were performed on the CosMx SMI instrument.

scan_protocol: Fluorescence imaging was performed on the NanoString CosMx SMI instrument. Multiple fields of view (FOVs) were acquired per tissue section. Transcript detection and cell segmentation were performed using NanoString AtoMx software.

data_processing:
Raw transcript counts were processed using NanoString AtoMx software. Cell segmentation was performed using DAPI and morphology marker channels. Downstream analysis including quality control, normalization (SCTransform), dimensionality reduction, and cell type annotation was performed in R using Seurat v5. Cells passing QC filters (nCount_RNA > 0, qcFlagsRNACounts = Pass) were retained for analysis.
Raw transcript counts per cell per gene

organism: Homo sapiens

source_name: skin biopsy

label_protocol: RNA targets were detected using the NanoString CosMx 980-plex RNA panel with fluorescently labeled probes according to the manufacturer's protocol (NanoString Technologies).

growth_protocol: N/A - clinical biopsy specimens

extract_protocol: Skin punch biopsies from patients with mycosis fungoides were formalin-fixed and paraffin-embedded (FFPE). FFPE sections (5 um) were prepared for CosMx SMI profiling according to the NanoString CosMx SMI FFPE sample preparation protocol.

treatment_protocol: N/A - clinical biopsy specimens

tag: disease

value: mycosis fungoides

tag: tissue

value: skin

tag: disease stage

value: plaque

tag: patient id


title: scPerturb_YoungtdLN2

city: Boston

first: Alex Chang-Yu

last: Chen

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

description:
Library name: scPerturb_YoungtdLN2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped files include 10x format single cell gene expression matrices, including barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and protospacer_calls_per_cell.csv

organism: Mus musculus

source_name: B16-OVA Tumor

extract_protocol:
Fifteen days after tumor inoculation, ametrine⁺ CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were isolated from tumors and tumor-draining lymph nodes (tdLNs) of young and aged mice using a BD FACSAria™ Fusion sorter. Sorted cells from independent mice were pooled into two biological replicates per group, counted, and loaded onto a Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells per run. Libraries were prepared with the 10x Single Cell 5′ Reagent Kits v2 (Dual Index) and Feature Barcode technology for CRISPR screening, following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq X or NextSeq 1000/2000 system using 100-cycle kits with paired-end reads.
Library was performed according to the manufacter’s instructions (10x Single Cell 5′ Reagent Kits v2, CG00511 RevD, 10x Genomics).

value: tdLN, B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells


title: Zebra finch Gonadal culture timecourse, DIV5 replicate 1

description:
Library name: zT5_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 5 days in vitro


title: Zebra finch Gonadal culture timecourse, DIV4 replicate 1

description:
Library name: zT4_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 4 days in vitro


title: GBM8_ChIPseq_PPARD_rep1

first: Evgeny

last: Deforzh

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: Sample 12

library_source: genomic

data_processing:
Low-quality reads (MAPQ<=30) were filtered out.
The remaining reads were alignedusing Bowtie2 (v2.5.3) with default end-to-end sensitive parameters.
PCR duplicates were removed from the aligned BAM files using SAMtools (rmdup, v1.13.7).
aligned BAM files were converted to BigWig format using deepTools (v3.5.0) bamCoverage without additional scaling or normalization
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

growth_protocol: GBM8 were maintained as neurospheres in serum-free Neurobasal medium (Gibco) supplemented with: B-27 Plus and N-2 supplements (Gibco), 3 mM GlutaMAX (Gibco), 20 ng/mL recombinant human FGF2 and EGF (Sigma-Aldrich), 2 μg/mL heparin (Sigma-Aldrich), 50 units/mL penicillin/streptomycin (Gibco). Normal human astrocytes, immortalized via E6/E7 and hTERT expression (a generous gift from Dr. Yukihiko Sonoda), served as non-malignant controls. These cells were cultured in Astrocyte Medium (ScienCell, Cat# 1801) according to the manufacturer’s instructions.

extract_protocol:
DNA was recovered using the Monarch PCR and DNA Cell Cleanup Kit (NEB, #T1030L).
Library Preparation and Sequencing ChIP-seq libraries were constructed from purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, #E7546S).

treatment_protocol: Glioma stem cells (GSCs) and normal human astrocytes (NHAs) were seeded in 6-well plates and transfected with 500 ng of both vectors using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s protocol. NHA cells were treated with All trans retinoic acid (SigmaAldrich,  R2500-25MG) diluted in DMSO according to manufacturer's protocol. Cross-linked NHA cells were incubated with Proteinase K (Thermo Scientific, EO0491) for 48 hours

value: low-passage glioma-initiating stem-like cells

tag: genotype

value: WT


title: Zebra finch Gonadal culture timecourse, DIV3 replicate 1

description:
Library name: zT3_r1
ZF_Gonad_timecourse_fcCounts.csv

value: 3 days in vitro


title: Zebra finch Gonadal culture timecourse, DIV2 replicate 1

description:
Library name: zT2_r1
ZF_Gonad_timecourse_fcCounts.csv

value: pooled male and female

value: 2 days in vitro


title: RNA_L1KD-2

city: Hangzhou

first: Yu

last: Qian

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

country: China

institute: Zhejiang University

description: Library name: RNA_L1KD-2

data_processing:
Illumina bcl2fastq (version 2.0)  for basecalling.
The sequencing data were processed using Easy_Ribo for trimming for adaptor sequences, masking low-complexity or low-quality reads, and mapping to the GRCh38 whole genome
RPKM were calculated to quantify gene expression levels, and differential expression analysis was performed using DESeq2.
Assembly: GRCh38 (Homo sapiens)
Supplementary files format and content: Comma-Separated Values file include the RPKM representing gene expression levels for each transcript.

source_name: Colon

growth_protocol: All RKO cells were grown to 80-90% confluence in DMEM supplemented with 10% FBS in 6cm dishes.

extract_protocol:
Cells were lysed in TRIzol, followed by chloroform extraction and isopropanol precipitation, with 1/5 of the RNA used for RNA-seq and 4/5 for ribosome profiling (Ribo-seq).
The library was constructed using Small RNA Library Prep Set for Illumina (E7330S, NEB).

value: Colon

value: RKO

value: colorectal carcinoma cell


title: Zebra finch Gonadal culture timecourse, DIV1 replicate 1

description:
Library name: zT1_r1
ZF_Gonad_timecourse_fcCounts.csv

value: primary cell culture

value: 1 day in vitro

value: embryonic gonadal cell cultures (HH28)

value: C


title: RNA_CTL-2

description: Library name: RNA_CTL-2

value: CTL


title: Ribo_RPL22L1-2

description: Library name: Ribo_RPL22L1-2


title: Ribo_RPL22L1IP-2

description: Library name: Ribo_RPL22L1IP-2


title: Ribo_L1KD-2

description: Library name: Ribo_L1KD-2


title: Ribo_CTL-2

description: Library name: Ribo_CTL-2


title: hTSC CT27, shDNMT1_B, hTSC-EVT, Rep 3

city: Philadelphia

first: Sanam

last: Kavari

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
Library name: hTSC-EVT shDNMT1_B Rep 3
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_B_3

data_processing:
Reads were first trimmed of adaptor sequences and low-quality bases using the trim-galore package (v0.6.11)
Trimmed reads were then aligned to the hg38 human genome using HISAT2 (v2.2.1) and resulting .sam files were sorted and converted to .bam files using SAMtools (v1.16.1)
Reads were then summarized using the featureCounts function in the Rsubread package (v2.0.6)
Read counts were then filtered to remove genes with a read count of zero for all samples and normalized using edgeR (v4.4.2), limma (v3.62.2), and Glimma (v2.16.0)
Assembly: hg38
Supplementary files format and content: .csv with filtered read counts, normalized to counts per million

source_name: Placenta

growth_protocol: hTSCs were cultured in human TSC medium (TSCM), composed of a basal medium (DMEM/F12 supplemented with 1% ITS-X, 0.3% BSA, 0.5X penicillin-streptomycin, 0.2 mM L-ascorbic acid) supplemented with 5 μM A83-01, 2 μM CHIR99021, 25 ng/mL EGF, 2.5 μM Y27632, and 0.8 mM VPA. Cells were cultured at 37°C, 5% CO2, and ambient O2, and the medium was changed or cells were passagedevery 2 days.

extract_protocol:
Cell pellets were collected and shipped to Azenta Life Sciences for RNA extraction
Library preparation was performed by Azenta Life Sciences from >= 500 ng RNA per sample

treatment_protocol: Cells were transduced with lentivirus containing an shRNA targeting DNMT1 or a control, non-targeting shRNA. Two days after transduction, cells were selected in 1 ug/mL puromycin in hTSC media for 4 days. For undifferentiated conditions, cells were maintained in hTSC media with puromycin until 13 days post-transduction. For EVT differentiated conditions, selected cells were differentiated using an eight-day defined protocol (Okae, et al. 2018, Cell Stem Cell) with continued puromycin selection.

value: Placenta

value: hTSC CT27

value: human trophoblast stem cell

value: DNMT1 knockdown

tag: treatment

value: Differentiated hTSC-EVT


title: hTSC CT27, shDNMT1_B, hTSC-EVT, Rep 2

description:
Library name: hTSC-EVT shDNMT1_B Rep 2
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_B_2


title: hTSC CT27, shDNMT1_B, hTSC-EVT, Rep 1

description:
Library name: hTSC-EVT shDNMT1_B Rep 1
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_B_1


title: hTSC CT27, shDNMT1_A, hTSC-EVT, Rep 3

description:
Library name: hTSC-EVT shDNMT1_A Rep 3
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_A_3


title: hTSC CT27, shDNMT1_A, hTSC-EVT, Rep 2

description:
Library name: hTSC-EVT shDNMT1_A Rep 2
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_A_2


title: hTSC CT27, shDNMT1_A, hTSC-EVT, Rep 1

description:
Library name: hTSC-EVT shDNMT1_A Rep 1
column name in GEO_filtered_normalized_readcounts.csv: EVT_DNMT1_A_1


title: hTSC CT27, shControl, hTSC-EVT, Rep 3

description:
Library name: hTSC-EVT shControl Rep 3
column name in GEO_filtered_normalized_readcounts.csv: EVT_control_3

value: control


title: hTSC CT27, shControl, hTSC-EVT, Rep 2

description:
Library name: hTSC-EVT shControl Rep 2
column name in GEO_filtered_normalized_readcounts.csv: EVT_control_2


title: hTSC CT27, shControl, hTSC-EVT, Rep 1

description:
Library name: hTSC-EVT shControl Rep 1
column name in GEO_filtered_normalized_readcounts.csv: EVT_control_1


title: hTSC CT27, shDNMT1_B, hTSC, Rep 2

description:
Library name: hTSC shDNMT1_B Rep 2
column name in GEO_filtered_normalized_readcounts.csv: hTSC_DNMT1_B_2

value: Undifferentiated hTSC


title: hTSC CT27, shDNMT1_B, hTSC, Rep 1

description:
Library name: hTSC shDNMT1_B Rep 1
column name in GEO_filtered_normalized_readcounts.csv: hTSC_DNMT1_B_1


title: hTSC CT27, shDNMT1_A, hTSC, Rep 2

description:
Library name: hTSC shDNMT1_A Rep 2
column name in GEO_filtered_normalized_readcounts.csv: hTSC_DNMT1_A_2


title: hTSC CT27, shDNMT1_A, hTSC, Rep 1

description:
Library name: hTSC shDNMT1_A Rep 1
column name in GEO_filtered_normalized_readcounts.csv: hTSC_DNMT1_A_1


title: hTSC CT27, shControl, hTSC, Rep 2

description:
Library name: hTSC shControl Rep 2
column name in GEO_filtered_normalized_readcounts.csv: hTSC_control_2


title: hTSC CT27, shControl, hTSC, Rep 1

description:
Library name: hTSC shControl Rep 1
column name in GEO_filtered_normalized_readcounts.csv: hTSC_control_1


title: Erythroid cells, Control rep1, Day3

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description: Library name: ATAC_D3_rep1

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential atac peaks of were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The ATAC peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The day of CD34+ cell harvest was recorded as day 0. The cell culture procedure consisted of 3 phases. The basic culture medium consisted of Iscove's Modified Dulbecco's Medium (IMDM), 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human holo-transferrin, 3 IU/mL heparin and 10 μg/mL insulin. From day 0 to day 7, CD34+ cells were cultured at a concentration of 105/mL in the presence of 10 ng/mL stem cell factor (SCF), 1 ng/mL interleukin-3 (IL-3) and 3 IU/mL erythropoietin (EPO).  The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature.20,000 cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.03% Tween-20), and centrifuged at 500 g for 8 min at 4 °C. The supernatant was carefully removed, and the nuclei was resuspended with Tn5 transposase reaction mix (25 μl 2 × TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free water) (Illumina) at 37 °C for 30 min. Immediately after the transposition reaction, DNA was purified using a Qiagen MinElute kit. Libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China) under manufacturer’s instructions and were then sequenced on an Illumina HiSeq X Ten sequencer to an average read depth of 52 million pair-end reads per sample. The ATAC-seq experiment and library sequencing were performed by Frasergen Bioinformatics Co., Ltd, Wuhan, China.
ATAC libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China) under manufacturer’s instructions and were then sequenced on an Illumina HiSeq X Ten sequencer to an average read depth of 52 million pair-end reads per sample.

treatment_protocol: Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. After transfection with lentivirus for 5 days, we performed ATAC assay of  shLuciferase and shTAL1 erythroblasts.

value: Cord blood

value: Erythroid cells

value: Control


title: Erythroid cells, Control rep2, Day3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_D3_rep2


title: Erythroid cells, Control rep1, Day0

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_D0_rep1


title: Erythroid cells, Control rep2, Day0

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_D0_rep2


title: Erythroid cells, H3K27ac shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27ac_shTAL1_rep1

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-TAL1, BRG1, GATA1, H3K27ac and H3K9me3 antibodys, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. After transfection with lentivirus for 5 days, we performed CUT&Tag of shLuciferase and shTAL1 erythroblasts.


title: Erythroid cells, H3K27ac Control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27ac_Control_rep2


title: Erythroid cells, H3K27ac shTAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27ac_shTAL1_rep2


title: Erythroid cells, H3K9me3 shTAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K9me3_shTAL1_rep2


title: Erythroid cells, H3K9me3 shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K9me3_shTAL1_rep1


title: Erythroid cells, H3K27ac Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K27ac_Control_rep1


title: Erythroid cells, H3K9me3 Control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K9me3_Control_rep2


title: Erythroid cells, H3K9me3 Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_H3K9me3_Control_rep1


title: Erythroid cells, GATA1 shTAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_GATA1_shTAL1_rep2


title: PETCC2610, DOX+PeptideE, rep1

city: Wuhu

last: Du

address: No. 8, Yinhe Avenue, Fanchang Economic Development Zone, Fanchang District

institute: Nourse Centre for Pet Nutrition

description: Library name: DOX_taiE1

data_processing:
Raw sequencing reads (FASTQ format) were quality-controlled using FastQC (v0.11.9). Low-quality reads and adapter sequences were trimmed using fastp (v0.19.5) with default parameters.
Assembly: Felis catus reference genome assembly F.catus_Fca126_mat1.0 (GCF_018350175.1)
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing the gene expression count matrix for all six samples. Columns include gene ID, gene name, gene description, and raw read counts for each sample (DOX1, DOX2, DOX3, DOX_taiE1, DOX_taiE2, DOX_taiE3).

molecule: polyA RNA

organism: Felis catus

source_name: kidney

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (TIANGEN; Cat. No. DP424) according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated by agarose gel electrophoresis and Agilent 5300 (RIN > 6.5).
mRNA was enriched from total RNA using Oligo(dT)-coated magnetic beads. The enriched mRNA was fragmented into approximately 300 bp fragments using fragmentation buffer. First-strand cDNA was synthesized using random primers and reverse transcriptase, followed by second-strand cDNA synthesis to generate double-stranded cDNA. The cDNA products were end-repaired, A-tailed, and ligated with sequencing adaptors. The adaptor-ligated products were purified and size-selected, followed by PCR amplification to enrich the final library. Library quality was assessed, and sequencing was performed on the Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: kidney

value: PETCC 2610

value: DOX+PeptideE


title: Erythroid cells, GATA1 shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_GATA1_shTAL1_rep1


title: Erythroid cells, TAL1 PROTEC_BRG1 rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_PROTEC_BRG1_rep3


title: liver male control rep8

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: OCSPP

institute: US EPA

description: Library name: L_08

data_processing:
RNA-seq data quality was assessed using FASTQC (v0.12.1) and summarized with MultiQC (v1.28)
PCR duplicates were removed by deduplicating sequencing reads with UMI-tools (v1.1.5)
Low-quality bases were trimmed using Cutadapt (v4.9) and Trim Galore (v0.6.10)
The cleaned reads were then aligned to the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1) using STAR (v2.7.11b)
Quantification of transcript abundance was performed with Salmon (v1.10.3)
Assembly: the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcrit level generated by salmon  (*.gene_counts.tsv )
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcript level generated by salmon  (*.transcript_counts.tsv )

organism: Rattus norvegicus

source_name: liver

growth_protocol: Rats were fed a standard rodent chow

extract_protocol:
A 50% (v/v) solution of Antifoam A (cat. no. A5633; Sigma, St. Louis, MO) was prepared in propylene glycol (cat. no. W294004; Sigma St. Louis, MO). The solution was vortexed prior to use. Homogenization buffer was prepared by adding 10 µl of β-mercaptoethanol (cat no. 0482, VWR, Radnor, PA) and 60 µl antifoam solution per milliliter of Buffer RLT Plus (Qiagen, Germantown, MD).
Prior to homogenization, large tissue samples were broken into smaller pieces using a mortar and pestle cooled with liquid nitrogen (LN2). Several of the resulting pieces (each approximately 3–5 mm) were then pulverized together to produce the final sample. For homogenization, 400 µl of buffer was added to a 3 ml, flat-bottom polystyrene tube (Globe Scientific, Mahwah, NJ). The tube was placed into a CoolRack CF15 (Corning Inc., Corning, NY) cooled with LN2. A cooled 30 µl plastic scoop was used to transfer pulverized tissue to the tube. The target mass of tissue was 50 µg, although the actual mass varied due to the need to work quickly and differences in the sizes of the pulverized samples.
The tube was placed on ice, and 600 µl of ice-cold homogenization buffer was added to the sample. The sample was homogenized using a model 985-370 TissueTearor rotor-stator homogenizer with a 7 mm probe (BioSpec Products, Bartlesville, OK) until no remnants of intact tissue were visible. If the homogenate appeared significantly darker than other samples, suggesting an excess of tissue, additional buffer was added until the color of the sample was similar to that of the other samples. Homogenates were stored at -80 °C until used for RNA isolation. The homogenizer was rinsed between samples within a treatment by running it at the highest speed for 30 s in three changes of deionized water. Between treatments, the rotor and stator were disassembled and cleaned with a polyester test tube brush before rinsing in water.
For RNA isolation, homogenized samples were removed from the freezer and placed on ice to thaw. The samples were vortexed, and 100 µl of the homogenate was transferred to the well of a 96-well round bottom plate (Caplugs Evergreen, Buffalo, NY). RNA was isolated using the MagMAX-96 Total RNA Isolation Kit (Fisher Scientific, Hampton, NH) according to the manufacturer’s protocol, except for the substitution of RLT Plus buffer for the lysis/binding solution as described above.
Isolated RNA was quantified on a Synergy HTX plate reader using a Take3 microvolume plate (Agilent, Santa Clara, CA). The integrity of the RNA was analyzed on an Agilent TapeStation using RNA Screen Tapes and reagents (Agilent, Santa Clara, CA). Concentrations of samples ranged from 75 to 470 ng/µl. RNA integrity numbers (RIN) ranged from 8.0 to 10.0; nearly 90% of samples had a RIN higher than 9.0.
Isolated RNA was next used to prepare RNA-Seq libraries. Samples were blocked so that about eight samples of each tissue and treatment combination were included in one of two plates. RNA was normalized to 25 ng/uL with nuclease-free water (Ambion, USA). 250 ng total RNA (10 uL of normalized RNA) was input into mRNA purification with magnetic beads using a PolyA Selection Module (Lexogen, USA). Purified mRNA was then used directly in CORALL mRNA-Seq V2 library preparation with set A unique dual indexes (UDIs). Each batch was checked by qPCR to determine the appropriate number of PCR cycles for library amplification with Add-On PCR V2 kit (Lexogen, USA), SYBR Green (ThermoFisher, USA), and a QuantStudio 6 Flex real-time PCR instrument (ThermoFisher, USA). After final PCR amplification, libraries were quantified with Quant-iT PicoGreen (ThermoFisher, USA). The distribution of library size was checked by TapeStation D1000 assay (Agilent, USA). The average library size was 508 – 517 bp. Samples below 1 ng/uL were re-amplified.

value: liver

tag: strain

value: Sprague-Dawley

tag: developmental stage

value: adult

value: WT

value: Male-Vehicle Control

value: Batch 3


title: Erythroid cells, GATA1 Control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_GATA1_Control_rep2


title: Erythroid cells, GATA1 Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_GATA1_Control_rep1


title: Erythroid cells, TAL1 PROTEC_BRG1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_PROTEC_BRG1_rep2


title: Erythroid cells, TAL1 Control rep3, Day3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D3_rep3


title: Erythroid cells, TAL1 PROTEC_BRG1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_PROTEC_BRG1_rep1


title: Erythroid cells, TAL1 Control rep2, Day0

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D0_rep2


title: Erythroid cells, TAL1 Control rep2, Day3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D3_rep2


title: Erythroid cells, TAL1 Control rep1, Day3

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D3_rep1


title: Erythroid cells, TAL1 Control rep3, Day0

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D0_rep3


title: NTC_2

city: Montreal

first: Tamiko

last: Nishimura

address: 740 ave Dr Penfield

country: Canada

institute: McGill University

description: Library name: NTC_2

library_source: other

data_processing:
The raw data (FASTQ) was converted to DCC files for upload into Bruker Spatial's proprietary software. Data was Q3 normalized and target mRNAs that were detected in at least 1% of the AOIs were retained in the analysis, resulting in inclusion of 12,489 targets.
Assembly: Nanostring synthetic WTA and custom respiratory microbe barcode reference
Supplementary files format and content: Q3 normalized count matrix table for 184 libraries with 12,489 targets
Library strategy: Spatial Transcriptomics

molecule: other

source_name: water

extract_protocol:
Clinical biopsies were fixed in formalin, embedded in paraffin, and sectioned onto positively charged slides (4 biopsies per slide) for GeoMx DSP WTA analysis. Barcodes attached to antisense probes were released by UV-illumination and collected.
Releasates from each area-of-illumination (PanCK+ or PanCK-/stroma) were collected into a well of a 96-well plate and dual-index Illumina sequencing adapters were added by PCR amplification. Libraries were pooled and sequenced on an Illumina NovaSeq 6000.

value: water

value: Not applicable

tag: caucasian

tag: age

tag: bmi

tag: diagnosis (asthma_or_healthy_control)

tag: asthma severity

tag: ever smoked


title: NTC_3

description: Library name: NTC_3

tag: Sex


title: Erythroid cells, TAL1 Control rep1, Day0

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_D0_rep1

tag: cell type


title: NTC_1

description: Library name: NTC_1


title: Patient 22  008 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 008 | stroma

source_name: lung needle biopsy

value: lung needle biopsy

value: Male

value: Yes

value: No


title: Patient 22  008 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 008 | PanCK+


title: Patient 22  007 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 007 | stroma


title: Patient 22  007 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 007 | PanCK+


title: Patient 19  006 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 006 | stroma

value: Asthma

value: Non-severe


title: Patient 19  006 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 006 | PanCK+


title: SW480, P2RY2 KO, ATP treated, rep3

city: Heidelberg

first: Chong

last: Sun

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Immune Regulation in Cancer

country: Germany

institute: German Cancer Research Center

description:
Library name: Sample 18
Column name in all_cnt_FeatureCounts.tsv: SW480_KO_3

data_processing:
Raw reads from the paired-end fastq files were aligned to GRCh38 using STAR (2.7.10a).
Raw read counts per gene were measured by FeatureCounts (2.0.1) with the default parameters.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw read counts for each sample

growth_protocol: KBM7 cells were cultured in IMDM, while BxPC3 and SW480 cells were maintained in RPMI 1640 medium. All media were supplemented with 10% fetal bovine serum, 100 U/mL penicillin-streptomycin, and GlutaMAX. The cells were incubated in a humidified atmosphere at 37 °C with 5% CO₂.

extract_protocol:
RNeasy Mini Kit (QIAGEN) was used for RNA isolation. 1μg total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using the Hieff NGS Ultima Dual-Mode mRNA Library Prep Kit for Illumina (Yeasen, model: 13533ES96), following the manufacturer's protocol.

treatment_protocol: All the cells were treated with 200 μM ATP for 8 hours.

tag: cell line

value: Colorectal cancer cells

value: P2RY2 knockout

value: 200 μM ATP


title: Patient 19  005 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 005 | stroma


title: Patient 19  005 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 005 | PanCK+


title: Patient 6  004 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 004 | stroma

value: Female


title: Patient 6  003 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 003 | PanCK+


title: Patient 6  003 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 003 | stroma


title: Patient 6  004 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 004 | PanCK+


title: Patient 5  001 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 001 | stroma

value: Severe


title: Patient 5  002 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 002 | PanCK+


title: Patient 5  001 PanCK+

description: Library name: 1_WTA_PanCK_CD68_real | 001 | PanCK+


title: Patient 5  002 stroma

description: Library name: 1_WTA_PanCK_CD68_real | 002 | stroma


title: Patient 301  009 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 009 | PanCK+

value: Control


title: Patient 309  008 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 008 | stroma


title: Patient 309  006 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 006 | stroma


title: Patient 309  008 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 008 | PanCK+


title: Patient 309  006 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 006 | PanCK+


title: Patient 54  004 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 004 | stroma


title: Patient 301  005 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 005 | PanCK+


title: Patient 53  003 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 003 | stroma


title: Patient 53  001 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 001 | stroma


title: Patient 53  003 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 003 | PanCK+


title: Patient 54  002 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 002 | stroma


title: Patient 54  002 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 002 | PanCK+


title: Patient 323  010 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 010 | PanCK+

value: Unknown


title: Patient 323  009 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 009 | stroma


title: Patient 322  008 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 008 | stroma


title: Patient 321  006 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 006 | stroma


title: Patient 322  007 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 007 | PanCK+


title: Patient 321  004 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 004 | stroma


title: Patient 321  005 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 005 | stroma


title: Patient 321  006 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 006 | PanCK+


title: Patient 321  005 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 005 | PanCK+


title: Patient 322  008 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 008 | PanCK+


title: Patient 316  001 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 001 | PanCK+


title: Patient 316  002 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 002 | PanCK+


title: Patient 370  008 stroma

description: Library name: 4_WTA_PanCK_CD68 | 008 | stroma


title: Patient 316  001 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 001 | stroma


title: Patient 321  004 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 004 | PanCK+


title: Patient 316  003 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 003 | PanCK+


title: Patient 365  007 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 370  006 stroma

description: Library name: 4_WTA_PanCK_CD68 | 006 | stroma


title: Patient 365  005 stroma

description: Library name: 4_WTA_PanCK_CD68 | 005 | stroma


title: aIgMKO4

first: Ana Maria

last: Hincapie

address: 1160 Pine avenue West

description: Library name: B008

data_processing:
SALMON
Assembly: MM_grch38_ens94
Supplementary files format and content: .xlsx

source_name: Isolated B lymphocytes

extract_protocol:
Qiagen Rneasy Plus Universal mini kit
NEBNext Ultra II RNA Library Prep Kit for Illumina

value: Isolated B lymphocytes

value: Ptpn2fl/fl mb1 Cre+

value: anti-IgM 6 hour treatment


title: aIgMKO3

description: Library name: B007


title: Patient 337  004 stroma

description: Library name: 4_WTA_PanCK_CD68 | 004 | stroma


title: Patient 365  005 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 301  009 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 009 | stroma

value: Not applicable


title: Patient 334  003 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 003 | PanCK+

value: lung needle biopsy


title: Patient 337  002 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 370  008 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 008 | PanCK+

value: Male


title: Patient 316  002 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 002 | stroma

value: Yes


title: Patient 365  007 stroma

description: Library name: 4_WTA_PanCK_CD68 | 007 | stroma

value: No


title: Patient 301  005 stroma

description: Library name: 2_WTA_PanCK_CD68_real | 005 | stroma


title: Patient 53  001 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 001 | PanCK+


title: Patient 323  010 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 010 | stroma

value: Asthma


title: Patient 334  001 stroma

description: Library name: 4_WTA_PanCK_CD68 | 001 | stroma

value: Non-severe


title: Patient 337  004 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 004 | PanCK+


title: ChIPseq, MED1, aux

city: Tokyo

first: Shoin

last: Tei

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

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

description: Library name: ChIPseq_MED1_aux

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

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

extract_protocol:
Mouse C2C12 cells were used as a spike-in control. HCT-116 and C2C12 cells were crosslinked with 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine for 5 min, washed with PBS, pelleted by centrifugation, and stored at –80°C until use. For standard ChIP-seq, thawed cells were resuspended in 1 mL of LB1 Buffer [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM PMSF, 10 mM DTT, 1x cOmplete EDTA-free (Roche)] and incubated on ice for 10 min. After centrifugation, the pellet was resuspended in 1 mL of LB2 Buffer [20 mM Tris-HCl (pH 7.5), 200 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1x cOmplete EDTA-free] and incubated on ice for 10 min. Following another centrifugation, the pellet was resuspended in 1 mL of LB3 Buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 0.1% SDS, 1x cOmplete EDTA-free] and incubated on ice for 10 min. The centrifugation and resuspension steps with LB3 buffer were repeated. Chromatin was sonicated on Sonifier 250D (BRANSON) at 17% of amplitude for six cycles of 12 sec each. Between each cycle, chromatin was collected by centrifugation. After chromatin fragmentation, insoluble debris was removed by centrifugation. HCT-116 and C2C12 chromatin were combined at a 4:1 ratio. To prepare antibody-conjugated beads, 50 μL of Dynabeads Protein A/G (Invitrogen) were washed twice with PBS containing 5 mg/mL BSA and resuspended in the same buffer. After the addition of 4 μg of antibody, the mixture was rotated for 3 hours at 4°C. The beads were then washed twice with BSA/PBS and once with LB3 buffer, followed by resuspension in LB3 buffer. Chromatin mixture was rotated with the antibody-conjugated beads for 14 hours at 4°C. The beads were washed with LB3 Buffer once, twice with LB3 High Buffer [20 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 0.1% SDS], three times with RIPA wash Buffer [50 mM HEPES-KOH (pH 7.4), 0.25 M LiCl, 1 mM EDTA, 0.5% Na-Deoxycholate, 1% NP-40], and once with TE50 Buffer [50 mM Tris-HCl (pH 7.5), 10 mM EDTA]. Bead-bound DNA was eluted with Elution Buffer [50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1% SDS] and incubated at 65°C for 6 hours, followed by sequential treatment with RNase A and proteinase K. The samples were purified with QIAquick PCR purification kit (QIAGEN).
The library for sequencing was prepared with NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete RAD21. 100 μM 5,6-Dichlorobenzimidazole 1-β-D-Ribofuranoside (DRB; TCI) was added concurrently with IAA for 3 hours, or 1 μM flavopiridol (Santa Cruz) during the final 1 hour of the 3-hour IAA treatment.

value: Auxin


title: Patient 54  004 PanCK+

description: Library name: 2_WTA_PanCK_CD68_real | 004 | PanCK+


title: Patient 337  002 stroma

description: Library name: 4_WTA_PanCK_CD68 | 002 | stroma


title: Patient 334  001 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 334  003 stroma

description: Library name: 4_WTA_PanCK_CD68 | 003 | stroma


title: Patient 601  008 stroma

description: Library name: 5_WTA_PanCK_CD68 | 008 | stroma


title: Patient 322  007 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 007 | stroma


title: Patient 323  009 PanCK+

description: Library name: 3_WTA_PanCK_CD68_real | 009 | PanCK+


title: Patient 601  008 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 601  007 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 415  006 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 601  007 stroma

description: Library name: 5_WTA_PanCK_CD68 | 007 | stroma


title: Patient 415  006 stroma

description: Library name: 5_WTA_PanCK_CD68 | 006 | stroma


title: IFN14_Baseline_cd34pos_GoT-ChA

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

description:
Library name: IFN14_Baseline_cd34pos_GoT-ChA
GoT-ChA

data_processing:
10x data was processed using Cell Ranger 1 and v6.1.2 using default parameters. RNA reads were aligned to the human referece genome. Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x RNA-seq dataATAC-seq 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-CALR genes and those matching no gene below a supporting read threshold.
CUT&RUN data were down-sampled to have same number of reads across all conditions within the sample replicate to account for difference in sequencing depth. Among the down-sampled reads, low-quality reads were filtered out using Trimmomatic, resulting reads were aligned with hg38 genome with Bowtie2, and PCR duplicates were removed with SAMtools with a previously described workflow. Aligned reads were then used for peak calling with MACS3 with a q-value threshold of 0.01 and reads from IgG antibody as the control. SPI1 over-enrichment in the called peaks was confirmed with Simple Enrichment Analysis (SEA, v5.5.5). Overlapping peaks between replicates of the same condition were kept for further processing. The peaks were processed with multiBamSummary function from deepTools to obtain counts matrix per sample for downstream analysis.
Genotyping data processing was performed according to the previously published instructions and available Gotcha R package. Briefly, initial FASTQ files were filtered based on base quality scores, and the Fastqsplit function was used to split FASTQ files for subsequent parallel computing. Mutations were determined via the BatchMutationCalling function, which identifies reads that are correctly primed, calculates the counts of reads per cell for each specified genotype (i.e., WT, JAK2-V617F).
Assembly: GRCh38
Supplementary files format and content: Processed 10X data is matrix table of gene/peak counts per cell for each sample
Supplementary files format and content: Output matrices processed from genotyping data have two columns: barcodes (BC) and Genotype

source_name: Bone marrow

extract_protocol:
GoT-IM Extraction Protocol: Cryopreserved bone marrow mononuclear cells approved by the Institutional Review Board of Weill Cornell Medicine were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, Miltenyi Biotec) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. To eliminate experimental batch effects, cells were labelled simultaneously with hashing antibodies with time-point-identifying barcodes using Hashtag Antibodies 1, 2 or 3 (TotalSeq-A, clone LNH-94, Biolegend) for GoT-IM. To link cell identities to expression of cell surface proteins, cells were also incubated with CITE-seq antibodies according to manufacturer protocol (TotalSeq-A, Biolegend). Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Genotyping of Transcriptomes (GoT) was performed by adapting the 10x Genomics platform. FACS-sorted CD34+ cells for each time-point from the same individual were pooled, targeting a total of 10,000-15,000 cells.  GoT-ATAC Extraction Protocol: Cryopreserved bone marrow mononuclear cells were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, MACS) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Nuclei were isolated from DAPI-, CD34+ cells according to 10x Genomics Demonstrated Low Cell Input Nuclei Isolation protocol. Lysis buffer was prepared following manufacturer’s recommendations and then split into aliquots for each serial sample. Either TotalSeq-A Anti-Nuclei Pore Complex Proteins Hashtag 9 or 10 Antibody (1uL at 1:5 dilution; BioLegend) was added to each aliquot of lysis buffer. Low-input nuclei isolation was otherwise performed following manufacturer’s recommendations. Subsequently, nuclei from each time-point were counted and pooled together at approximately equal proportions. For IFN03, additional nuclei from the IFNa-treated sample were available to be run on a separate lane.  RFX3-OE Extraction Protocol: Cells from frozen umbilical cord blood mononuclear cells were thawed rapidly at 37°C, red blood cell lysis was performed using ACK Lysis Buffer, then centrifuged, and cell pellet was resuspended in cold MACS buffer. Cells were centrifuged at 300g for 5min at 4°C, and resuspended in cold MACs buffer at a concentration of 1x10^7 cells/mL. CD34+ cells were then isolated with the EasySep™ Human CD34 Positive Selection Kit II (StemCell Technologies #17856) according to manufacturer’s protocol. After isolation, cells were counted and plated in 96-well round-bottom plates (Falcon) in StemSpan™ SFEM II media (StemCell Technologies) with StemSpan™ CD34+ Expansion Supplement (StemCell Technologies) and 1% Pen/Strep. After 24 hours in culture, cells were spun down and resuspended in minimal media consisting of StemSpan StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement, 1% Pen/Strep, 10μM prostaglandin E2 (StemCell Technologies #72192) and 100ng/μl poloxamer 407 (Millipore Sigma P2164030). Cells were split into 2 technical replicates each for untransduced condition, mCherry-control vector transduction, and RFX3-OE vector transduction. Lentivirus or PBS control was added at an MOI of 100, spinoculated at 300g, 32°C for 1 hour, and cells were incubated in same lentivirus-containing media for 24 hours at 37°C before resuspension in fresh media consisting of StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement and 1% Pen/Strep. After 48 hours of incubation, cells were stained with CD34-APC antibody (1:50). Cells were then FACS isolated for the CD34+ population in the untransduced condition and the CD34+ mCherry+ populations in the RFX3-OE and mCherrycontrol conditions. Three independent transduction experiments were completed with new units of umbilical cord blood cells. Untransduced, mCherry-Control, and RFX3-OE CD34+ cells were stained with Cell Hashing antibodies (HTO TotalSeq-A, BioLegend) for 30 min at 4°C. Cells were then washed with FACs Buffer three times, pooled, and counted for loading. scRNA-sequencing was then performed using the 10x 3’ v3.1 platform according to manufacturer’s protocol. HTO demultiplexing and downstream analyses such as differential gene expression and gene set enrichment were performed as in GoT-IM for CD34+ bone marrow samples. scRNA-seq experiment was completed on one replicate of three independent transduction experiments.  CUT&RUN Extraction Protocol: UT7 cell lines expressing MPL (thrombopoietin receptor) and either the mutant CALR (type 1, L367Tfs*46) or wildtype CALR transgene (93) were seeded in 10cm plates in DMEM supplemented with 10% FBS (Thomas Scientific) and 5 ng/ml GM-CSF (Miltenyi-Biotec). Cells were treated with 0.1μg/ml Recombinant Human IFN-alpha2a (RC217-14) or PBS-1X control for 24hrs. After treatment, cells were washed 1x with PBS and collected for use with the CUTANA™ CUT&RUN assay (EpiCypher) according to the manufacturer’s protocol. 0.5μg of anti-human rabbit monoclonal PU.1 antibody (ab76543) and IgG antibody (ab172730) were used in the assay.
GoT-IM Library Construction Protocol: The standard 10x Genomics Chromium 3′ (v.3.1 chemistry) was implemented according to the manufacturer’s recommendations up to the cDNA amplification step (10X Genomics, Pleasanton, CA). After cDNA amplification and SPRI cleanup, 10x scRNA-seq and ADT/HTO libraries were generated as recommended. A portion of the cDNA was used for somatic genotyping. Briefly, to capture the somatic genotypes of cells, cDNA was amplified with a locus-specific amplification (10 PCR cycles), using the generic forward SI-PCR primer and a following locus-specific reverse primer for the CALR mutations. The amplified locus-specific cDNAs are then cleaned using SPRI purification to remove unincorporated primers. Finally, the targeted amplicon libraries are generated through a PCR performed with a P5 generic forward PCR primer together with an RPI-x primer. The targeted amplicon libraries were spiked into the remainder of the gene expression and immunophenotyping libraries to be sequenced together on a NovaSeq (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 8 cycles for i7 sample index and 8 cycles for i5 sample index.  GoT-ATAC Library Construction Protocol: Single-nucleus gene expression (GEX) and chromatin accessibility libraries were constructed from the pooled nuclei according to the Chromium Next GEM Single Cell Multiome User Guide (10X Genomics). Genotyping libraries targeting the CALR mutant transcripts were constructed from the remaining amplified cDNA, similar to the original GoT method. The re-amplified sample was purified and concentrated via 0.7X SPRI cleanup, eluting it into 10uL Buffer EB. To pre-enrich the CALR mutation locus, a gene-specific PCR was performed with 3uL of cleaned re-amplified cDNA and Partial Read 1 and gene-specific primers. CALR locus-specific amplification was then performed with 3uL of cleaned gene-specific amplified cDNA and SI-PCR and loci-specific Primers. A 0.7X SPRI cleanup was performed, and cDNA was eluted into 11uL Buffer EB. Finally, to construct the targeted amplicon library, loci-amplified cDNA was mixed with P5 Generic and RPIx indexing primers and amplified. The constructed library was cleaned via 0.8X SPRI cleanup and eluted into 12uL Buffer EB. At the cDNA amplification stage of the Chromium Next GEM Single Cell Multiome protocol, supernatant from the 0.6X size selection was retained and was used to generate the hashing libraries as per HTO protocol25 with the following modification. For the hashing library construction step, the PCR reaction was prepared with 0.65uL of 10uM SI-PCR primer, 0.65uL of 10uM TruSeq DNA D7xx_s primer, 11.25uL cleaned supernatant and 12.5 uL Kapa HiFI HotStart Ready Mix (Roche, Basel, Switzerland). Hashing, gene expression, and genotyping libraries were pooled and sequenced together on a NovaSeq (Illumina).  Genotyping for JAK2-mutated samples (IFN14, IFN15): Nuclei were processed according to the 10x Genomics Chromium Next GEM Single-Cell ATAC v2 Kit guidelines, with several modifications specific to the GoT-ChA protocol. 1 µl of 22.5 µM GoT–ChA primer mix was added to the barcoding reaction mixture, containing the locus-specific primers GoT–ChA_R1N and GoT–ChA_Rev (primer sequences in Supplementary Table 32). During the post-GEM incubation clean-up, 45.5 µl of elution solution I was used to elute the SPRIselect bead reaction, and 5 µl was used for GoT-ChA library generation. GoT-ChA libraries were generated according to the published protocol.

value: Bone marrow

tag: disease state

value: Polycythemia vera


title: Patient 415  005 stroma

description: Library name: 5_WTA_PanCK_CD68 | 005 | stroma

tag: tissue


title: Patient 374  004 stroma

description: Library name: 5_WTA_PanCK_CD68 | 004 | stroma

value: Female


title: Patient 371  002 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 002 | PanCK+

value: Severe


title: Patient 374  003 stroma

description: Library name: 5_WTA_PanCK_CD68 | 003 | stroma


title: Patient 415  005 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 371  001 stroma

description: Library name: 5_WTA_PanCK_CD68 | 001 | stroma


title: Patient 374  003 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 003 | PanCK+


title: Patient 374  004 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 371  002 stroma

description: Library name: 5_WTA_PanCK_CD68 | 002 | stroma


title: Patient 371  001 PanCK+

description: Library name: 5_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 620  010 stroma

description: Library name: 6_WTA_PanCK_CD68 | 010 | stroma


title: Patient 620  010 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 010 | PanCK+


title: Patient 316  003 stroma

description: Library name: 3_WTA_PanCK_CD68_real | 003 | stroma

value: Control


title: Patient 620  009 stroma

description: Library name: 6_WTA_PanCK_CD68 | 009 | stroma


title: Patient 620  009 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 009 | PanCK+


title: Patient 612  008 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 612  008 stroma

description: Library name: 6_WTA_PanCK_CD68 | 008 | stroma


title: Patient 612  007 stroma

description: Library name: 6_WTA_PanCK_CD68 | 007 | stroma


title: Patient 610  006 stroma

description: Library name: 6_WTA_PanCK_CD68 | 006 | stroma


title: Patient 612  007 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 610  006 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 604  004 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 604  003 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 003 | PanCK+


title: Patient 610  005 stroma

description: Library name: 6_WTA_PanCK_CD68 | 005 | stroma


title: Patient 610  005 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 604  004 stroma

description: Library name: 6_WTA_PanCK_CD68 | 004 | stroma


title: Patient 604  001 stroma

description: Library name: 6_WTA_PanCK_CD68 | 001 | stroma


title: Patient 604  002 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 604  003 stroma

description: Library name: 6_WTA_PanCK_CD68 | 003 | stroma


title: Patient 604  001 PanCK+

description: Library name: 6_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 604  002 stroma

description: Library name: 6_WTA_PanCK_CD68 | 002 | stroma


title: Patient 652  008 stroma

description: Library name: 8_WTA_PanCK_CD68 | 008 | stroma


title: Patient 652  008 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 652  007 stroma

description: Library name: 8_WTA_PanCK_CD68 | 007 | stroma


title: Patient 649  006 stroma

description: Library name: 8_WTA_PanCK_CD68 | 006 | stroma


title: Patient 652  007 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 649  005 stroma

description: Library name: 8_WTA_PanCK_CD68 | 005 | stroma


title: Patient 649  006 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 649  005 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 642  004 stroma

description: Library name: 8_WTA_PanCK_CD68 | 004 | stroma


title: Patient 642  004 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 641  003 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 003 | PanCK+


title: Patient 642  002 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 642  002 stroma

description: Library name: 8_WTA_PanCK_CD68 | 002 | stroma


title: Patient 370  006 PanCK+

description: Library name: 4_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 637  008 stroma

description: Library name: 7_WTA_PanCK_CD68 | 008 | stroma


title: Patient 640  007 stroma

description: Library name: 7_WTA_PanCK_CD68 | 007 | stroma


title: Patient 641  001 PanCK+

description: Library name: 8_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 640  007 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 640  006 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 638  005 stroma

description: Library name: 7_WTA_PanCK_CD68 | 005 | stroma


title: Patient 638  005 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 637  003 stroma

description: Library name: 7_WTA_PanCK_CD68 | 003 | stroma


title: Patient 637  003 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 003 | PanCK+


title: Patient 635  002 stroma

description: Library name: 7_WTA_PanCK_CD68 | 002 | stroma


title: Patient 635  002 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 635  001 stroma

description: Library name: 7_WTA_PanCK_CD68 | 001 | stroma


title: Patient 635  001 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 664  008 stroma

description: Library name: 9_WTA_PanCK_CD68 | 008 | stroma


title: Patient 664  007 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 664  007 stroma

description: Library name: 9_WTA_PanCK_CD68 | 007 | stroma


title: Patient 660  006 stroma

description: Library name: 9_WTA_PanCK_CD68 | 006 | stroma


title: Patient 660  006 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 656  004 stroma

description: Library name: 9_WTA_PanCK_CD68 | 004 | stroma


title: Patient 656  004 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 656  003 stroma

description: Library name: 9_WTA_PanCK_CD68 | 003 | stroma


title: Patient 653  002 stroma

description: Library name: 9_WTA_PanCK_CD68 | 002 | stroma


title: Patient 653  002 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 675  010 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 010 | PanCK+


title: Patient 675  010 stroma

description: Library name: 10_WTA_PanCK_CD68 | 010 | stroma


title: Patient 675  009 stroma

description: Library name: 10_WTA_PanCK_CD68 | 009 | stroma


title: Patient 675  009 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 009 | PanCK+


title: Patient 675  008 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 674  007 stroma

description: Library name: 10_WTA_PanCK_CD68 | 007 | stroma


title: Patient 674  006 stroma

description: Library name: 10_WTA_PanCK_CD68 | 006 | stroma


title: Patient 670  004 stroma

description: Library name: 10_WTA_PanCK_CD68 | 004 | stroma


title: Patient 670  004 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 670  003 stroma

description: Library name: 10_WTA_PanCK_CD68 | 003 | stroma


title: Patient 666  002 stroma

description: Library name: 10_WTA_PanCK_CD68 | 002 | stroma


title: Patient 666  002 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 002 | PanCK+


title: Patient 666  001 stroma

description: Library name: 10_WTA_PanCK_CD68 | 001 | stroma


title: Patient 666  001 PanCK+

description: Library name: 10_WTA_PanCK_CD68 | 001 | PanCK+


title: Patient 679  009 stroma

description: Library name: 11_WTA_PanCK_CD68 | 009 | stroma


title: Patient 688  008 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 688  007 stroma

description: Library name: 11_WTA_PanCK_CD68 | 007 | stroma


title: Patient 641  001 stroma

description: Library name: 8_WTA_PanCK_CD68 | 001 | stroma


title: Patient 687  006 stroma

description: Library name: 11_WTA_PanCK_CD68 | 006 | stroma


title: Patient 688  007 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 007 | PanCK+


title: Patient 640  006 stroma

description: Library name: 7_WTA_PanCK_CD68 | 006 | stroma


title: Patient 638  004 PanCK+

description: Library name: 7_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 687  006 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 006 | PanCK+


title: Patient 686  005 stroma

description: Library name: 11_WTA_PanCK_CD68 | 005 | stroma


title: Patient 686  004 stroma

description: Library name: 11_WTA_PanCK_CD68 | 004 | stroma


title: Patient 686  005 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 686  004 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 004 | PanCK+


title: Patient 664  008 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 008 | PanCK+


title: Patient 687  003 stroma

description: Library name: 11_WTA_PanCK_CD68 | 003 | stroma


title: Patient 660  005 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 005 | PanCK+


title: Patient 687  003 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 003 | PanCK+


title: Patient 679  002 stroma

description: Library name: 11_WTA_PanCK_CD68 | 002 | stroma


title: Donor 479, B cell, HEK BCS (CD79B)

city: Oxford

first: Matt

last: Jackson-Wood

address: 9400 Business Park, Garsington Road

country: United Kingdom

institute: Gilead Sciences

description: Library name: E5_ID2276_479_S150

data_processing:
Residual ribosomal RNA reads were removed using SortMeRNA.
RNA-seq reads were processed to gene-level counts using the nf-core/rnaseq pipeline (v3.12).
Salmon was used for pseudoalignment to the Ensembl GRCh38.96 reference genome.
Assembly: Ensembl GRCh38.96
Supplementary files format and content: Processed data file is a comma-separated text file containing gene-level count matrix across samples.
Supplementary files format and content: Note: samples B2_ID2276_479_S149, E5_ID2276_479_S150, and B5_ID2276_479_S116 were excluded from downstream analyses reported in the manuscript (identified as PCA‑based outliers) but are included in the GEO deposition.

source_name: Blood

growth_protocol: Blood cones from healthy, de-identified donors were processed to obtain PBMCs using density-gradient centrifugation. Briefly, diluted blood cone cells were layered over Ficoll-Paque PLUS Media (Cytiva) in a 50 mL Leucosep tube (Greiner Bio-One GmbH). The resulting cells were seeded into Nunc™ Non-Treated 24-well plates (Thermo Fisher Scientific) at a density of 8x10^5/cm^2 in a final volume of 1 mL RPMI (Gibco), supplemented with Penicillin-Streptomycin-Neomycin (Gibco), 10% Foetal Bovine Serum (Gibco), and L-Glutamine (Gibco).

extract_protocol:
Following the 48-hour in vitro stimulation assay, major immune cell populations were isolated by fluorescence-activated cell sorting (FACS) on the BD FACSAria™ Fusion using lineage markers for monocytes (CD14+), CD4+ T cells (CD3+, CD4+), CD8+ T cells (CD3+, CD8+), and B cells (CD19+, CD20+). Between 3x10^5 and 1x10^6 cells were sorted into sorting buffer, and RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Bulk RNA-seq libraries were prepared from RNA isolated from FACS-sorted immune cell populations using the NEBNext rRNA Depletion Kit and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 S4 in 150 bp paired-end read mode to achieve at least 20 million reads per sample.

treatment_protocol: Isolated PBMCs were treated in vitro for 48 hours with a subset of immunomodulatory stimuli comprising B cell stimulator cells (BCS), CytoStim™, lipopolysaccharide (LPS), and IFN-α, alongside unstimulated baseline controls. BCS stimulation was performed using HEK293 cells transduced to express CD40L and an anti-CD79B ScFv construct, added at an 8:1 PBMC:BCS ratio together with 100 ng/mL IL-21 (BioLegend). CytoStim™ human (Miltenyi Biotec) was used at 20 µL/mL, and LPS (eBioscience) was used at 100 ng/mL.

value: Blood

value: B cell

value: HEK BCS (CD79B)


title: Donor 474, B cell, HEK BCS (CD79B)

description: Library name: E5_ID2258_474_S105


title: Donor 467, B cell, HEK BCS (CD79B)

description: Library name: E5_ID2226_467_S121


title: Donor 470, B cell, HEK BCS (CD79B)

description: Library name: E5_ID2236_470_S124


title: Patient 675  008 stroma

description: Library name: 10_WTA_PanCK_CD68 | 008 | stroma


title: Donor 464, B cell, HEK BCS (CD79B)

description: Library name: E5_ID2207_464_S17


title: Donor 477, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2271_477_S65


title: Donor 479, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2276_479_S76


title: Donor 474, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2258_474_S54


title: Donor 464, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2207_464_S12


title: Donor 470, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2236_470_S43


title: Donor 467, CD4, HEK BCS (CD79B)

description: Library name: E4_ID2226_467_S119


title: Donor 477, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2271_477_S130


title: Donor 474, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2258_474_S126


title: Donor 467, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2226_467_S82


title: Donor 464, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2207_464_S7


title: Patient 679  009 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 009 | PanCK+


title: Donor 477, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2271_477_S128


title: Donor 467, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2226_467_S27


title: Donor 479, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2276_479_S67

value: Whole PBMC


title: Donor 464, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2207_464_S2


title: Donor 477, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2271_477_S55


title: Donor 474, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2258_474_S96


title: Donor 470, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2236_470_S36


title: Donor 467, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2226_467_S22


title: Donor 479, B cell, LPS

description: Library name: D5_ID2276_479_S145

value: LPS


title: Donor 477, B cell, LPS

description: Library name: D5_ID2271_477_S132


title: Donor 474, B cell, LPS

description: Library name: D5_ID2258_474_S104


title: Donor 470, B cell, LPS

description: Library name: D5_ID2236_470_S47


title: Donor 467, B cell, LPS

description: Library name: D5_ID2226_467_S85


title: Donor 479, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2276_479_S71


title: Donor 464, B cell, LPS

description: Library name: D5_ID2207_464_S16


title: Donor 470, CD8, HEK BCS (CD79B)

description: Library name: E3_ID2236_470_S137


title: Donor 479, CD4, LPS

description: Library name: D4_ID2276_479_S75


title: Donor 479, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2276_479_S69


title: Donor 477, CD4, LPS

description: Library name: D4_ID2271_477_S64


title: CHI190 Active Het

city: Memphis

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Pl, M2426

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Library name: CHI190

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

source_name: dorsal striatum

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

value: dorsal striatum

tag: group

value: Active

value: cholinergic interneuron

value: Het

value: male

tag: batch

tag: date ephys

tag: dob

tag: age days

tag: electrophysiologist

tag: mouse id

tag: rt lot

tag: date lp

tag: lp lot

tag: index lot

tag: date seq

tag: seq srm_sample_id


title: Donor 474, CD4, LPS

description: Library name: D4_ID2258_474_S53

tag: cell type

tag: treatment


title: Donor 470, CD4, LPS

description: Library name: D4_ID2236_470_S92


title: Donor 470, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2236_470_S38


title: Donor 474, CD14, HEK BCS (CD79B)

description: Library name: E2_ID2258_474_S48


title: Donor 467, CD4, LPS

description: Library name: D4_ID2226_467_S32


title: Patient 641  003 stroma

description: Library name: 8_WTA_PanCK_CD68 | 003 | stroma

value: lung needle biopsy

tag: Sex

tag: caucasian

value: Yes

tag: age

tag: bmi

tag: diagnosis (asthma_or_healthy_control)

value: Asthma

tag: asthma severity

value: Non-severe

tag: ever smoked

value: No


title: Patient 638  004 stroma

description: Library name: 7_WTA_PanCK_CD68 | 004 | stroma

tag: tissue

value: Female


title: Donor 464, CD4, LPS

description: Library name: D4_ID2207_464_S11


title: Donor 477, CD8, LPS

description: Library name: D3_ID2271_477_S60


title: Donor 479, CD8, LPS

description: Library name: D3_ID2276_479_S144


title: Donor 474, CD8, LPS

description: Library name: D3_ID2258_474_S140


title: Donor 467, CD8, LPS

description: Library name: D3_ID2226_467_S136


title: Donor 464, CD8, LPS

description: Library name: D3_ID2207_464_S6


title: Donor 479, CD14, LPS

description: Library name: D2_ID2276_479_S115


title: Patient 653  009 PanCK+

description: Library name: 9_WTA_PanCK_CD68 | 009 | PanCK+

value: Severe


title: Donor 470, CD8, LPS

description: Library name: D3_ID2236_470_S123

value: Blood


title: Donor 467, CD14, LPS

description: Library name: D2_ID2226_467_S26


title: Donor 479, Whole PBMC, LPS

description: Library name: D1_ID2276_479_S114


title: Donor 477, Whole PBMC, LPS

description: Library name: D1_ID2271_477_S107


title: Donor 474, Whole PBMC, LPS

description: Library name: D1_ID2258_474_S138


title: Donor 464, CD14, LPS

description: Library name: D2_ID2207_464_S1


title: Donor 467, Whole PBMC, LPS

description: Library name: D1_ID2226_467_S21


title: Donor 477, CD14, LPS

description: Library name: D2_ID2271_477_S57


title: Donor 464, Whole PBMC, LPS

description: Library name: D1_ID2207_464_S79


title: Donor 479, B cell, IFNa

description: Library name: C5_ID2276_479_S146

value: B cell

value: IFNa


title: Donor 477, B cell, IFNa

description: Library name: C5_ID2271_477_S131


title: Donor 474, B cell, IFNa

description: Library name: C5_ID2258_474_S103


title: Donor 470, B cell, IFNa

description: Library name: C5_ID2236_470_S46


title: Donor 467, B cell, IFNa

description: Library name: C5_ID2226_467_S84


title: Donor 464, B cell, IFNa

description: Library name: C5_ID2207_464_S15


title: Donor 479, CD4, IFNa

description: Library name: C4_ID2276_479_S74


title: Donor 477, CD4, IFNa

description: Library name: C4_ID2271_477_S63


title: Donor 474, CD4, IFNa

description: Library name: C4_ID2258_474_S52


title: Donor 470, CD4, IFNa

description: Library name: C4_ID2236_470_S42


title: Donor 464, CD4, IFNa

description: Library name: C4_ID2207_464_S10


title: Donor 479, CD8, IFNa

description: Library name: C3_ID2276_479_S143


title: Donor 477, CD8, IFNa

description: Library name: C3_ID2271_477_S59


title: Donor 474, CD8, IFNa

description: Library name: C3_ID2258_474_S100


title: Donor 470, CD8, IFNa

description: Library name: C3_ID2236_470_S91


title: Donor 467, CD8, IFNa

description: Library name: C3_ID2226_467_S81


title: Donor 467, CD14, IFNa

description: Library name: C2_ID2226_467_S25


title: Donor 470, Whole PBMC, LPS

description: Library name: D1_ID2236_470_S86

value: Whole PBMC


title: Donor 470, CD14, IFNa

description: Library name: C2_ID2236_470_S88


title: Donor 474, CD14, IFNa

description: Library name: C2_ID2258_474_S125


title: Donor 479, Whole PBMC, IFNa

description: Library name: C1_ID2276_479_S113


title: Donor 464, CD8, IFNa

description: Library name: C3_ID2207_464_S5


title: Donor 467, CD4, IFNa

description: Library name: C4_ID2226_467_S31


title: Donor 477, Whole PBMC, IFNa

description: Library name: C1_ID2271_477_S106


title: Donor 474, Whole PBMC, IFNa

description: Library name: C1_ID2258_474_S95


title: Patient 679  002 PanCK+

description: Library name: 11_WTA_PanCK_CD68 | 002 | PanCK+

value: Male

value: Control

value: Not applicable


title: Donor 464, CD14, IFNa

description: Library name: C2_ID2207_464_S135


title: Donor 477, B cell, HEK BCS (CD79B)

description: Library name: E5_ID2271_477_S111

value: HEK BCS (CD79B)


title: Donor 470, Whole PBMC, IFNa

description: Library name: C1_ID2236_470_S35


title: Donor 467, Whole PBMC, IFNa

description: Library name: C1_ID2226_467_S20


title: Donor 464, Whole PBMC, IFNa

description: Library name: C1_ID2207_464_S118


title: Donor 479, B cell, Cytostim

description: Library name: B5_ID2276_479_S116

value: Cytostim


title: Donor 477, B cell, Cytostim

description: Library name: B5_ID2271_477_S66


title: Donor 474, B cell, Cytostim

description: Library name: B5_ID2258_474_S102


title: Donor 470, B cell, Cytostim

description: Library name: B5_ID2236_470_S45


title: Donor 467, B cell, Cytostim

description: Library name: B5_ID2226_467_S33


title: Donor 464, B cell, Cytostim

description: Library name: B5_ID2207_464_S14


title: Donor 479, CD14, IFNa

description: Library name: C2_ID2276_479_S68


title: Donor 479, CD4, Cytostim

description: Library name: B4_ID2276_479_S73


title: Donor 477, CD14, IFNa

description: Library name: C2_ID2271_477_S56


title: Donor 474, CD4, Cytostim

description: Library name: B4_ID2258_474_S51


title: Donor 467, CD4, Cytostim

description: Library name: B4_ID2226_467_S30


title: Donor 470, CD4, Cytostim

description: Library name: B4_ID2236_470_S41


title: Donor 464, CD4, Cytostim

description: Library name: B4_ID2207_464_S9


title: Donor 479, CD8, Cytostim

description: Library name: B3_ID2276_479_S70


title: Donor 477, CD4, Cytostim

description: Library name: B4_ID2271_477_S62


title: Donor 477, CD8, Cytostim

description: Library name: B3_ID2271_477_S58


title: Donor 474, CD8, Cytostim

description: Library name: B3_ID2258_474_S49


title: Donor 470, CD8, Cytostim

description: Library name: B3_ID2236_470_S39


title: Donor 467, CD8, Cytostim

description: Library name: B3_ID2226_467_S80


title: Donor 464, CD8, Cytostim

description: Library name: B3_ID2207_464_S4


title: Donor 479, CD14, Cytostim

description: Library name: B2_ID2276_479_S149


title: Donor 477, CD14, Cytostim

description: Library name: B2_ID2271_477_S109


title: Donor 470, CD14, Cytostim

description: Library name: B2_ID2236_470_S87


title: Donor 477, Whole PBMC, Cytostim

description: Library name: B1_ID2271_477_S127


title: Donor 474, CD14, Cytostim

description: Library name: B2_ID2258_474_S139


title: Donor 467, CD14, Cytostim

description: Library name: B2_ID2226_467_S24


title: Donor 479, Whole PBMC, Cytostim

description: Library name: B1_ID2276_479_S112


title: Donor 464, CD14, Cytostim

description: Library name: B2_ID2207_464_S134


title: Donor 474, Whole PBMC, Cytostim

description: Library name: B1_ID2258_474_S94


title: Donor 467, Whole PBMC, Cytostim

description: Library name: B1_ID2226_467_S19


title: Donor 464, Whole PBMC, Cytostim

description: Library name: B1_ID2207_464_S117


title: Donor 470, Whole PBMC, Cytostim

description: Library name: B1_ID2236_470_S34


title: Donor 479, B cell, Baseline

description: Library name: A5_ID2276_479_S77

value: Baseline


title: Donor 464, Whole PBMC, HEK BCS (CD79B)

description: Library name: E1_ID2207_464_S29


title: Donor 477, B cell, Baseline

description: Library name: A5_ID2271_477_S110


title: Donor 470, B cell, Baseline

description: Library name: A5_ID2236_470_S44


title: Donor 474, B cell, Baseline

description: Library name: A5_ID2258_474_S101


title: Donor 464, B cell, Baseline

description: Library name: A5_ID2207_464_S13


title: Donor 467, B cell, Baseline

description: Library name: A5_ID2226_467_S120


title: Donor 479, CD4, Baseline

description: Library name: A4_ID2276_479_S72


title: Donor 467, CD4, Baseline

description: Library name: A4_ID2226_467_S83


title: Donor 464, CD4, Baseline

description: Library name: A4_ID2207_464_S8


title: Donor 477, CD4, Baseline

description: Library name: A4_ID2271_477_S61


title: Donor 474, CD4, Baseline

description: Library name: A4_ID2258_474_S50


title: Donor 470, CD4, Baseline

description: Library name: A4_ID2236_470_S40


title: Donor 477, CD8, Baseline

description: Library name: A3_ID2271_477_S129


title: Donor 479, CD8, Baseline

description: Library name: A3_ID2276_479_S142


title: Donor 474, CD8, Baseline

description: Library name: A3_ID2258_474_S99


title: Donor 467, CD8, Baseline

description: Library name: A3_ID2226_467_S28


title: Donor 470, CD8, Baseline

description: Library name: A3_ID2236_470_S90


title: Donor 479, CD14, Baseline

description: Library name: A2_ID2276_479_S147


title: Donor 477, CD14, Baseline

description: Library name: A2_ID2271_477_S108


title: Donor 464, CD8, Baseline

description: Library name: A3_ID2207_464_S3


title: Donor 470, CD14, Baseline

description: Library name: A2_ID2236_470_S37


title: Donor 467, CD14, Baseline

description: Library name: A2_ID2226_467_S23


title: Donor 474, CD14, Baseline

description: Library name: A2_ID2258_474_S97


title: Donor 479, Whole PBMC, Baseline

description: Library name: A1_ID2276_479_S141


title: Donor 474, Whole PBMC, Baseline

description: Library name: A1_ID2258_474_S93


title: Donor 477, Whole PBMC, Baseline

description: Library name: A1_ID2271_477_S148


title: Donor 467, Whole PBMC, Baseline

description: Library name: A1_ID2226_467_S18


title: Donor 470, Whole PBMC, Baseline

description: Library name: A1_ID2236_470_S122


title: Donor 464, Whole PBMC, Baseline

description: Library name: A1_ID2207_464_S78


title: KYSE410 siADAR1-2

city: Jinan

first: Liangchao

address: Jiyan Road No.440, Jinan, 250012, P. R. China.

institute: Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences

description:
Library name: Sample 5
RNA-seq of KYSE410 siADAR1 cells

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly.
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: esophageal tissue

growth_protocol: KYSE410 cells and their knockdown derivatives (siADAR1) cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol reagent (Accurate Biotechnology (Hunan) Co., Ltd., Hunan, China). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: No

value: esophageal tissue

tag: cell line

value: Esophageal squamous cell carcinoma cell

tag: genotype

value: ADAR1 knockdown

tag: batch


title: KYSE410 siADAR1-3

description:
Library name: Sample 6
RNA-seq of KYSE410 siADAR1 cells


title: KYSE410 siADAR1-1

description:
Library name: Sample 4
RNA-seq of KYSE410 siADAR1 cells


title: KYSE410 NC-3

description:
Library name: Sample 3
RNA-seq of KYSE410 control cells

value: wild type


title: KYSE410 NC-1

description:
Library name: Sample 1
RNA-seq of KYSE410 control cells

value: No


title: White Preeclamptic 4

city: Augusta

first: Jessica

last: Faulkner

state: Georgia

address: 1120 15th Street

department: Physiology

institute: Augusta Univeristy

description:
Library name: WP4
White Preeclamptic 4

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

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

value: Placenta


title: White Preeclamptic 5

description:
Library name: WP5
White Preeclamptic 5


title: KYSE410 NC-2

description:
Library name: Sample 2
RNA-seq of KYSE410 control cells


title: White Preeclamptic 6

description:
Library name: WP6
White Preeclamptic 6


title: Donor 464, CD14, Baseline

description: Library name: A2_ID2207_464_S133


title: White Preeclamptic 2

description:
Library name: WP2
White Preeclamptic 2


title: White Preeclamptic 1

description:
Library name: WP1
White Preeclamptic 1


title: White Preeclamptic 3

description:
Library name: WP3
White Preeclamptic 3


title: White Normal 5

description:
Library name: WN5
White Normal 5


title: White Normal 6

description:
Library name: WN6
White Normal 6


title: White Normal 4

description:
Library name: WN4
White Normal 4


title: White Normal 3

description:
Library name: WN3
White Normal 3


title: White Normal 1

description:
Library name: WN1
White Normal 1


title: White Normal 2

description:
Library name: WN2
White Normal 2


title: Black Preeclamptic 6

description:
Library name: BP6
Black Preeclamptic 6


title: Black Preeclamptic 5

description:
Library name: BP5
Black Preeclamptic 5


title: Black Preeclamptic 4

description:
Library name: BP4
Black Preeclamptic 4


title: Black Preeclamptic 3

description:
Library name: BP3
Black Preeclamptic 3


title: Donor 474, CD14, LPS

description: Library name: D2_ID2258_474_S98

value: LPS


title: Black Preeclamptic 2

description:
Library name: BP2
Black Preeclamptic 2


title: Black Preeclamptic 1

description:
Library name: BP1
Black Preeclamptic 1


title: Black Normal 6

description:
Library name: BN6
Black Normal 6


title: Black Normal 4

description:
Library name: BN4
Black Normal 4


title: Black Normal 5

description:
Library name: BN5
Black Normal 5


title: Black Normal 3

description:
Library name: BN3
Black Normal 3


title: Donor 470, CD14, LPS

description: Library name: D2_ID2236_470_S89

value: Blood


title: Black Normal 2

description:
Library name: BN2
Black Normal 2


title: Black Normal 1

description:
Library name: BN1
Black Normal 1


title: Human-NK-T co-culture (Boosted), biol repl3

city: Homburg

first: Sijia

state: Saarland

address: Saarland University. Center for Integrative Physiology and Molecular Medicine (CIPMM). Kirrberger Straße 100, 66424 Homburg, Germany.

department: Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine

institute: Saarland University

description:
Library name: BstNK_1_3
Column name in gene_count.xls: BstNK_3

data_processing:
Gene expression levels were quantified using Fragments Per Kilobase of exon model per Million mapped fragments, which accounts for sequencing depth and gene length in fragment counting.
Assembly: hg38
Supplementary files format and content: Excel read count of genes for each sample

source_name: Human-NK-T

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors as previously described. Primary human NK cells, CD4+ T cells and CD8+ T cells were negatively isolated from PBMCs according to the manufacturer’s instruction using NK Cell Isolation Kit human (Miltenyi Biotec), CD4+ T Cell Isolation Kit human (Miltenyi Biotec), CD8+ T Cell Isolation Kit human (Miltenyi Biotec), respectively. NK cells and T cells were cultured in AIMV medium (ThermoFisher Scientific) with 10% FCS at a density of 2×106 and 3×106 cells/mL. T cells were stimulated with Dynabeads Human T-Activator CD3/CD28 (ThermoFisher Scientific) for 2 days at a bead to cell ratio of 0.8:1.

extract_protocol:
RNA extraction was performed simultaneously for all samples using the NucleoSpin RNA Plus kit (Macherey-Nagel), following the manufacturer’s protocol.
RNA sequencing was conducted by Novogene using Illumina platforms based on sequencing-by-synthesis (SBS) technology.

value: Human-NK-T


title: Human-NK-T co-culture (Boosted), biol repl5

description:
Library name: BstNK_1_5
Column name in gene_count.xls: BstNK_5


title: Human-NK-T co-culture (Boosted), biol repl4

description:
Library name: BstNK_1_4
Column name in gene_count.xls: BstNK_4


title: Human-NK-T co-culture (Boosted), biol repl2

description:
Library name: BstNK_1_2
Column name in gene_count.xls: BstNK_2


title: Human-NK-T co-culture (Boosted), biol repl1

description:
Library name: BstNK_1_1
Column name in gene_count.xls: BstNK_1


title: Human-NK cultured alone (NK), biol repl4

description:
Library name: NK_1_4
Column name in gene_count.xls: NK_4

source_name: Human-NK

value: Human-NK


title: Human-NK cultured alone (NK), biol repl5

description:
Library name: NK_1_5
Column name in gene_count.xls: NK_5


title: Human-NK cultured alone (NK), biol repl2

description:
Library name: NK_1_2
Column name in gene_count.xls: NK_2


title: Human-NK cultured alone (NK), biol repl3

description:
Library name: NK_1_3
Column name in gene_count.xls: NK_3


title: Human-NK cultured alone (NK), biol repl1

description:
Library name: NK_1_1
Column name in gene_count.xls: NK_1


title: D73_R1_ISO_NSC

first: Nick

last: Gatford

address: Dorothy Crowfoot Hodgkin Building, South Parks Road

department: NDCN

institute: University of Oxford

description: 10X Genomics

data_processing:
Fastq files were aligned to Homo sapiens GRCh38, in Cellranger (v6.1.1).
Filtering: removed genes with no UMI counts and gens with less than <1 UMI count across 3 cells at least
PercellQCmetrics to decide outliers based on 3 MADS (scuttle)
Evaluate doublets using scdblfinder
Assembly: hg38 2020
Supplementary files format and content: *.h5 file type

source_name: hiPSC

growth_protocol: iPSC differentiation into dopaminergic neurons to DIV 73

extract_protocol:
Cells were first dissociated in Accutase for 30 minutes at 37 C to generate a single cell suspension. Cells were fixed in 100% methanol following the 10X Genomics established protocol.
Library preparation and mRNA barcoding was performed using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), following the manufacturer’s instructions. 10,000-cell recovery was the targeted for each sample. One library was prepared for each condition (Clone 1-13 and ND34391G). Libraries were sequenced with NovaSeq 6000 (Illumina).

treatment_protocol: Non-seeded control (NSC)

value: hiPSC

value: Induced pluripotent stem cell derived dopaminergic neurons

value: Isogenic control (Clone 1-13)

value: Non-seeded control (NSC)


title: D73_R2_TRIP_NSC

description: 10X Genomics

value: SNCA Triplication (ND34391G)


title: D73_R2_ISO_NSC

description: 10X Genomics


title: D73_R1_TRIP_NSC

description: 10X Genomics


title: D60_R6_NSC

data_processing:
Paired end files (150 bp) were generated for each sample
Kallisto (v0.46.2) was used to estimate transcript abundance for Ensembl (release 102) protein-coding genes from RNAseq reads
Count data was imported into R using tximport and genes with less than 10 reads across the six samples used in the comparison were filtered out
Differential gene expression was performed in DESeq2 using the Wald test with an FDR threshold of 0.05 and a log2 fold change threshold on 0.25
Assembly: GRCh38 (Ensemble release 102)
Supplementary files format and content: Kallisto quantification files (tsv files and HDF5 binary files) for each sample with run info, transcript abundance estimates, TPM, bootstrap estimates, and transcript length information length

growth_protocol: iPSC differentiation into dopaminergic neurons to DIV 52 or DIV 60

extract_protocol:
RNeasy Plus Mini Kit, Qiagen (Cat No./ID: 74134)
Library preparation was performed with the NEB Next Ultra RNA Library Prep Kit, following standard Illumina protocols. Libraries were sequenced with NovaSeq 6000 (Illumina).
Unstranded library, poly-A enriched RNA-Seq

treatment_protocol: NSC

value: NSC

tag: time

value: day 60


title: D60_R3_NSC


title: D60_R5_NSC


title: D60_R4_NSC


title: D60_R2_NSC


title: D60_R1_NSC


title: D52_R6_NSC

value: day 52


title: D52_R5_NSC


title: D52_R4_NSC


title: D52_R3_NSC


title: D52_R2_NSC