title: RNA-Seq of naive CD4 T cells activated  for 3 days_WT3

description: Library name: RNA_A_WT3


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 2, for BnNAC038-OE

status: Public on Sep 15 2025

type: SRA

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

country: China

institute: China Agricultural Universtiy

description:
Library name: Sample23
Column name in OE_RNAseq_All_samples.txt: WT_ABA3h_rep2

library_source: transcriptomic

data_processing:
For RNA-seq analysis of knockout line, high-quality reads were mapped to the Brassica napus reference genome (zs11) using HISAT2.2.1. Fragment per kilobase of transcript per million mapped reads (FPKM) values were calculated for each transcript using StringTie2.2.1 to quantify gene expression. Differentially expressed genes (DEGs) were identified using the DESeq2_1.38.3 package with a fold change (FC) ≥ 1.5 and a p-value < 0.05.
For RNA-seq analysis of overexpression line, high-quality reads were used to quantify each transcript using Kallisto_0.51.1. The transcripts per million (TPM) values for each transcript were calculated. Differentially expressed genes between wild-type and BnNAC038-OE plants were identified using the Sleuth_0.30.1 package with FC ≥ 1.5 and a p-value < 0.05.
Assembly: zs11
Supplementary files format and content: For RNA-seq, txt files include FPKM or TPM value for each Sample

molecule: total RNA

organism: Brassica napus

source_name: leaves

growth_protocol: Brassica napus seedlings are cultivated in Hoagland's nutrient solution at 25°C under long-day conditions (16 hours of light and 8 hours of darkness).

extract_protocol:
Total RNA from each sample was extracted using TRIzol™ Reagent (Invitrogen) following the manufacturer's protocol.
The mRNA was isolated and used for RNA-seq library construction following the NEBNext Ultra II RNA Library Kit instructions.

treatment_protocol: Wild-type, knockout lines (BnNAC038-KO-1), and overexpression lines (BnNAC038-OE-1, BnNAC038-OE-2) were subjected to treatment with 50 μM ABA and 20% PEG for the specified durations.

tag: tissue

value: leaves

tag: genotype

value: wild-type

tag: treatment

value: 50 μM ABA treatment for 3 hours


title: RNA-Seq of naive CD4 T cells activated  for 3 days_KO3

city: NEW YORK

first: Jingyao

last: Zhao

state: NY

address: 701 W 168th Street Room 1204

department: Microbiology and Immunology

country: USA

institute: Columbia University Medical Center

description: Library name: RNA_A_KO3

data_processing:
Galaxy RNA-seq platform.
Assembly: mm10
Supplementary files format and content: csv DEG for RNA-seq. BED  for ATAC-seq

organism: Mus musculus

source_name: Spleen and Lymph nodes

extract_protocol:
RNA was harvested using Quick-RNA Microprep Kit (Zymo Research). 0.5 ug of total RNA was used for the construction of sequencing libraries.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina(NEB) or ATAC-Seq Kit(Active Motif)

value: Spleen and Lymph nodes

tag: cell type


title: LoVo_M_2

city: London

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Medical Research Council

data_processing:
HiSeq Control Software 2.2.58, RTA 2.11.3 and bcl2fastq2_2.20.0 were used for raw reads quality control and treatment
Raw sequences were quality filtered and trimmed with trimmomatic (v.0.39)
The resulting reads were mapped to the human reference transcriptome from ensembl database.
Quantification of samples was made via salmon (v 1.5.0) with mapping validation and gcbias options activated
Assembly: GRCh38.p13, version 103
Supplementary files format and content: tab-separated file of raw reads from Salmon mapping
Supplementary files format and content: tab-separated file of normalised reads done in deseq2 in R

organism: Homo sapiens

source_name: Colon

growth_protocol: HCT116, LoVo, DLD-1 and SW948 cells were plated in 6 wells plates with complete medium

extract_protocol:
Samples were prepared using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
RNA-seq libraries were prepared using Illumina Stranded mRNA Prep kit and protocols

treatment_protocol: 10 mM of 2-MiCit was used as a treatment, or vehicle (water) for control condition

value: Colon

tag: cell line

value: LoVo

value: epithelial

value: Micit


title: wilt-type, normal cultural condition, biological replicate 3, for BnNAC038-OE

description:
Library name: Sample21
Column name in OE_RNAseq_All_samples.txt: WT_CK_rep3

value: non treatent


title: WA_KO 0hr _Serum Stimulation-3

city: Sudbury

first: Sujeenthar

last: Tharmalingam

state: Ontario

address: 935 Ramsey Lake Road

country: Canada

institute: NOSM University

description:
Library name: TLab_206
0hCas9dCas9_vs_0hKO.genes.counts.csv

data_processing:
The sequencing data was processed in-house using various bioinformatics toolkits available through the Illumina Sequence Hub (San Diego, CA, USA), powered by DRAGEN Inc. Briefly, DRAGEN FASTQ was used to assess sequencing quality and perform read trimming. DRAGEN RNA was employed to align reads to the human reference genome (GRCh38.p14; hg38) and quantify transcript abundance. Differential expression analysis was conducted using the DRAGEN Differential Expression pipeline, which incorporates the DESeq2 algorithm. Genes were considered differentially expressed if they exhibited a fold change < −1.5 or > 1.5, an FDR-adjusted p-value < 0.05, and an average transcript abundance of at least 30 transcripts per million (TPM).
Assembly: GRCh38.p14; hg38
Supplementary files format and content: CSV file describing the number of reads mapped to each gene for each sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using the TRIzol reagent and further purified with the NEB Monarch® RNA Cleanup Kit (T2040L, NEB).
100 ng of high-quality RNA (A260/280 ~2.0 ± 0.1) was used to generate strand-specific libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (E7765S, NEB), which enriches for poly-A mRNA and incorporates the dUTP method for strand specificity.

value: hybrid of fibroblast and HeLa

value: Cas9; FRA1 KO

value: Baseline


title: LoVo_C_2

value: control


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_KO3

description: Library name: RNA_FSK_KO3


title: wilt-type, normal cultural condition, biological replicate 2, for BnNAC038-OE

description:
Library name: Sample20
Column name in OE_RNAseq_All_samples.txt: WT_CK_rep2


title: Skin, 70 days not irradiated, rep 1

city: Pisa

first: Giulia

last: Furini

address: Via Giuseppe Moruzzi 1

department: Institute of Clinical Physiology (IFC)

country: Italy

institute: National Research Council (CNR)

description: Library name: 1CNT_Skin

data_processing:
Dragen BCLConvert (for demultiplexing): raw data
Kallisto 0.5.0
Assembly: mm10
Supplementary files format and content: tsv from kallisto, gene counts

source_name: Skin

extract_protocol:
Total RNA was extracted from 10–15 mg of frozen skin and muscle tissues, collected from the left hindlimb of both control and irradiated mice. Homogenization was performed with a Qiagen TissueLyser II in 700 µL of TRIzol reagent using stainless steel beads at 30 Hz for 5×30 sec. The aqueous phase obtained after chloroform addition (1/5 volume) and centrifugation (12000 × g for 15 min at 4 °C) was loaded onto Direct-zol RNA Microprep columns (Zymo Research,) and RNA eluted in 15 uL RNAse-free water, as indicated by the manufacturer protocol.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus

treatment_protocol: C57BL/6J mice were exposed to 35 Gy electron irradiation using the ElectronFlash linear accelerator (Linac) available at the Centro Pisano FLASH Radiotherapy (CPFR). The instrument was set on either FLASH or conventional (CONV) modality.  Sham, not irradiated mice served as controls.

value: Skin

tag: strain

value: WT

value: sham

tag: batch


title: WA_KO 0hr _Serum Stimulation-2

description:
Library name: TLab_205
0hCas9dCas9_vs_0hKO.genes.counts.csv


title: WA_KO 0hr _Serum Stimulation-1

description:
Library name: TLab_204
0hCas9dCas9_vs_0hKO.genes.counts.csv


title: DLD1_M_2


title: HCT116_C_3


title: ATAC-Seq of naive CD4 T cells_KO3

description: Library name: ATAC_N_PKAKO3

library_source: genomic

molecule: genomic DNA


title: DLD1_C_2


title: WA_Cas9 0hr _Serum Stimulation-3

description:
Library name: TLab_203
0hCas9dCas9_vs_0hKO.genes.counts.csv


title: BnNAC038 knock out, 20% PEG treatment for 6 hours, biological replicate 3

description:
Library name: Sample18
Column name in KO_RNAseq_All_samples.txt: NAC38ko_PEG6h_rep3

value: BnNAC038 knock out

value: 20% PEG treatment for 6 hours


title: HCT116_M_2

value: wild-type


title: RNA-Seq of naive CD4 T cells_KO3

description: Library name: RNA_N_KO3


title: wilt-type, normal cultural condition, biological replicate 1, for BnNAC038-OE

description:
Library name: Sample19
Column name in OE_RNAseq_All_samples.txt: WT_CK_rep1

value: leaves


title: ATAC-Seq of naive CD4 T cells activated  for 3 days_WT3

description: Library name: ATAC_A_WT3

value: Spleen and Lymph nodes


title: BnNAC038 knock out, 20% PEG treatment for 6 hours, biological replicate 2

description:
Library name: Sample17
Column name in KO_RNAseq_All_samples.txt: NAC38ko_PEG6h_rep2


title: WA_Cas9 0hr _Serum Stimulation-2

description:
Library name: TLab_202
0hCas9dCas9_vs_0hKO.genes.counts.csv


title: WA_Cas9 0hr _Serum Stimulation-1

description:
Library name: TLab_201
0hCas9dCas9_vs_0hKO.genes.counts.csv


title: iPSC-CM_IndA_Untr_Input

city: Galveston

first: Michelle

middle: C.

last: Ward

address: 301 University blvd.

institute: UTMB

description: Library name: IndA_Untr_Input

data_processing:
Paired-end ChIP and Input reads were assessed for quality using FastQC (v0.11.9), then aligned to the human genome (GRCh38/hg38) using Bowtie2 (v2.5.1). Uniquely mapped read pairs were retained with bamtools filter, and PCR duplicates were removed using Picard MarkDuplicates with optical duplicate detection. MACS2 (v2.2.7.1) was used for broad peak calling (--broad) with matched input control, using a q-value threshold of 0.05 and broad cutoff of 0.1. Fragment size was estimated with mfold=5–50 and bandwidth=300.
Assembly: hg38
Supplementary files format and content: PAUL_TOP2B_ChIP.bed

growth_protocol: Human iPSC-dervied cardiomyocytes were maintained in Cardiomyocyte Maintenance Media (500 mL DMEM without glucose (A14430-01, ThermoFisher Scientific), 50 mL FBS (MT35015CV, Corning), 990 mg Galactose (G5388, Sigma-Aldrich), 5 mL 100 mM sodium pyruvate (11360-070, ThermoFisher Scientific), 2.5 mL 1 M HEPES (H3375, Sigma-Aldrich), 5 mL 100X GlutaMAX (35050-061, ThermoFisher Scientific), and 5 mL Penicillin/Streptomycin) on Matrigel-coated dishes at 37°C, 5% CO2 and atmospheric O2.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed to map TOP2B binding sites in untreated iPSC-derived cardiomyocytes from individual UCSD143i-87-1. Approximately 40 million cells were fixed in 1% formaldehyde, quenched with glycine, and flash-frozen. Chromatin was extracted, sequentially lysed, and sonicated using a Covaris system to generate 250–400 bp fragments. Immunoprecipitation was performed overnight at 4 °C using anti-TOP2B antibody (Abcam ab72334) pre-bound to Dynabeads Protein G. After stringent washes, chromatin was eluted and crosslinks reversed. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then resuspended for library preparation.
ChIP and Input DNA libraries were constructed using the TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1012) following manufacturer instructions with minor modifications. Starting with all the ChIP DNA and 50ng of  input DNA, end repair and A-tailing were performed prior to ligation of indexed adapters (ACAGTG for ChIP, GCCAAT for Input). Adapter-ligated DNA was PCR-amplified for 18 cycles and purified using AMPure XP beads. Libraries were size-selected (250–400 bp) by gel excision, then purified with the MinElute Gel Extraction Kit (Qiagen). Library concentration and size distribution were assessed by Qubit and Agilent Bioanalyzer. Final libraries were sequenced as 40 bp paired-end reads: ChIP library on the Illumina NextSeq 550 (generated 40,380,049 reads) and Input library on the Illumina MiniSeq (20,968,544 reads).

treatment_protocol: Chromatin immunoprecipitation was performed to map endogenous TOP2B binding sites in untreated human iPSC-derived cardiomyocytes. ChIP and matched input DNA were collected from 40 million cells each, derived from a single female donor line (UCSD143i-87-1). No drug treatment was applied prior to cell harvesting.

tag: Sex

value: female

value: induced pluripotent stem cell-derived cardiomyocytes

value: Untreated

tag: antibody


title: HCT116_C_2

value: Colon

value: epithelial


title: BnNAC038 knock out, 20% PEG treatment for 6 hours, biological replicate 1

description:
Library name: Sample16
Column name in KO_RNAseq_All_samples.txt: NAC38ko_PEG6h_rep1


title: ATAC-Seq of naive CD4 T cells_WT3

description: Library name: ATAC_N_WT3


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_WT2

description: Library name: RNA_FSK_WT2


title: SW948_M_1

value: Micit


title: BnNAC038 knock out, 50 μM ABA treatment for 3 hours, biological replicate 3

description:
Library name: Sample15
Column name in KO_RNAseq_All_samples.txt: NAC38ko_ABA3h_rep3

value: 50 μM ABA treatment for 3 hours


title: RNA-Seq of naive CD4 T cells_WT2

description: Library name: RNA_N_WT2


title: 3_EV_rep3

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexander Solzhenitsyn Street 25

country: Russia

institute: ISP RAS

description: Library name: 3_EV_2

data_processing:
nf-core/rnaseq
Assembly: Rnor_6.0
Supplementary files format and content: comma delimeted text files included counts for each Sample

organism: Rattus norvegicus

source_name: Brain cortex

extract_protocol:
The extraction was obtained with RNeasy Plus Mini Kit (Qiagen, Германия) according to the manufacturer's instructions. https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/rna-purification/total-rna/rneasy-plus-kits
DNBSEQ Eukaryotic Strand-specific mRNA library

value: Brain cortex

value: Primary neuro-glial culture

value: extracellular vesicles


title: LoVo_M_1

value: LoVo


title: RNA-Seq of naive CD4 T cells_KO2

description: Library name: RNA_N_KO2


title: SW948_C_1

value: control


title: BnNAC038 knock out, 50 μM ABA treatment for 3 hours, biological replicate 1

description:
Library name: Sample13
Column name in KO_RNAseq_All_samples.txt: NAC38ko_ABA3h_rep1

value: BnNAC038 knock out


title: BnNAC038 knock out, 50 μM ABA treatment for 3 hours, biological replicate 2

description:
Library name: Sample14
Column name in KO_RNAseq_All_samples.txt: NAC38ko_ABA3h_rep2


title: ATAC-Seq of naive CD4 T cells activated for 3 days_KO3

description: Library name: ATAC_A_PKAKO3


title: 3_EV_rep2

description: Library name: 3_EV_1


title: LoVo_C_1


title: 3_EV_rep1

description: Library name: 3_EV_0


title: 3_many_rep3

description: Library name: 3_many_2

value: total secretome


title: BnNAC038 knock out, normal cultural condition, biological replicate 2

description:
Library name: Sample11
Column name in KO_RNAseq_All_samples.txt: NAC38ko_CK_rep2

value: non treatent


title: DLD1_M_1

value: wild-type


title: RNA-Seq of naive CD4 T cells activated  for 3 days_KO2

description: Library name: RNA_A_KO2

value: Spleen and Lymph nodes


title: BnNAC038 knock out, normal cultural condition, biological replicate 3

description:
Library name: Sample12
Column name in KO_RNAseq_All_samples.txt: NAC38ko_CK_rep3

value: leaves


title: DLD1_C_1


title: 3_many_rep2

description: Library name: 3_many_1


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_KO2

description: Library name: RNA_FSK_KO2


title: BnNAC038 knock out, normal cultural condition, biological replicate 1

description:
Library name: Sample10
Column name in KO_RNAseq_All_samples.txt: NAC38ko_CK_rep1


title: ATAC-Seq of naive CD4 T cells activated for 3 days_KO2

description: Library name: ATAC_A_PKAKO2


title: HCT116_M_1


title: HCT116_C_1


title: 3_100_rep3

description: Library name: 3_100_2

value: 3-100 kDa proteins


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 3

description:
Library name: Sample9
Column name in KO_RNAseq_All_samples.txt: K407_PEG6h_rep3

value: 20% PEG treatment for 6 hours


title: 3_many_rep1

description: Library name: 3_many_0


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 2

description:
Library name: Sample8
Column name in KO_RNAseq_All_samples.txt: K407_PEG6h_rep2


title: ATAC-Seq of naive CD4 T cells_KO2

description: Library name: ATAC_N_PKAKO2


title: ATAC-Seq of naive CD4 T cells activated  for 3 days_WT2

description: Library name: ATAC_A_WT2


title: 3_100_rep2

description: Library name: 3_100_1


title: 3_100_rep1

description: Library name: 3_100_0


title: wilt-type, 20% PEG treatment for 6 hours, biological replicate 1

description:
Library name: Sample7
Column name in KO_RNAseq_All_samples.txt: K407_PEG6h_rep1


title: RNA-Seq of naive CD4 T cells activated  for 3 days_WT2

description: Library name: RNA_A_WT2


title: eΔmenFΔubiC_D_1

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

country: India

institute: TIFR

description: Library name: Sample 9

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2
Maximum insert size of 1000 and two maximum mismatches after trimming 3 bp at the 3' ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments packageintersection mode
The dispersion and differential expression level of each gene were estimated using DESeq2
Transcripts per Million (TPM) were calculated by DESeq2
Assembly: NC_000913.3
Supplementary files format and content: csv, TPM counts

organism: Escherichia coli

source_name: Whole cell

extract_protocol:
RNA was isolated from the cells pelleted from the mid-log phase of the culture.
Nextera XT kit (illumina FC-1311024) following thermanufactures protocol

value: Whole cell


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 3

description:
Library name: Sample6
Column name in KO_RNAseq_All_samples.txt: K407_ABA3h_rep3


title: K_rep3

description: Library name: K_2


title: ATAC-Seq of naive CD4 T cells_WT2

description: Library name: ATAC_N_WT2


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 2

description:
Library name: Sample5
Column name in KO_RNAseq_All_samples.txt: K407_ABA3h_rep2


title: eΔmenFΔubiC_C_2

description: Library name: Sample 8


title: RNA-Seq of naive CD4 T cells_WT1

description: Library name: RNA_N_WT1


title: RNA-Seq of naive CD4 T cells_KO1

description: Library name: RNA_N_KO1


title: eΔmenFΔubiC_C_1

description: Library name: Sample 7


title: eΔmenFΔubiC_D_2

description: Library name: Sample 10


title: eΔmenFΔubiC_B_2

description: Library name: Sample 6


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_WT1

description: Library name: RNA_FSK_WT1


title: wilt-type, normal cultural condition, biological replicate 3

description:
Library name: Sample3
Column name in KO_RNAseq_All_samples.txt: K407_CK_rep3


title: eΔmenFΔubiC_B_1

description: Library name: Sample 5


title: RNA-Seq of naive CD4 T cells activated  for 3 days_WT1

description: Library name: RNA_A_WT1


title: Glutamate_BPC_3

address: Alexandra Solzhenitsina

department: Information Systems

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
STAR – 2.7.0a
Salmon - 1.9.0
Assembly: rn6
Supplementary files format and content: comma delimeted text files include RPKM values for each Sample

extract_protocol:
The extraction was obtained with RNeasy Plus Mini Kit (Qiagen, Germany) according to the manufacturer's instructions. https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/rna-purification/total-rna/rneasy-plus-kits
DNBSEQ Eukaryotic Strand-specific mRNA library


title: wilt-type, normal cultural condition, biological replicate 1

description:
Library name: Sample1
Column name in KO_RNAseq_All_samples.txt: K407_CK_rep1


title: wilt-type, normal cultural condition, biological replicate 2

description:
Library name: Sample2
Column name in KO_RNAseq_All_samples.txt: K407_CK_rep2


title: RNA-Seq of naive CD4 T cells stimulated by Forskolin_KO1

description: Library name: RNA_FSK_KO1


title: Glutamate_BPC_2


title: eΔmenFΔubiC_A_2

description: Library name: Sample 4


title: eΔmenFΔubiC_A_1

description: Library name: Sample 3


title: Glutamate_secret_3


title: Exp3 Lane 1 HASH

city: Palo Alto

first: Christopher

last: McGinnis

state: CA

address: Biomedical Innovations Building 4600, 240 Pasteur Drive

department: Pathology

institute: Stanford University

description:
Library name: Experiment 3 Lane 1 HASH
Cell Hashing; Untreated LN

library_source: other

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the mm-10-3.0.0 reference transcriptome.
MULTI-seq and HTO FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: mm10
Supplementary files format and content: Cellranger output files: mRNA barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: deMULTIplex2 output files: MULTI-seq count table csv

molecule: other

source_name: LN

extract_protocol:
Experiment 1: Spleens were obtained from 7-8 week-old EpoR-loxp/loxp or EpoR-loxp/loxp-Xcr1-Cre mice after TLI/ATS treatment or from untreated controls. Samples were dissociated and subjected to MACS negative enrichment with Pan Dendritic Cell Isolation Kit and were tagged by genotpye using TotalSeq-A hashtag antibodies. Lin(CD3e, NK1.1, CD19, B200)-SiglecH-PDCA-1-F4/80-CD11c+MHCII+XCR1+SIRPa- cDC1s were FACS isolated and used for 10x Genomics scRNA-seq. Experiment 2: Spleens and LNs were obtained from 7-8 week-old EpoR-TdTomato-Cre mice after TLI/ATS treatment. Samples were dissociated and subjected to MACS negative enrichment with Pan Dendritic Cell Isolation Kit, split into 2 aliquots per tissue and MULTI-seq barcoded. cDC1s were then FACS isolated according to EpoR expression status (tracked with MULTI-seq barcode), pooled by EpoR status, and used for 10x Genomics scRNA-seq. Experiment 3: LNs were obtained from 7-8 week-old EpoR-loxp/loxp or EpoR-loxp/loxp-Xcr1-Cre mice. Samples were dissociated and subjected to MACS negative enrichment with Pan Dendritic Cell Isolation Kit and were tagged by genotpye using TotalSeq-A hashtag antibodies. Lin(CD3e, NK1.1, CD19, B200)-SiglecH-PDCA-1-F4/80-CD11c+MHCII+XCR1+SIRPa- cDC1s were FACS isolated and used for 10x Genomics scRNA-seq.
Libraries were prepared according to manufacturers instructions (10x Genomics V3.1; BioLegend Total-Seq-A) with a separate MULTI-seq library prep workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019)

value: LN


title: Glutamate_secret_2


title: ATAC-Seq of naive CD4 T cells activated for 3 days_KO1

description: Library name: ATAC_A_PKAKO1


title: K_rep2

description: Library name: K_1


title: ΔmenFΔubiC_1

description: Library name: Sample 1


title: Glutamate_BPC_1


title: ΔmenFΔubiC_2

description: Library name: Sample 2


title: Patient 6 PDAC_6

type: RNA

city: Dallas

first: Huocong

last: Huang

state: TX

address: NB8.212A, 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research, Department of Surgery and Immunology

institute: UT Southwestern Medical Center

description: Xenium PDAC

hyb_protocol: Probe hybridization was performed at 50 °C overnight, followed by the removal of unhybridized probes. Locked DNA probes bound to target mRNA were ligated at 37 °C for 2 hours (Xenium ligase A/B). Circular DNA probes for each gene underwent rolling circle amplification, producing multiple copies of specific DNA barcodes. After washing, background fluorescence was chemically quenched.

scan_protocol: Xenium In Situ Analyzer

data_processing: The slides were then analyzed using a Xenium analyzer (10X Genomics) for image acquisition. The morphological image of DAPI nuclear staining was used for cell assignment, and built-in machine learning algorithms were applied for cell segmentation. Output files generated by the instrument's pipeline were used for downstream analysis.

label: Xenium Human Probe Set

source_name: 5 µm section Pancreatic ductal adenocarcinoma (PDAC)

label_protocol: Xenium Human Probe Set

extract_protocol: Tissue sections were prepared according to the Xenium In Situ for FFPE-Tissue Preparation Guide protocol (10X Genomics). Briefly, FFPE sections were cut to 5 μm and placed in the designated sample area (10.45mm x 22.45mm) on a Xenium slide (10X Genomics). The sections were then dewaxed in xylene, rehydrated through a gradient ethanol series, and treated with enzyme to facilitate mRNA accessibility.

value: chemoradiotherapy-treated


title: Exp3 Lane 1

description:
Library name: Experiment 3 Lane 1
10x Genomics; Untreated LN

library_source: transcriptomic single cell


title: ATAC-Seq of naive CD4 T cells_KO1

description: Library name: ATAC_N_PKAKO1


title: wilt-type, 50 μM ABA treatment for 3 hours, biological replicate 1

description:
Library name: Sample4
Column name in KO_RNAseq_All_samples.txt: K407_ABA3h_rep1

value: 50 μM ABA treatment for 3 hours


title: Immature anthers containing meiocytes undergoing meiosis I in WT (Mo17/B73;+/+) replicate 3

city: Gainesville

first: Meixia

state: FL

address: 1355 Museum Drive

department: Microbiology and Cell Science

institute: University of Florida

description:
Library name: W44A
Column name in normalized_counts_all_samples.csv: W44A

data_processing:
Reads were quality trimmed and adapters removed using Trimmomatic v0.39 with the TruSeq3-PE adapter file under the parameters of LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Cleaned paired reads were aligned to the Zea mays B73 reference genome using HISAT2 with default settings.
SAM files with mapping alignments were converted to BAM format using samtools. BAM files were sorted by read names using samtools sort -n.
Gene-level counts were generated using HTSeq-count in the intersection-nonempty mode with unstranded settings and GFF3 annotation.
Differential gene expression analysis was performed using DESeq2 in R, comparing specified sample groups (e.g., mop1 vs. wild type).
Assembly: Zm-B73-REFERENCE-NAM-5.0.fa
Supplementary files format and content: comma separated .csv file containing normalized read counts for each of the samples.

organism: Zea mays

source_name: immature anthers

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit (Cat no. / ID. 74904).
Library construction and sequencing were conducted at Biomarker Technologies (BMKGENE) in the Illumina Nova PE150 platform.

value: immature anthers

value: meiocytes

value: WT


title: Immature anthers containing meiocytes undergoing meiosis I in WT (Mo17/B73;+/+) replicate 2

description:
Library name: W40A
Column name in normalized_counts_all_samples.csv: W40A


title: ATAC-Seq of naive CD4 T cells_WT1

description: Library name: ATAC_N_WT1


title: Patient 5 PDAC_5

description: Xenium PDAC

value: treatment-naïve


title: K_rep1

description: Library name: K_0

value: Brain cortex

value: Primary neuro-glial culture

value: control


title: Patient 4 PDAC_4

description: Xenium PDAC


title: ATAC-Seq of naive CD4 T cells activated  for 3 days_WT1

description: Library name: ATAC_A_WT1


title: Glutamate_secret_1


title: lung cells,old mouse IAV infected 3

city: Oklahoma City

first: Jordan

last: Metcalf

address: 800 Research PKWY, Rm425

institute: The university of Oklahoma Health Sciences Center

description: Library name: IAV infected old lung cell 10

data_processing:
Data were demultiplexed and aligned to the mm10 2020-A reference transcriptome (10x Genomics) using Cell Ranger (v8.0, 10x Genomics).
Assembly: mouse mm10
Supplementary files format and content: Tab seperated values and matrix file

source_name: total lung cells

extract_protocol:
Seven days after IAV infection, mice were euthanized, and their lungs were perfused. Whole lungs were collected, fixed and frozen according to the Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling kit (10X Genomics, Pleasanton, CA) and the 10x Genomics Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit. Dissociation of fixed Tissue and creation of single cell suspension were done according to the manufacturers protocol.
Cells were loaded onto the Chromium X (10X Genomics), then the Mouse Transcriptome 10x Genomics Chromium Fixed RNA Kit, was used to generate cDNA libraries. All samples were handled so that approximately 10,000 cells were captured as 10X Genomics Gel Beads-in-emulsion (GEMs). Barcoded libraries were sequenced on an Illumina NovaSeq X Plus 25B PE300 instrument using the 10X genomics’ suggested cycling conditions.

treatment_protocol: influenza A virus infection

tag: age

value: 70 weeks

value: total lung cells

value: male

value: influenza virus PR8

value: day 7 after infection


title: RNA-Seq of naive CD4 T cells activated  for 3 days_KO1

description: Library name: RNA_A_KO1

value: Spleen and Lymph nodes


title: Immature anthers containing meiocytes undergoing meiosis I in WT (Mo17/B73;+/+) replicate 1

description:
Library name: W25A
Column name in normalized_counts_all_samples.csv: W25A


title: Patient 3 PDAC_3

description: Xenium PDAC


title: Glutamate_vesicles_1


title: lung cells,old mouse IAV infected 1

description: Library name: IAV infected old lung cell 8


title: Memantine_3

value: Memantine


title: Immature anthers containing meiocytes undergoing meiosis I in mop1 mutants (Mo17/B73;mop1/mop1) replicate 2

description:
Library name: P43A
Column name in normalized_counts_all_samples.csv: P43A


title: lung cells,old mouse mock treated 1

description: Library name: mock old lung cell 6

value: PBS


title: lung cells,old mouse mock treated 2

description: Library name: mock old lung cell 7


title: Memantine_1


title: Memantine_2


title: Glutamate_vesicles_3


title: Immature anthers containing meiocytes undergoing meiosis I in mop1 mutants (Mo17/B73;mop1/mop1) replicate 1

description:
Library name: P34A
Column name in normalized_counts_all_samples.csv: P34A


title: Patient 8 PM8

description: Xenium PM

source_name: colorectal peritoneal metastasis

tag: molecular subtype

value: PM-adjacent tissue


title: Patient 7 PM7

description: Xenium PM


title: Patient 5 PM5

description: Xenium PM


title: Glutamate_2

value: Glutamate


title: lung cells,young mouse IAV infected 2

description: Library name: IAV infected young lung cell 4

value: 12 weeks


title: Glutamate_3


title: lung cells,young mouse IAV infected 1

description: Library name: IAV infected young lung cell 3


title: Glutamate_vesicles_2


title: Immature anthers containing meiocytes undergoing meiosis I in mop1 mutants (Mo17/B73;mop1/mop1) replicate 3

description:
Library name: P9A
Column name in normalized_counts_all_samples.csv: P9A

value: immature anthers

value: meiocytes


title: lung cells,young mouse IAV infected 3

description: Library name: IAV infected young lung cell 5


title: Patient 4 PM4

description: Xenium PM


title: lung cells,old mouse IAV infected 2

description: Library name: IAV infected old lung cell 9


title: LDLR_KO

city: New York

first: Ira

middle: J

last: Goldberg

address: 435 E. 30th St, Science Building, 617

department: Division of Endocrinology, Diabetes and Metabolism

institute: New York University Grossman School  of Medicine

description: Library name: Sample 1

data_processing:
Raw sequencing reads were processed using the PIPseeker™ pipeline. FASTQ files were demultiplexed and cell barcodes filtered for quality. Hashtag oligo (HTO) demultiplexing was performed using k-medoid clustering and negative binomial modeling to assign cells to sample groups. Reads were aligned to the Mus musculus reference genome (mm10) with STAR. Aligned data were quantified to generate single-cell gene expression matrices. Downstream analysis included normalization, identification of variable features, clustering, and differential expression using Seurat v5 (RStudio v4.4.1).
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: AORTIC ARCH

growth_protocol: Male iLpl-/-/Ldlr-/- and Lplfl/fl/Ldlr-/- mice were maintained on a Western Diet for 12 weeks prior to sacrifice.

extract_protocol:
Aortic arches were dissected and maintained in HypoThermosol® FRS Preservation Solution with transcription inhibitor flavopiridol on ice. Tissues were minced and digested at 37 °C for 15 minutes in an enzyme cocktail containing 1 mg/ml collagenase I, 1 mg/ml dispase, 150 mg/ml DNase I, and Liberase™ TL. Dissociated cells were filtered through a 100 µm strainer, stained with live/dead dye, and subjected to FACS sorting. Live singlets were collected for single-cell RNA sequencing
FACS-sorted single-cell suspensions of aortic arches from iLpl-/-/Ldlr-/- and Lplfl/fl/Ldlr-/- mice were used to generate barcoded single-cell cDNA libraries using the PIPseq™ V3 T20 Single Cell RNA Kit (Fluent Biosciences), which profiles up to 20,000 cells per reaction. Sequencing libraries were constructed from one pooled sample of four mouse aortic arch samples across four libraries and combined for downstream processing. Sample multiplexing was performed with TotalSeq™-A Hashtag Antibodies (BioLegend; A0301, A0302, A0303, A0304) for cell hashing. Libraries were loaded onto an Illumina NextSeq-600 platform for sequencing.

treatment_protocol: Mice were anesthetized with ketamine–xylazine and perfused with PBS to remove circulating blood before tissue collection.

value: AORTIC ARCH

value: endothelial cells, muscle cells, monocytes

value: LDL receptor knockout (LDLR KO)

value: 12 weeks western diet


title: Glutamate_1

value: Brain cortex

value: Primary neuro-glial culture


title: Patient 2 PDAC_2

description: Xenium PDAC

value: chemoradiotherapy-treated


title: lung cells,young mouse mock treated 2

description: Library name: mock young lung cell 2

value: total lung cells

value: male


title: 5 wk Ovarian cells, scRNAseq

city: Baltimore

first: Allan

last: Spradling

state: MD

address: 3520 San Martin Drive

department: Department of Embryology

institute: Carnegie Institution for Science

data_processing:
Raw data were processed by following the standard protocols including the initial processing using the Cell Ranger pipeline (v3.1.0 and v6.0.1) with default settings. Further analyses were performed using the Seurat package (v4.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 5 wk ovaries

extract_protocol:
The ovaries were dissected from the mice and dissociated into single cells for twenty minutes at 37°C using 0.25% trypsin.
The cells were then subjected to library construction using the Chromium Next GEM Single Cell 3 Reagent Kits v3.1 from 10X Genomics.

value: 5 wk ovaries

value: 5 wk Ovarian cells

value: No treatment


title: Patient 1 PDAC_1

description: Xenium PDAC

value: treatment-naïve


title: LDLR_KO_LPL_KO

description: Library name: Sample 2

value: LDL receptor knockout (LDLR KO), inducible LPL knockout (LPL KO)


title: Patient 3 PM3

description: Xenium PM


title: Patient 6 PM6

description: Xenium PM


title: Patient 2 PM2

description: Xenium PM


title: lung cells,young mouse mock treated 1

description: Library name: mock young  lung cell 1

value: 12 weeks

value: PBS

value: day 7 after infection


title: Control 2

value: Control


title: 2 wk Ovarian cells, scRNAseq

source_name: 2 wk ovaries

value: 2 wk ovaries

value: 2 wk Ovarian cells


title: Control 3


title: 3 wk Ovarian cells, scRNAseq

source_name: 3 wk ovaries

value: 3 wk ovaries

value: 3 wk Ovarian cells


title: 6 wk Ovarian cells, scRNAseq

source_name: 6 wk ovaries

value: 6 wk ovaries

value: 6 wk Ovarian cells


title: Control 1

value: Brain cortex

value: Primary neuro-glial culture


title: Patient 1 PM1

description: Xenium PM


title: UMUC3 cells, si-CPSF3, rep3

status: Public on Sep 14 2025

city: Shanghai

first: Zhiyang

last: Ma

address: 197 Ruijin Second Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medcine

description: Library name: NATSI3U

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: bladder

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bladder

value: human bladder cancer cell line


title: UMUC3 cells, si-CPSF3, rep2

description: Library name: NATSI2U


title: UMUC3 cells, si-CPSF3, rep1

description: Library name: NATSI1U


title: UMUC3 cells, Negative control, rep2

description: Library name: NATNC2U


title: UMUC3 cells, Negative control, rep3

description: Library name: NATNC3U


title: UMUC3 cells, Negative control, rep1

description: Library name: NATNC1U


title: Naïve ESC replicate2

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: Library name: Naive_2

data_processing:
Sequence reads passed quality control were trimmed before mapping to human genome by HISAT2
Assembly: Homo_sapiens GRCh38
Supplementary files format and content: csv file included all raw counts of each sample
Supplementary files format and content: csv file of fpkm table of all samples

growth_protocol: hPSC cells were maintained in StemFlex medium in humidified atmosphere with 5% CO2 at 37 degrees

extract_protocol:
RNA was extracted by using the Rneasy mini plus preparation kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA seq libraries were prepared with TruSeq Stranded mRNA kit following the manufacturer's protocol

value: Naive ESC


title: Naïve ESC replicate1

description: Library name: Naive_1


title: MULTI-seq data labelling the distinct three conditions

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

description:
Library name: multi-RYL1
The MULTI-seq fastq file contains the same cellular barcode information and sample designation to multiplex the RYL1 library

data_processing:
The library was mapped using cellranger (7.1.0) and the custom reference with EGFP (files present in GSE258895).
Samples of different groups were demultiplexed using the deMULTIplex package in RStudio (https://github.com/chris-mcginnis-ucsf/MULTI-seq) based on the counts of MULTI-seq barcodes (Ch_E3.5_GFP (Control E3.5), Ch_E4_Ctrl (Control E4.0), Ch_E4_Cyclop (Cyclopamine E4.0)). Leveraging the intrinsic genetic variation of chick embryos, each cells were assigned to individual embryos, within each sample using the vireo package (https://github.com/single-cell-genetics/vireo) (Huang et al., 2019). Doublets identified from both MULTI-seq as well as vireo analysis were excluded from downstream analysis.
Assembly: Galgal6a (NCBI)
Supplementary files format and content: Seurat object in .RDS format that includes all the annotation and demultiplexed information as well as the gene expression information

organism: Gallus gallus

source_name: Foregut

growth_protocol: Fertilized Specific Pathogen Free (SPF) white Leghorn chicken eggs (Charles River and AVS Bio) and transgenic Roslin Green (expressing cytoplasmic GFP) chicken eggs (Susan Chapman, Clemson University) were used. Eggs were incubated in a 38°C humidified chamber up to 4.5 days before collection.

extract_protocol:
Foreguts were dissected and dissociated subject to MULTI-seq labelling based on conditions and processed according to 10X Chromium protocol
10X scRNA-seq v3.1 chemistry

treatment_protocol: To inhibit SHH signaling in vivo, we developed an in ovo cyclopamine treatment protocol for chick embryos. 3 mL of albumen was drawn from the bottom of the egg at E2 to prevent the embryo from sticking to the eggshell. The egg was sealed with tape and incubated to E3 when it was windowed. 50 µL 10 mM cyclopamine (ApexBio, A8340) dissolved in ethanol was mixed with 250 µL PBS by gentle pipetting, and the mixture, usually in a form of cloudy suspension, was carefully added on top of the chick embryo. The treated egg was immediately sealed and returned to the incubator.

value: Foregut

value: wildtype

value: cyclopamine treatment in subset of the samples


title: Primed ESC replicate3

description: Library name: Prime_3

value: Primed ESC


title: Multiplexed E3.5&E4.0 control and cyclopamine-treated foreguts

description:
Library name: RYL1
The whole library can be demultiplexed by accompanying MULTI-seq fastq file and genotype demtuliplexing by vireoSNP


title: Primed ESC replicate1

description: Library name: Prime_1


title: Naïve ESC replicate3

description: Library name: Naive_3


title: NT hPSC differentiated ectoderm cells replicate2

description: Library name: NT_EctoD2_2

value: Ectoderm

value: Nontargeting

value: Doxycycline

tag: time

value: Day 2


title: 4 wk Ovarian cells, scRNAseq

source_name: 4 wk ovaries

value: 4 wk ovaries

value: 4 wk Ovarian cells

value: No treatment


title: NT hPSC differentiated ectoderm cells replicate1

description: Library name: NT_EctoD2_1


title: ZIC2 IF hPSC differentiated ectoderm cells replicate3

description: Library name: ZIC2_EctoD2_3

value: ZIC2 knock down


title: ZIC2 IF hPSC differentiated ectoderm cells replicate1

description: Library name: ZIC2_EctoD2_1


title: NT Naïve hPSC replicate2

description: Library name: NT_Naive_2

value: Naive hPSC


title: NT Naïve hPSC replicate3

description: Library name: NT_Naive_3


title: ZNF8 IF naïve hPSC replicate3

description: Library name: ZNF8_Naive_3

value: ZNF8 knock down


title: ZNF8 IF naïve hPSC replicate1

description: Library name: ZNF8_Naive_1


title: NT Primed hPSC replicate2

description: Library name: NT_Prime_2

value: Primed hPSC


title: NT Primed hPSC replicate3

description: Library name: NT_Prime_3


title: ZNF8 IF naïve hPSC replicate2

description: Library name: ZNF8_Naive_2


title: NT Primed hPSC replicate1

description: Library name: NT_Prime_1


title: CARHSP1 IF hPSC replicate1

description: Library name: CARHSP1_1

value: CARHSP1 knock down


title: CARHSP1 IF hPSC replicate2

description: Library name: CARHSP1_2


title: Primed ESC replicate2

description: Library name: Prime_2


title: NT hPSC differentiated ectoderm cells replicate3

description: Library name: NT_EctoD2_3


title: CK biol rep 3

first: xinyue

last: wang

address: No. 2, Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description:
Library name: Sample 3
Column name in All_Samples.csv: CK_rep3

data_processing:
CASAVA 1.7
The raw sequencing data were processed with Cutadapt (v1.15) for adapter trimming and quality control.
The filtered reads were mapped to Brara_Chiifu_V3.5.fa using HISAT2 v2.0.5.
Assembly: Brara_Chiifu_V3.5.fa
Supplementary files format and content: the csv file includes FPKM values for each Sample

organism: Brassica rapa subsp. pekinensis

source_name: stems and roots

extract_protocol:
RNA was harvested using RNAprep pure plant plus kit (polysaccharides&polyphenolics-rich, Tiangen).
RNA libraries for RNA-seg were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocols.

value: stems and roots

value: inoculation with P. brassicae

value: 0 DAI


title: 10 DAI biol rep 3

description:
Library name: Sample 9
Column name in All_Samples.csv: T10d_rep3

value: 10 DAI


title: 10 DAI biol rep 2

description:
Library name: Sample 8
Column name in All_Samples.csv: T10d_rep2


title: 3 DAI biol rep 3

description:
Library name: Sample 6
Column name in All_Samples.csv: T3d_rep3

value: 3 DAI


title: CK biol rep 2

description:
Library name: Sample 2
Column name in All_Samples.csv: CK_rep2


title: 3 DAI biol rep 2

description:
Library name: Sample 5
Column name in All_Samples.csv: T3d_rep2


title: 3 DAI biol rep 1

description:
Library name: Sample 4
Column name in All_Samples.csv: T3d_rep1


title: CK biol rep 1

description:
Library name: Sample 1
Column name in All_Samples.csv: CK_rep1


title: ZIC2 IF hPSC differentiated ectoderm cells replicate2

description: Library name: ZIC2_EctoD2_2

value: Ectoderm


title: 10 DAI biol rep 1

description:
Library name: Sample 7
Column name in All_Samples.csv: T10d_rep1


title: SHEP, INPUT

city: Gent

first: Louis

last: Delhaye

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

description: Library name: NESPR_SHEP_INPUT

data_processing:
Reads were quality controlled using FastQC (v0.11.8) and trimmed with cutadapt (v1.18) to remove any low quality bases and Illumina adapter sequences.
Trimmed reads were aligned using bowtie2 (v2.3.1) to the human hg19 reference genome assembly (GRCh37)
Peak calling was performed using MACS2 with a 5% q-value threshold.
Bedgraph files generated by MACS2 were converted to bigWig format using bedGraphToBigWig and used as input to generate coverage plots in R using the Gviz (v1.46) package.
Assembly: hg19
Supplementary files format and content: narrowPeak and bed files contain MACS2 peak calling output of NESPR ChIRP-seq pulldown samples contrasted to LacZ, RNase, or input control samples.
Supplementary files format and content: bigWig files contain ChIRP-seq signal across the genome
Library strategy: ChIRP-seq

source_name: SHEP

growth_protocol: IMR32 and SHEP cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 2 mM glutamine, and 30 U/mL Penicillin-Streptomycin. Cell cultures were maintained under 60-70% confluency and passaged twice a week. Cells lines were confirmed mycoplasma-free on a regular basis by a mycoplasma colorimetric detection assay on medium of 48 h-confluent cultures. STR genotyping was performed to validate cell line authenticity. Cells were cultured in designated incubators at 37°C with a humidified atmosphere containing 5% CO2.

extract_protocol:
20-30 million IMR32 or SHEP cells per sample were cultured and harvested. In cellulo cross-linking was done by resuspending the cell pellets in 1% grade I glutaraldehyde. The reaction was quenched by adding 1.25 M glycine. Pellets were lysed in SDS lysis buffer (50 mM Tris-HCl pH7.5, 10 mM EDTA, and 1% SDS) supplemented fresh with 60 U/mL SuperaseIn RNase inhibitor, 1 mM DTT, 0.5 mM PMSF, and protease inhibitor cocktail. Lysates were sonicated untill the bulk of fragments was 500 bp. Sonicated lysates were cleared, transferred to a new tube,  incubated with Dynabeads MyOne Streptavidin C1 bound to 625 pmol NESPR- or LacZ-targeting probe set, and rotated at 4°C for 3 h. Beads were washed 3 times with unsupplemented SDS lysis buffer. DNA was eluted in two consecutive round by incubation with a cocktail of 10 mg/mL RNase A and 10 U/uL RNase H in DNA elution buffer (50 mM NaHCO3 and 1% SDS). Eluates were incubated with 150 ug/uL proteinase K at 50°C for 45 min, and DNA was purified using PhOH:Chloroform:Isoamyl extraction. The aqueous phase was transferred, and 3 ug GlycoBlue, 30 uL 3 M NaOAc, and 900 uL 100% EtOH were added and stored overnight at -20°C. Samples were spinned at 16.000 x g for 30 min at 4°C, supernatant was removed, and the pellet was washed in 1 mL 70% EtOH. Pellets were then airdryed, and resuspended in 30 uL nuclease-free water.
NEBNext II library prep according to the manufacturer's instructions

treatment_protocol: For RNase control sample, lysates were treated with 10 mg/mL RNase A and 10 U/uL RNase H

value: SHEP

value: Neuroblastoma cell line


title: IMR32, LacZ, ChIRP, Rep1

description: Library name: LacZ_IMR32_ChIRP_rep1


title: IMR32, INPUT

description: Library name: NESPR_IM32_INPUT


title: IMR32, NESPR, ChIRP, Rep1

description: Library name: NESPR_IMR32_ChIRP_rep1


title: IMR32, NESPR, ChIRP, RNase

description: Library name: NESPR_IMR32_ChIRP_RNase

value: RNase A and RNase H


title: IMR32, NESPR, ChIRP, Rep2

description: Library name: NESPR_IMR32_ChIRP_rep2


title: SHEP, NESPR, ChIRP, Rep1

description: Library name: NESPR_SHEP_ChIRP_rep1


title: NT Naïve hPSC replicate1

description: Library name: NT_Naive_1

value: Nontargeting

value: Doxycycline


title: 1928ZAP327 CAR with stimulation rep3

city: Los Angeles

first: Rongfu

last: Wang

address: 1441 Eastlake Ave., NRT5517

institute: Keck School of Medicine, USC

description: Library name: mCAR_19pTu

data_processing:
Partek Flow Genomic Analysis Software (Ver: 10.0.21.0509)
trim base
STAR - 2.7.3a
Quantify to annotation model (Partek E/M)
Normalization, GSA
Assembly: hg38
Supplementary files format and content: txt file includes raw count of all samples
Supplementary files format and content: txt file includes normalized count of samples

source_name: Human T cells

extract_protocol:
Total RNA was extracted using Rneasy kit (Qiagen)
Per Novogene's SOP.

value: Human T cells


title: CARHSP1 IF hPSC replicate3

description: Library name: CARHSP1_3


title: 1928ZAP327 CAR with stimulation rep1

description: Library name: mCAR_14pTu


title: 1928ZAP327 CAR no stimulation rep3

description: Library name: mCAR_19


title: 1928ZAP327 CAR no stimulation rep2

description: Library name: mCAR_16


title: 1928ZAP327 CAR no stimulation rep1

description: Library name: mCAR_14


title: 1928z CAR with stimulation rep3

description: Library name: a1928z_19pTu


title: 1928z CAR with stimulation rep1

description: Library name: a1928z_14pTu


title: 1928z CAR no stimulation rep2

description: Library name: a1928z_16


title: 1928z CAR no stimulation rep3

description: Library name: a1928z_19


title: scRNA-seq data from hypertrophic scar sample 1 (female, 4 y)

city: 杭州市

first: Yao

last: Jie

state: 浙江

address: 浙江大学紫金港校区农学院A

institute: ZheJiang University

description: Library name: Hy01_scRNA

data_processing:
scRNA-seq data were initially aligned to the reference genome using Cell Ranger (v7.1.0) (10x Genomics, 2023a). Downstream analysis was performed using Seurat (v5.0) (Hao et al., 2024) in R. Cells with fewer than 200 or more than 5,000 detected genes, or with mitochondrial gene percentages exceeding 20%, were excluded to remove low-quality cells and potential doublets. The filtered expression matrix was normalized and scaled, and highly 3000 variable genes were identified for downstream analyses. Dimensionality reduction was performed using principal component analysis (PCA), and the top 30 principal components were selected for downstream analysis. Batch effects across samples were corrected using Harmony (Korsunsky et al., 2019), followed by uniform manifold approximation and projection (UMAP) for visualization. Cell type annotation was assigned based on marker genes from the ScarCellMarker database (Zheng et al., 2023).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Processed data files are provided as gzipped tar archives (.tar.gz).  - scRNA-seq processed data: scar_Integration_0427_seurat_annotated.tar.gz, contains Seurat objects with filtered gene-barcode matrices for 4 samples (2 keloid, 2 hyperplastic).  - Spatial transcriptomics processed data: ST_keloid_spaceranger_results.tar.gz and ST_hyper_spaceranger_results.tar.gz, each contains filtered_feature_bc_matrix/, spatial/ directories, and web_summary.html for 1 keloid and 1 hyperplastic scar sample respectively.  All files are ready for downstream analysis using Seurat or other single-cell/spatial transcriptomics analysis tools.

source_name: hypertrophic scar tissue

extract_protocol:
Total RNA was extracted from scar tissue samples (keloid and hyperplastic scars) using standard tissue dissociation and RNA isolation protocols. For scRNA-seq, single cells were captured and RNA was reverse-transcribed into cDNA using 10x Genomics Chromium platform. For spatial transcriptomics (ST), RNA was captured directly from tissue sections using 10x Genomics Visium platform.
For scRNA-seq samples, libraries were prepared using 10x Genomics Chromium Single Cell 3’ v3.1 kit according to the manufacturer's instructions. For ST samples, libraries were prepared using 10x Genomics Visium Spatial Gene Expression kit, including reverse transcription, cDNA amplification, and library construction per the standard protocol.

value: hypertrophic scar tissue


title: spatial transcriptomic data from hypertrophic scar sample 1 (female, 4y)

address: 浙江大学紫金港校区农学院A

description: Library name: Hy_ST

data_processing:
scRNA-seq data were initially aligned to the reference genome using Cell Ranger (v7.1.0) (10x Genomics, 2023a). Downstream analysis was performed using Seurat (v5.0) (Hao et al., 2024) in R. Cells with fewer than 200 or more than 5,000 detected genes, or with mitochondrial gene percentages exceeding 20%, were excluded to remove low-quality cells and potential doublets. The filtered expression matrix was normalized and scaled, and highly 3000 variable genes were identified for downstream analyses. Dimensionality reduction was performed using principal component analysis (PCA), and the top 30 principal components were selected for downstream analysis. Batch effects across samples were corrected using Harmony (Korsunsky et al., 2019), followed by uniform manifold approximation and projection (UMAP) for visualization. Cell type annotation was assigned based on marker genes from the ScarCellMarker database (Zheng et al., 2023).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Processed data files are provided as gzipped tar archives (.tar.gz).  - scRNA-seq processed data: scar_Integration_0427_seurat_annotated.tar.gz, contains Seurat objects with filtered gene-barcode matrices for 4 samples (2 keloid, 2 hyperplastic).  - Spatial transcriptomics processed data: ST_keloid_spaceranger_results.tar.gz and ST_hyper_spaceranger_results.tar.gz, each contains filtered_feature_bc_matrix/, spatial/ directories, and web_summary.html for 1 keloid and 1 hyperplastic scar sample respectively.  All files are ready for downstream analysis using Seurat or other single-cell/spatial transcriptomics analysis tools.
Library strategy: Spatial Transcriptomics


title: spatial transcriptomic data from keloid sample 1 (male, 6y)

address: 浙江大学紫金港校区农学院A

description: Library name: Ke_ST

source_name: keloid tissue

value: keloid tissue


title: scRNA-seq data from hypertrophic scar sample 2 (male, 4 y)

address: 浙江大学紫金港校区农学院A

description: Library name: Hy02_scRNA


title: scRNA-seq data from keloid sample 1 (male, 6 y)

address: 浙江大学紫金港校区农学院A

description: Library name: Ke01_scRNA


title: 1928z CAR no stimulation rep1

description: Library name: a1928z_14


title: scRNA-seq data from keloid sample 2 (male, 20y)

address: 浙江大学紫金港校区农学院A

description: Library name: Ke02_scRNA


title: MCF-7 H3K27ac CUT&Tag

city: Beijing

first: Zijun

last: Peng

address: Xueyuan road number 38

institute: Peking University

description: Library name: MCF-7 H3K27ac CUT_Tag

data_processing:
The raw sequencing data were first conducted quality control via the Fastp toolkit for the reliability of the following analysis with a quality score > 20. Remained sequences were aligned to the unmasked human reference genome ( hg19) using Bowtie Version 2. MACS Version 2 was used for the identification of YEATS4-, H3K14cr-, h3K27ac-specific binding peaks at p-value < 10^-5. Genomic distributions of YEATS4, H3K14cr, and H3K27ac binding sites were analyzed by ChIPseeker.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
Briefly, approximately 1 × 10^6 MCF-7 cells were collected and incubated with NovoNGS® ConA Beads. Then antibodies and ChiTag transposons were bonded to the chromatin in order.
DNA fragments were obtained, amplified, and purified according to the NovoNGS® CUT&Tag High‐Sensitivity Kit.

value: human breast cancer cell


title: Bulk_Healthy_6

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample 48
3' RNA

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the human reference genome (GRCh38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies. Differential expression analysis was conducted using the Seurat package in R, which included scaling, principal component analysis, and clustering to identify cell populations and marker genes.
Bulk 3' sequencing used for 10x cell demultiplexing using Freemuxlet https://demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/Freemuxlet.html
Assembly: refdata-cellranger-GRCh38-1.2.0
Supplementary files format and content:
For each library:
10x output that contain features barcodes and matrix
feature_ref with antibody barcodes
mapping of patients to 10x cell name and unique cell name in this work
GEO_metadata.tsv: Annotated cells csv format
Seurat_annotated_GEO.rds: Easy to load all main data normalized and annotated

source_name: Peripheral Blood

extract_protocol:
PBMCs separation by Ficoll centrifugation
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

value: Peripheral Blood

value: PBMCs

tag: patient in_sample


title: Anna_CART_4_gene_expression

description:
Library name: Sample 49
10x Genomics


title: 1928ZAP327 CAR with stimulation rep2

description: Library name: mCAR_16pTu


title: Bulk_Healthy_10

description:
Library name: Sample 44
3' RNA


title: Bulk_Healthy_8

description:
Library name: Sample 47
3' RNA


title: Bulk_Healthy_11

description:
Library name: Sample 45
3' RNA


title: Bulk_Healthy_9

description:
Library name: Sample 46
3' RNA


title: Bulk_Axi-23

description:
Library name: Sample 38
3' RNA


title: Bulk_Healthy_5

description:
Library name: Sample 42
3' RNA


title: Bulk_Axi-24

description:
Library name: Sample 39
3' RNA


title: Anna_CART_5_gene_expression

description:
Library name: Sample 41
10x Genomics


title: OMB1846, control

city: Oxford

first: Edmund

middle: C R

last: Watson

address: Windmill Road

department: NDORMS

institute: University of Oxford

description: Library name: omb1846

data_processing:
FASTQ files were processed by running a singularity image of the wf-single-cell pipeline (EPI2ME) on a high-performance cluster, with the reference genome GRCh38 and expected cells set to 5000.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Bone marrow

extract_protocol:
For myeloma samples: bone marrow aspirates in EDTA underwent Ficoll separation to extract bone marrow mononuclear cells (BMMNCs), and were then viably frozen for long-term nitrogen storage. Samples then defrosted in small batches, and kept at 4ºC pending encapsulation into 10X GEM-X. For control samples: Femoral head and necks acquired during elective arthroplasty for non-malignant conditions were taken directly for processing, where trabecular bone marrow was washed with ice cold PBS and agitated. The resulting eluate was spun on a Ficoll gradient and the buffy coat taken forward for 10X Next-GEM (OMB1791, 1798, 1846) or GEM-X (OMB 2148).
Single cell encapsulation performed as per manufacturer's instructions. GEM-X single cell 3', protocol CG000731 Rev A (or Next-GEM single cell 3' v3.1, protocol CG000315 Rev E). Briefly, cells encapsulated with v4 (or v3.1) reagents; GEM-RT incubation; then clean-up, cDNA amplification (13 cycles of PCR) and cDNA clean-up. Samples were quantified with Agilent TapeStation. 10 ng of cDNA library then taken through to legacy Oxford Nanopore (ONT) SQK-PCS111 protocol, using PCS114 reagents, where cDNA biotin-tagged, followed by Streptavidin bead pull down before final PCR with clean up. Adapters then added, and Promethion R10.4.1 flow cell loaded (or R9 chemistry for OMB1791, 1798, 1846), one sample per flow cell. Samples were sequenced on a Promethion 48, with super accurate base calling.

value: Bone marrow

value: Bone marrow mononuclear cell

tag: disease state

value: non-malignant control

value: control


title: OMB1798, control

description: Library name: omb1798


title: 1928z CAR with stimulation rep2

description: Library name: a1928z_16pTu


title: OMB2148, control

description: Library name: omb2148


title: Bulk_Healthy_7

description:
Library name: Sample 43
3' RNA


title: Bulk_Axi-25

description:
Library name: Sample 40
3' RNA


title: Bulk_Poc-4

description:
Library name: Sample 36
3' RNA


title: Bulk_Poc-2

description:
Library name: Sample 34
3' RNA


title: Bulk_Poc-3

description:
Library name: Sample 35
3' RNA


title: OMB1791, control

description: Library name: omb1791


title: Bulk_Axi-22

description:
Library name: Sample 33
3' RNA


title: Bulk_Poc-11

description:
Library name: Sample 31
3' RNA


title: Bulk_Poc-10

description:
Library name: Sample 30
3' RNA


title: PROM00006, screening

description: Library name: prom00006_bl

value: myeloma

value: Belantamab mafodotin

value: screening (pre-treatment start)


title: Anna_CART_7_gene_expression

description:
Library name: Sample 32
10x Genomics


title: MM00099, follow-up, remission

description: Library name: mm00099_fu1

value: follow-up


title: Bulk_Poc-9

description:
Library name: Sample 29
3' RNA


title: Bulk_Poc-8

description:
Library name: Sample 28
3' RNA


title: Bulk_Poc-7

description:
Library name: Sample 27
3' RNA


title: Bulk_Poc-6

description:
Library name: Sample 26
3' RNA


title: Bulk_Poc-5

description:
Library name: Sample 37
3' RNA


title: MM00098, follow-up, active

description: Library name: mm00098_fu1


title: MM00075, follow-up, remission

description: Library name: mm00075_fu1


title: Anna_CART_6_gene_expression

description:
Library name: Sample 25
10x Genomics


title: MM00075, screening

description: Library name: mm00075_bl


title: Rpb1 WT RNA-seq Rep3

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description:
Library name: Sample 3
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed

data_processing:
Reads were aligned using hisat2 version 2.1.0
PCR duplicates were removed using bbtools clumpify version 39.01
rMATS version 4.0.2
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: bigwig

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

growth_protocol: cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep

extract_protocol:
Trizol extraction rRNA deletion by the method of [1] Baldwin A, Morris AR, Mukherjee N. . Curr Protoc. 2021;1:e176.
KAPA RNA HyperPrep KR1350

treatment_protocol: Amr Rpb1 was induced with doxycycline (2.0 mg/ml)  for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before harvesting  RNA for RNA-seq.

value: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr WT

value: doxycycline induced, a-amanitin (2.5 mg/ml) 42 hr


title: MM00063, follow-up, remission

description: Library name: mm00063_fu1


title: Rpb1 R749H RNA-seq Rep2

description:
Library name: Sample 5
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed

source_name: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H


title: Rpb1 R749H RNA-seq Rep3

description:
Library name: Sample 6
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed

value: HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H


title: Rpb1 WT RNA-seq Rep2

description:
Library name: Sample 2
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed


title: ORB7320, follow-up, active

description: Library name: orb7320_fu1


title: Rpb1 R749H RNA-seq Rep1

description:
Library name: Sample 4
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed


title: HEK293FlpIN_R749H Rpb1 CAR-SPLASH Rep2

description: Library name: Sample 4

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
clusters of hybri-reads were identifeid with TOSCA (Chakrabarti et al NAR, 51, 3573, 2023)
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: GTF, hybri-reads

molecule: nuclear RNA

growth_protocol: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep. Doxycylcine 2 mg/ml 48 hr a-amanitin 5mg/ml 24 hr

extract_protocol:
chromatin associated RNA was isolated from urea washed nuclei, and fragmented with RNAse III. Psoralen cross-linked RNA was isolated on magnetic  streptavidinMyOne beads, and proximity ligated with RNA ligase 1 on the beads. Eluted RNA was reverse cross linked with 254 nm UV (4.25mW/cm2) for 10 minutes.
QIAseq miRNA UDI  kit (#331505) with 12 base UMI.using SuperScript IV RT

treatment_protocol: cells were permeabilised with 0.01% digitonin .2mM AMT-PEG3-Biotin (AP3B),  1X dPBS for 5 minutes at 37°C then crosslinked at 365 nm UV at dose of 2.5 mW/cm2 for 20 minutes.


title: Rpb1 WT RNA-seq Rep1

description:
Library name: Sample 1
DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
RNA seq of rRNA depleted RNA random +oligo dT primed


title: MM00265, screening

description: Library name: mm00265_bl


title: HEK293FlpIN_R749H Rpb1 CAR-SPLASH Rep1

description: Library name: Sample 3

value: DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin,  pen/strep. Doxycylcine 2 mg/ml 48 hr a-amanitin 5mg/ml 24 hr


title: HEK293FlpIN_WT Rpb1 CAR-SPLASH Rep2

description: Library name: Sample 2


title: ORB6049, screening

description: Library name: orb6049_bl


title: Ecto_CBC_GBC

description:
Library name: Ecto_CBC_GBC
10X Genomics

data_processing:
The origin sequence data was aligned to human genome GRCH38 and processed by STARsolo software and gene expression matrix was generated.
Assembly: Homo_sapiens GRCh38
Supplementary files format and content: STAR index
Supplementary files format and content: matix file

source_name: cell barcode and gene barcode correlation for sample 2

extract_protocol:
The hPSC cells were infected with lentivirus and sorted based on fluorescence protein expression. The sorted cells were recovered for one week, followed by induced differentiation towards ectoderm lineage. Cells were washed with PBS and digested to single cell with Accutase (Stem Cell Tech), then washed again with PBS and resuspended to the concentration suggested by 10X Genomics library preparation instruction.
The library was prepared according to 10X Genomics single cell 3' v2 protocol.

treatment_protocol: lentivirus infection

value: Ectoderm

value: gene barcode and cell barcodes were PCR amplified from cDNA retained following the whole transcriptome amplification step of the 10x Genomics scRNA-seq library preparation protocol


title: HEK293FlpIN_WT Rpb1 CAR-SPLASH Rep1

description: Library name: Sample 1


title: ESC_CBC_GBC

description:
Library name: ESC_CBC_GBC
10X Genomics

source_name: cell barcode and gene barcode correlation for sample 1

value: hPSC


title: ESC_perturb

description:
Library name: ESC_perturb
10X Genomics

source_name: hPSC

value: lentivirus infection and sorting


title: MM00263, follow-up, active

description: Library name: mm00263_fu1


title: MM00263, screening

description: Library name: mm00263_bl


title: seqrun3_donor5-6-7_HTO

city: Zürich

first: Aline

last: Bauer

address: Vladimir-Prelog-Weg 1-5/10

department: D-CHAB

country: Switzerland

institute: ETH Zürich

data_processing:
CellRangerMulti v7.1.0 used for demultiplexing + read mapping + barcode assignment + UMI counting
R package Seurat used for quality control + normalization + dimensionality reduction + clustering
Assembly: GRCh 38.p13
Supplementary files format and content: 10X v3 count matrices in HDF5 format
Supplementary files format and content: Seurat object of final analysis
Library strategy: CITE-seq

molecule: protein

source_name: Skin and adipose tissue

extract_protocol:
Human skin and subcutaneous tissue were enzymatically digested, the stromal vascular fraction isolated and stained with antibodies before FACS sorting lymphatic endothelial cells (LECs). Sorted cells were loaded on into the 10X Chromium controller.
The library preparation followed the manufacturer's guidelines specified in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) with Feature Barcoding technology for Cell Surface Protein.

value: Skin and adipose tissue

value: FACS-sorted LECs

tag: library type

value: HTO

tag: hto

value: TotalSeq-B0256 anti-human Hashtag 6 antibody (donor 6_skin), TotalSeq-B0257 anti-human Hashtag 7 antibody (donor 6_fat), TotalSeq-B0258 anti-human Hashtag 8 antibody (donor 7_skin), TotalSeq-B0259 anti-human Hashtag 9 antibody (donor 7_fat)


title: ORB4718, follow-up, active

description: Library name: orb4718_fu1

value: Bone marrow

value: Bone marrow mononuclear cell


title: seqrun3_donor5-6-7_GEX

value: mRNA


title: seqrun2_donor3-4_HTO

value: TotalSeq-B0256 anti-human Hashtag 6 antibody (donor 3_skin), TotalSeq-B0257 anti-human Hashtag 7 antibody (donor 3_fat), TotalSeq-B0258 anti-human Hashtag 8 antibody (donor 4_skin), TotalSeq-B0259 anti-human Hashtag 9 antibody  (donor 4_fat)


title: ORB4718, screening

description: Library name: orb4718_bl

value: myeloma

value: Belantamab mafodotin

value: screening (pre-treatment start)


title: seqrun1_donor1-2_HTO

value: TotalSeq-B0256 anti-human Hashtag 6 antibody (donor 1_skin), TotalSeq-B0257 anti-human Hashtag 7 antibody (donor 1_fat), TotalSeq-B0258 anti-human Hashtag 8 antibody (donor 2_fat)


title: seqrun2_donor3-4_GEX


title: LEC donor 433Z032_3_4dyn_flowOSS_R1

data_processing:
Sequencing depth was at least 22.9 million reads per sample. Sequencing reads were aligned using the STAR package, counted using the Rsubread package, and differential expression analysis was conducted using the DESq2 package (with grouping according to treatment and donor), done by the FGCZ (functional genomic center zurich), all in R version 4.0.4.
Assembly: GRCh38
Supplementary files format and content: tab-delimited raw counts

source_name: Skin

growth_protocol: Human dermal LECs (passages 3-5) were grown on dishes coated with human plasma fibronectin in PBS (10 µg/mL, Millipore, FC010) in complete EBM-2 medium (Lonza CC-3156, 5% FBS including VEGF-A) in humidified atmosphere at 37°C with 5% CO2

extract_protocol:
Total RNA was isolated with the kit #740955 from Macherey Nagel and stored at -80°C until further processing.
RNA libraries for RNA-seq were prepared using Illumina Truseq Stranded mRNA following manufacturer's instructions.

treatment_protocol: The parallel plate system (Ibidi, 10902) was used to create isolated laminar and oscillatory shear stress conditions. Ibidi slides (µ-slides I0.8 Luer slides, Ibidi, 80196) were coated with the appropriate coating solution depending on the cell type for 30 min at RT. Subsequently, the coating was removed, and the cells were seeded on the slides at a density of 200,000 cells per slide and cultured for 24 h at 37 °C. The cells were subjected to laminar flow (4 dyn/cm2), oscillatory flow (4 dyn/cm2; 0.25 Hz, flow changes direction every 4 sec), or kept under static conditions for 48 h. The red tubing set (Ibidi, 10962) was used. The medium was renewed on the day of shear stress induction and after 24 h in the case of the static condition.

value: Skin

value: primary cells

value: Lymphatic endothelial cells

value: oscillatory flow


title: seqrun1_donor1-2_GEX


title: LEC donor 433Z032_3_4dyn_flowLam_R1

value: laminar flow


title: LEC donor 439Z007_2_4dyn_flowOSS_R1


title: LEC donor 431Z006_2_4dyn_flowOSS_R1


title: panicles, OsM2L_MT2

city: Bengaluru

first: Usha

last: Vijayraghavan

state: Karnataka

address: New biological Sciences, Indian Institute of Sciences

department: MCB

institute: Indian Institute of Science

data_processing:
QC of the sequenced reads is performed with fastqc and low qulaity reads and adapters are trimmed with fastp algorithm.
The filtered reads are Aligned to rice genome (https://rapdb.dna.affrc.go.jp/) using STARaligner.
FeatureCounts tools is used to extract raw counts using "IRGSP-1.0_representative_transcript_exon_2022_09-01.gtf" as reference.
Differential expression analysis was carried out using the edgeR package.
Assembly: IRGSP-1.0_genome.fasta (September 2022)
Supplementary files format and content: OsM2_E_M_L_WT_MT_RawCounts.xlsx : Result of FeatureCount algorithm over 15 indvidual samples in one Excel file (Rap gene id column + 15 columns).
Supplementary files format and content: OsM2_E_M_L_WT_MT_NormalizedCounts.xlsx : Respective Normalized counts (TPM) as single Excel file (Rap gene id column + 15 columns).
Supplementary files format and content: Dataset_S2.xlsx : Result of differential expression analysis for the respective developmental pool (WT vs mutant). Information of raw and aligned reads is provided. The similarity plots are provided as images in XLSX file.
Supplementary files format and content: Dataset_S3.xlsx : Result of Gene ontology analysis for the respective data sets.
Supplementary files format and content: Dataset_S4.xlsx : List of DEGs in osmads2 that have orthologs deregulated in Arabidopsis pi-1 mutant.
Supplementary files format and content: Dataset_S5.xlsx : List of DEGs in early and middle osmads2 expression datasets with respective occurrence number for DNA binding motifs of the different nodal transcription factors. Selected enriched motifs are provided in seperate sheet. Information of occurrence of enriched motifs in OsM2 directly regulated genes is provided in seperate sheet.

organism: Oryza sativa

source_name: Inflorescence Meristem (1.0- 2.0 cm panicle)

growth_protocol: RNA-sequencing of WT and osmads2d8/d8 tissues was performed for three and two biological  replicates, respectively.

extract_protocol:
First, total RNA was extracted from panicle tissue using the TRIzol R  reagent (Invitrogen, Carlsbad, CA, USA). RNA was then treated with DNAse I (M0303S  NEB, Massachusetts, USA) to remove contaminating gDNA according to the manufacturer’s  protocol. RNA quality and concentration were examined on a 4150 TapeStation (Catalog:  G2992AA, Agilent Technologies, California, USA) and Qubit (Life Technologies, California,  USA), respectively.
RNA of integrity number (RIN) > 7 was used for library construction.  Total RNA of 500 ng was used to enrich mRNA using the NEBNext Poly (A) mRNA magnetic isolation module (Catalog: E7490, New England Biolabs) following the  manufacturer’s protocol. Enriched mRNAs were used for library preparation using the  NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England  Biolabs).
Sequence data was generated using the Illumina HiSeq, pair-end 2X150bp chemistry.

value: osm2 mutant (crispar-cas9)


title: panicles, OsM2L_MT1

value: Inflorescence Meristem (1.0- 2.0 cm panicle)


title: LEC donor 433Z032_3_4dyn_ss_R1

value: steady-state


title: Cisplatin + 84-B10 biological replicate 4

city: Nanjing

first: Fan

middle: Jiao

last: Jiao

address: 72 Guangzhou Road

institute: Children’s Hospital of Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
Supplementary files format and content: xls, include FPKM values for each Sample

source_name: kidney

growth_protocol: C57BL/6 mice were maintained in a Specific Pathogen Free (SPF) room in the Animal Core Facility of Nanjing Medical University with 12-h light/12-h dark cycle and constant temperature (22 ± 2 °C), with free access to food and water.

extract_protocol:
Kidney tissues were harvested and rapidly frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the instruction manual.
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Mice were pre-treated with 84-B10 for 48h before cisplatin (25mg/kg, intraperitoneal) challenge in both cisplatin and cisplatin +84-B10 group, then treatment groups were received 84-B10 daily. After 72h cisplatin challenge, mice of all groups were sacrificed.

value: kidney

value: Cisplatin +84-B10 after 72 h


title: Ectoderm_perturb

description:
Library name: Ectoderm_perturb
10X Genomics

source_name: hPSC derived ectodem cells with selected targets knock out

value: Ectoderm

value: lentivirus infection, sorting and differentiation


title: panicles, OsM2L_WT3

value: Wildtype


title: LEC donor 439Z007_2_4dyn_ss_R1


title: Cisplatin + 84-B10 biological replicate 3


title: Cisplatin + 84-B10 biological replicate 2


title: LEC donor 431Z006_2_4dyn_ss_R1


title: LEC donor 439Z007_2_4dyn_flowLam_R1


title: panicles, OsM2L_WT2


title: Cisplatin + 84-B10 biological replicate 1


title: pre-treatment PBMCs, Library_9_hashing

description: 10x Genomics

value: Peripheral Blood

value: PBMCs

value: HTO


title: panicles, OsM2L_WT1


title: panicles, OsM2M_MT2

source_name: Inflorescence Meristem (0.5- 1.0 cm panicle)


title: pre-treatment PBMCs, Library_9_gene_expression

description: 10x Genomics

value: GEX


title: pre-treatment PBMCs, Library_8_hashing

description: 10x Genomics


title: ORB1444, follow-up, remission

description: Library name: orb1444_fu1

value: Bone marrow

value: Bone marrow mononuclear cell

value: myeloma

value: Belantamab mafodotin

value: follow-up


title: panicles, OsM2M_MT1

value: Inflorescence Meristem (0.5- 1.0 cm panicle)

value: osm2 mutant (crispar-cas9)


title: Oculina patagonica 4 clicktags

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
Library name: Sample 12
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.

data_processing:
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
Assembly: Acropora millepora: GCF_013753865.1, Stylophora pistillata: GCF_002571385.2
Supplementary files format and content: TSV file with the gene IDs (in the same order as in the UMI matrix, mtx file)
Supplementary files format and content: TSV file with CellIDs and associated metadata (in the same order as in the UMI matrix, mtx file)
Supplementary files format and content: MTX file containin gene x cell UMI counts

organism: Oculina patagonica

source_name: Whole adult specimens

extract_protocol:
Whole-adult specimens were fixed and dissociated before sorting single-cells for scRNAseq.
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.

value: Whole adult specimens


title: pre-treatment PBMCs, Library_8_gene_expression

description: 10x Genomics


title: Cisplatin biological replicate 3

value: kidney

value: Cisplatin after 72 h


title: PROM00016, screening

description: Library name: prom00016_bl

value: screening (pre-treatment start)


title: Cisplatin biological replicate 2


title: Cisplatin biological replicate 1


title: panicles, OsM2M_WT2


title: LEC donor 431Z006_2_4dyn_flowLam_R1

value: Skin

value: primary cells

value: Lymphatic endothelial cells

value: laminar flow


title: pre-treatment PBMCs, Library_6_hashing

description: 10x Genomics

value: Peripheral Blood

value: PBMCs

value: HTO


title: pre-treatment PBMCs, Library_6_gene_expression

description: 10x Genomics

value: GEX


title: Oculina patagonica 2 clicktags

description:
Library name: Sample 10
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.


title: Oculina patagonica 3 clicktags

description:
Library name: Sample 11
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.


title: pre-treatment PBMCs, Library_2_hashing

description: 10x Genomics


title: panicles, OsM2M_WT1

value: Wildtype


title: Oculina patagonica 1 clicktags

description:
Library name: Sample 9
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.


title: Vehicle biological replicate 4

value: Vehicle after 72 h


title: Vehicle biological replicate 3


title: panicles, OsM2E_MT2

source_name: Inflorescence Meristem (0.2-0.5 cm panicle)


title: Oculina patagonica 4

description: Library name: Sample 8


title: pre-treatment PBMCs, Library_14_hashing

description: 10x Genomics


title: panicles, OsM2E_MT1

value: Inflorescence Meristem (0.2-0.5 cm panicle)


title: pre-treatment PBMCs, Library_2_gene_expression

description: 10x Genomics


title: Vehicle biological replicate 2


title: Cisplatin biological replicate 4


title: Oculina patagonica 3

description: Library name: Sample 7


title: pre-treatment PBMCs, Library_14_gene_expression

description: 10x Genomics


title: panicles, OsM2E_WT3


title: Oculina patagonica 2

description: Library name: Sample 6


title: Vehicle biological replicate 1


title: pre-treatment PBMCs, Library_11_hashing

description: 10x Genomics


title: panicles, OsM2M_WT3

value: Inflorescence Meristem (0.5- 1.0 cm panicle)


title: panicles, OsM2E_WT2


title: Oculina patagonica 1

description: Library name: Sample 5


title: pre-treatment PBMCs, Library_11_gene_expression

description: 10x Genomics


title: R254AKlf3MEFs RNA-seq Rep 2

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

data_processing:
ChiP-seq - After quality filtering and adaptor trimming using Trimmomatic v0.3.3 using the default parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36) (Bolger et al. 2014), reads were aligned to the mm10/GRCm38 Mus musculus genome using Bowtie v2.2.9 (Langmead & Salzberg 2012) set to –very-sensitive. Aligned reads were filtered using samtools v1.3.1 (Danecek et al. 2021) to remove unmapped reads, non-primary alignments, and alignments with a mapping quality less than 10 (-F 1804 -q 10).
ChiP-seq - Peak calling for all datasets was done using the spp package (Kharchenko et al. 2008, Landt et al. 2012) after removing duplicates with Picard MarkDuplicates v1.109. A set of consistent peaks (IDR = 0.01 for KLF3-V5 or 0.05 for WDR5) were then identified using IDR2 (Landt et al. 2012, Li et al. 2011).
ChIP-seq - Read coverage tracks were generated using deepTools bamcoverage (Ramírez et al. 2016) with the filtered mapped reads, extending reads based on predicted fragment sizes from spp, and normalizing all samples to have the equivalent of 1 million mapped reads (-bs 1 --normalizeUsing CPM).
RNA-seq - Raw fastq files were quantified using Salmon v1.6.0 (Patro et al. 2017) in selective alignment mapping mode (--validateMappings --rangeFactorizationBins 4) using a GENCODE vM20 (Frankish et al. 2019) (based on Mus musculus mm10 genome). A decoy-aware index was built by concatenating the GRCm38 primary assembly genome to the end of the GENCODE vM20 transcriptome. The quantified .sf files are provided for each RNA-seq sample
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak, sf - plain-text, tab separated file with header generated after quantification by salmon

source_name: RNA-Seq in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

growth_protocol: Mouse embryonic fibroblast (MEF) cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Life Technologies, CA, USA) supplemented with 1% (v/v) Penicillin-Streptomycin-Glutamine (PSG) solution (Life Technologies, CA, USA) and 10% (v/v) fetal bovine serum (FBS) (Life Technologies, CA, USA). Cells were grown at 37°C in a 5% CO2 water-jacketed incubator.

extract_protocol:
Total RNA was extracted from MEF wildtype KLF3 cells and MEFs R254A mutant KLF3 cells with Tri-reagent according to the manufacturer’s protocol (Qiagen, Cat#74004). 200 mL of chloroform was added to 1 mL Tri-reagent and vortexed for 10 seconds. The mixture was spun at 12,000 x g for 5 minutes. The aqueous phase was transferred into a new Eppendorf tube. The aqueous phase was mixed with  an equal volume of ethanol. The RNA-ethanol mixture was added to the column and washed once with wash buffer. RNA retained in the column was treated with DNA removal kit (Qiagen, Cat#79254) to ensure the purity of RNA samples. After DNase treatment, bound RNA was washed with wash buffer and then eluted with RNase A free water.  RNA concentration was determined by UV-light absorbance at 260 nm using a Nanodrop machine (Thermo Fisher Scientific). The integrity of RNA was checked by Bioanalyzer (Agilent).
TruSeq Stranded mRNA

value: R254A Klf3-V5

value: Klf3-null MEF cells


title: panicles, OsM2E_WT1


title: panicles, MOCK_B6

data_processing:
QC, filtering of low quality reads and adopter trimming is perfomed with fastp tool.
Alignment of filtered fastq files is performed with bowtie2 Aligner.
Uniquely aligned reads are extracted using samtools and dupliactes are marked with SAMBAMBA tools.
deeptools tools is used to create bigwig files.
Peakcalling is perfomed using MACS2 tool using IP as test and MOCK as control to identify high confident reagions bound by OsMADS2
Genomic size of 3.5e8 and keep dup AUTO parameter are used while calling peaks with MACS2
Assembly: MSUv7
Supplementary files format and content: deeptools tools is used to create bigwig files for respective samples.
Supplementary files format and content: Dataset_S1.xlsx : ChIP-Seq peaks enriched in OsMADS2 IP. Information of raw and mapped reads of OsMADS2 IP and MOCK samples are provided. Information of enriched motifs in ChIP seq data and enriched biological pathways are provided.

source_name: Inflorescence Meristem (0.3-2.0 cm)

growth_protocol: Wild-type TP309 panicles of 0.3-2 cm size (~200mg) were used for the ChIP.

extract_protocol:
MNaseI based chromatin was prepared with DNA fragments ranging from 150bp to 900bp. For the ChIP, 8μg of chromatin was used and incubated with 6μg of affinity-purified anti-OsMADS2 antibody. The DNA-protein complexes were pulled down using protein-A magnetic beads.  Simultaneously, a negative control sample using rabbit IgG antibody (mock IP) instead of the  anti-OsMADS2 antibody was processed in the same way. Immunoprecipitated DNA was eluted using the elution buffer provided in the kit and reverse cross-linked using 2M RNase A  and 4M proteinase K in 5M NaCl for 6 hours at 65˚C. Reverse-crosslinked ChIP DNA was purified using the phenol/chloroform purification and precipitation method.
Approximately 6ng of ChIP DNA was processed to prepare a library for NGS by using the Kapa kit, library amplification was performed before the double-size selection.
ChIP-Seq was performed using the Illumina HiSeq2500 machine at the Functional Genomics Center Zurich

treatment_protocol: The tissues were fixed with 1% formaldehyde in a fixation buffer. OsMADS2 ChIP was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Cat #9002, CST, Massachusetts, USA). MNaseI based chromatin was prepared with DNA fragments ranging from 150bp to 900bp.

value: Inflorescence Meristem (0.3-2.0 cm)

tag: tissue region

value: 0.3-2.0 cm panicle

tag: chip antibody

value: IgG


title: pre-treatment PBMCs, Library_10_hashing

description: 10x Genomics

source_name: Peripheral Blood

tag: tissue


title: panicles, MOCK_B5

tag: genotype


title: R254AKlf3MEFs RNA-seq Rep 1


title: WTKlf3MEFs RNA-seq Rep 1

source_name: RNA-Seq in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5

value: WT Klf3-V5


title: pre-treatment PBMCs, Library_10_gene_expression

description: 10x Genomics

tag: cell type


title: WTKlf3MEFs RNA-seq Rep 2

tag: cell line


title: pre-treatment PBMCs, Library_1_hashing

description: 10x Genomics


title: R254AKlf3MEFs Wdr5 ChIP-seq Rep 2 INPUT

source_name: Wdr5 ChIP-seq (INPUT) in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

extract_protocol:
ChIP experiments were performed as previously described (Schmidt et al. 2009). Approximately, 7x107-1x108 cells were used for each ChIP. Cells were crosslinked with 1% formaldehyde for 10 min and the reaction was quenched by 2.5 mM glycine. Fixed cells were washed with cold PBS and centrifuged at 2000 x g for 5 min. Fixed cells were sonicated at high voltage for 20 min (30 seconds on, 30 seconds off) using a Bioruptor (Diagenode) to obtain 200-300 bp DNA fragments. The fragmented chromatin was pulled down at 4°C overnight using an antibody against V5 (Life Technologies, #R960CUS) or WDR5 (Australian Biosearch, #13105S). Chromatin cross-linking was then reversed at 65°C overnight followed by DNA purification. Real-time qPCR was performed on ChIP DNA on an Applied Biosystems ViiA7 Real-time PCR system (Applied Biosystems) to confirm the success of the ChIP experiments before sending to next generation sequencing.
TruSeq DNA Sample Prep Kit

value: input


title: R254AKlf3MEFs Wdr5 ChIP-seq Rep 1 INPUT


title: panicles, OsM2_IP_B6


title: R254AKlf3MEFs Wdr5 ChIP-seq Rep 2

source_name: Wdr5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

value: WDR5 (Australian Biosearch, #13105S)


title: pre-treatment PBMCs, Library_0_hashing

description: 10x Genomics


title: crMGRN1_4

city: Murcia

first: José

last: Sánchez Beltrán

state: Murcia

address: Av. Buenavista, 32, 30120 El Palmar, Murcia

department: Biochemistry and Molecular Biology and Immunology

institute: University of Murcia

description:
Library name: Sample 8
Column name in processed data files: crMGRN1_4

data_processing:
Assembly: not provided
Alignments were performed using HISAT2
Data was processed and normalized with RStudio (version 4.3.1), using the DESeq2 R package.
Supplementary files format and content: TXT files include RAW counts.
Supplementary files format and content: TXT files include RAW counts.
Supplementary files format and content: TXT files include normalisez counts.

source_name: HBL

growth_protocol: The cell line was a kind gift from Prof. G. Ghanem. Cells were grown in DMEM-GlutaMAX enriched with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin sulfate, using cell culture reagents from Gibco (Gaithersburg, MD, USA).

extract_protocol:
Total RNA from MGRN1-KO (clone 4.9) and control cells (n = 4 for each condition) were isolated and purified with RNeasy® Mini kit (QIAGEN, Germantown, MD, USA) as per instructions.
Novogene Co., Ltd. (Cambridge, UK) performed  quality control evaluations (all samples showed an RNA integrity number, RIN = 10), as well as cDNA synthesis, library construction (poly A enrichment), and transcriptomic analysis (Illumina Sequencing PE150, Illumina Inc., San Diego, CA, USA) yielding 15 G of raw data per sample.

treatment_protocol: Cells were transfected with 0.5 μg of CRISPR plasmid (pSpCas9(sgRNA2, sgRNA3 or sgRNA4)) and 1 mg/mL Lipofectamine 2000, using the empty plasmid (pSpCas9) for control cells (CTR). After incubation for 72 h at 37 ◦C, puromycin-resistant clones were selected. The confirmation and selection of KO clones were performed by automated sequencing after PCR amplification of a 500 pb fragment on exon 1 using genomic DNA as a template, and Western blot for MGRN1 detection in all selected clones.

value: HBL

value: human melanoma cells

value: triple-WT

tag: treatment

value: transfection with CRISPR plasmid

tag: sample group

value: MGRN1-KO (CRISPR-Cas9) HBL


title: pre-treatment PBMCs, Library_1_gene_expression

description: 10x Genomics

value: Peripheral Blood

value: PBMCs

value: GEX


title: crMGRN1_3

description:
Library name: Sample 7
Column name in processed data files: crMGRN1_3


title: pre-treatment PBMCs, Library_0_gene_expression

description: 10x Genomics


title: R254AKlf3MEFs Wdr5 ChIP-seq Rep 1


title: pre-treatment PBMCs, Anna_CART_3_hashing

description: 10x Genomics

value: HTO


title: R254AKlf3MEFs Klf3 ChIP-seq Rep 2 INPUT

source_name: Klf3-V5 ChIP-seq (INPUT) in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

value: R254A Klf3-V5


title: crMGRN1_2

description:
Library name: Sample 6
Column name in processed data files: crMGRN1_2


title: pre-treatment PBMCs, Anna_CART_3_gene_expression

description: 10x Genomics


title: crMGRN1_1

description:
Library name: Sample 5
Column name in processed data files: crMGRN1_1


title: pre-treatment PBMCs, Anna_CART_2_hashing

description: 10x Genomics


title: crCTR_4

description:
Library name: Sample 4
Column name in processed data files: crCTR_4

value: CTR HBL


title: R254AKlf3MEFs Klf3 ChIP-seq Rep 1 INPUT

value: Klf3-null MEF cells


title: R254AKlf3MEFs Klf3 ChIP-seq Rep 2

source_name: Klf3-V5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing R254A Klf3-V5

value: V5 tag (Life Technologies, #R960CUS)


title: pre-treatment PBMCs, Anna_CART_2_gene_expression

description: 10x Genomics


title: crCTR_3

description:
Library name: Sample 3
Column name in processed data files: crCTR_3


title: panicles, OsM2_IP_B5

value: Inflorescence Meristem (0.3-2.0 cm)

value: Wildtype

value: 0.3-2.0 cm panicle


title: pre-treatment PBMCs, Anna_CART_1_hashing

description: 10x Genomics


title: WTKlf3MEFs Wdr5 ChIP-seq Rep 2 INPUT

source_name: Wdr5 ChIP-seq (INPUT) in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5

value: WT Klf3-V5

value: input


title: pre-treatment PBMCs, Anna_CART_1_gene_expression

description: 10x Genomics


title: crCTR_2

description:
Library name: Sample 2
Column name in processed data files: crCTR_2

value: HBL

value: human melanoma cells


title: crCTR_1

description:
Library name: Sample 1
Column name in processed data files: crCTR_1

value: triple-WT

value: transfection with CRISPR plasmid


title: WTKlf3MEFs Wdr5 ChIP-seq Rep 1 INPUT


title: MCF-7 H3K14cr CUT&Tag

data_processing:
The raw sequencing data were first conducted quality control via the Fastp toolkit for the reliability of the following analysis with a quality score > 20. Remained sequences were aligned to the unmasked human reference genome ( hg19) using Bowtie Version 2. MACS Version 2 was used for the identification of YEATS4-, H3K14cr-specific binding peaks at q-value < 0.05. Genomic distribution of YEATS4 and H3K14cr binding sites was analyzed by ChIPseeker.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Briefly, approximately 1 × 106 MCF-7 cells were collected and incubated with NovoNGS® ConA Beads. Then antibodies and ChiTag transposons were bonded to the chromatin in order.
After that, DNA fragments were obtained, amplified, and purified according to the NovoNGS® CUT&Tag High‐Sensitivity Kit.

value: H3K14cr (PTMlab, PTM-535RM)


title: WTKlf3MEFs Wdr5 ChIP-seq Rep 2

source_name: Wdr5 ChIP-seq in Klf3-null MEF cells rescued by overexpressing  WT Klf3-V5

value: WDR5 (Australian Biosearch, #13105S)


title: Stylophora pistillata 1 clicktags

description:
Library name: Sample 14
Clicktag barcodes reads necessary to demultiplex conditions. See Readme_ClickTag_demultiplexing.xlsx file for detailed description and barcodes used.

organism: Stylophora pistillata

value: Whole adult specimens


title: Stylophora pistillata 1

description: Library name: Sample 13


title: MCF-7 YEATS4 CUT&Tag

value: YEATS4 (Abcam, ab205018)