title: Setaria viridis leaf H3K27ac CUT&Tag validation sample GWCCSY2

city: Xi'an

first: Huiying

last: Shang

address: Cuihua Road No. 17

institute: Xi'an Botanical Garden

description:
Library name: SVIRIDIS_leaf_H3K27ac_GWCCSY2
Single-sample leaf H3K27ac CUT&Tag dataset used only for S. viridis candidate-locus validation. Source sample id GWCCSY2. Plant material: green foxtail germplasm, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity. Sequencing instrument and antibody were filled as the same as the S. italica CUT&Tag samples based on user-provided experimental judgment. Tissue was filled as leaf based on user-provided confirmation that the S. viridis sampling part matched the Xiaomi leaf sampling scheme.

data_processing:
Raw paired-end reads were quality controlled and aligned to the corresponding reference genome using Bowtie 2 compatible workflows.
Duplicate reads were evaluated using Picard MarkDuplicates outputs where available, and deduplicated alignments were used for downstream summaries.
Normalized signal tracks were generated in bigWig format for H3K27ac signal visualization.
Sample-level H3K27ac peaks were called and exported as broadPeak files. S. italica source peak sets were merged to generate a nonredundant consensus H3K27ac atlas.
The S. viridis CUT&Tag dataset was processed as a single validation sample and used only for representative locus-level support.
Assembly: Setaria italica v1.0, Setaria viridis v4.0 GCA_005286985.2
Supplementary files format and content: bigWig files contain normalized H3K27ac signal tracks for each CUT&Tag library.
Supplementary files format and content: broadPeak files contain sample-level H3K27ac peak calls, and the BED file contains the merged S. italica consensus H3K27ac peak atlas.
Library strategy: CUT&Tag

organism: Setaria viridis

source_name: leaf

growth_protocol: Plants were grown under standard conditions for the source experiment. Heading-stage stem, leaf, and panicle tissues were used where tissue information was available.

extract_protocol:
Nuclei or chromatin-associated material was prepared for CUT&Tag profiling of H3K27ac. Antibody details must be confirmed before final submission, including vendor, catalog number, and lot number.
CUT&Tag libraries were prepared for H3K27ac profiling and sequenced as paired-end genomic DNA libraries. Sequencing platform and instrument model must be confirmed before final submission.

treatment_protocol: No experimental treatment was applied. Samples represent tissue-specific H3K27ac CUT&Tag profiling and one S. viridis validation library.

value: leaf

value: not collected

tag: antibody

value: H3K27ac antibody, Active Motif, catalog 39685, mouse polyclonal; lot not available


title: A549 cells, siControl (NT), 6h Control (biological replicate 2)

status: Public on Jun 30 2026

type: SRA

city: L'Hospitalet de Llobregat

first: Cristina

last: Muñoz-Pinedo

state: Barcelona

address: Hospital Duran i Reynals, 3a planta - Avinguda de la Gran Via, 199

department: ONCOBELL

country: Spain

institute: Institut d'Investigació Biomédica de Bellvitge

description:
Library name: Sample 1 (biol rep 2)
Column name in RSEM_RawCounts.txt: A549n2_6h1

library_source: transcriptomic

data_processing:
Reads were trimmed using fastp and aligned to the human genome (GRCh38) with STAR using ENCODE parameters.
Gene quantification was performed with RSEM.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Lung carcinoma

growth_protocol: A549 cells were cultured in pyruvate-free high-glucose DMEM (25mM Glc) supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine and incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the PureLink RNA Mini Kit (Invitrogen), following the manufacturer’s instructions. 2.5 ug of total RNA was used for construction of sequencing libraries. Total RNA quality was assessed prior to library preparation to ensure suitability for sequencing (OD 260/280 ≥ 2.00; OD 260/230 ≥ 2.00).
Libraries were prepared using a poly(A) enrichment, non-stranded protocol and sequenced on an Illumina platform (paired-end, 150 bp), yielding approximately 50 million reads per sample, with ≥80% of bases at Q30.

treatment_protocol:
Glucose deprivation experiments were performed by seeding 300,000 cells per well in 6-well plates. 48h later (see below transfetion protocol) they were washed twice with FBS-pyruvate-and glucose-free DMEM media and incubated with glucose-free DMEM (0mM), while the control cells were supplemented with 25mM Glucose. Both conditions were supplemented with 10% dialysed FBS (dFBS) and 2mM L-glutamine.
For siRNA transfections, cells were seeded in 6-well plates, trypsinised and transfected while plated with a transfection mixture of unsupplemented media with 1μL/mL DharmaFECT and either non-targeting (NT, siControl) siRNA or specific siRNAs (ATF4 and ATF6) at a final concentration of 100nM. 24h later, cells were trypsinised, plated in two wells and incubated for 24h before treatment.

tag: tissue

value: Lung carcinoma

tag: cell line

tag: cell type

value: Human lung adenocarcinoma

tag: genotype

value: WT (siControl)

tag: treatment

value: Control

tag: time

value: 6 hours


title: seedlings_T1_col-0_ZT0.5_R1

city: York

first: Gina

last: Vong

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description: Library name: C43

data_processing:
fastq files were merged across lanes
Illumina adaptors were trimmed with Trim_Galore/0.6.10-GCCcore-11.3.0 --clip_R1 12 --clip_R2 12
Reads were mapped using Salmon/1.10.0-GCC-11.3.0
quantified reads were processed into abundance, counts and length tables using tximport v.1.34.0 in R v.4.5
Assembly: AtRTD3
Supplementary files format and content: Salmon quant output for each sample.
Supplementary files format and content: abundance_table_salmon.txt, counts_table_salmon.txt and length_table_salmon.txt are tab separated tables containing gene expression data for TPM, counts and read leangths respectively. Each row is a gene and each column is a sample.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seeds were surface sterilised and plated on 1xMS plates with 1% sucrose and 3% agar, in clusters of ~50 seeds. We stratified 3 genotypes of Arabidopsis thaliana (col-0, elf3-1, pifq) seeds at 4C for 3 days. To initiate germination, we exposed all plates to 24h continuous light with blue, red, far-red LEDs at 1:1:1 ratio. We grew the seedlings (on plates) in Snijders (Tilburg, Netherlands) MC1750 growth chamber at 22C and 60% room humidity under 4 light regimes: a) linear dawn; b) extreme dawn; c) 8h photoperiod control; d) 7h photoperiod control. After 7 days of growth, the seedlings were sampled every 30 mins from ZT-0.5 to ZT3 (i.e. 8 timepoints) for 2 replicates of  RNA-seq transcriptome analysis.

extract_protocol:
RNA was extracted using the Omega BioTek EZNA Plant RNA kit, following their protocols
NEBNext Ultra II Directional Library Prep Kit for Illumina, with NEBNext ploy(A) magnetic isolation

treatment_protocol: a) linear dawn (T1): blue, red and far red lights with a 1:1:1 ratio which increased in irradiance stepwise every 10 minutes, for 2h until a maximum PAR of 27.8 umol m-2 s-1. The maximum was sustained for a further 6h before lights turned off. b) extreme dawn (T2): using the same blue, red, far red light settings as the linear dawn treatment, but increasing the slope of the red channel and starting that 0.5h later than the other channels. This resulted in a <1 ratio initially (red relative to the other channels) but increasing as time progressed until the maximum PAR of 27.8 umol m-2 s-1. At the maximum, the B:R:FR ratio was 1:1:1 and was sustained for a further 6h before lights turned off. c) 8h control (C1): on/off square wave 8h photoperiod, with B:R:FR ratios at 1:1:1 d) 7h contro (C2)l: on/off square wave 7h photoperiod, with B:R:FR ratios at 1:1:1

value: seedling


title: IP_P14_GEX

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

description: Library name: IP_P14_GEX

library_source: transcriptomic single cell

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

source_name: CAR T cells

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: CAR T cells

value: Primary cells

value: Normal

value: Pre-treatment

tag: batch


title: d0-3

city: Yang Zhou

first: Yi

last: Du

address: Shuangqiao Street

country: China

institute: Yang Zhou University

description: Library name: Sample 12

data_processing:
CLC Genomics Workbench v11.0
Assembly: The tra nsc ripto me seque ncing and ana lysis were conducted by OE biotech Co., Ltd.(Shang hai, China)
Supplementary files format and content: Tab-delimited text file include RPKM value for each sample

organism: Auxenochlorella pyrenoidosa

source_name: Whole cell

extract_protocol:
RNA was harvested using Rneasy mini plus kit.1.3μg of total RNA was used for the construction of sequencing libraries
Illumina TruSeq RNA

value: Whole cell

value: Chlorella pyrenoidosa cell

value: control


title: A549 cells, siControl (NT), 6h Control (biological replicate 1)

description:
Library name: Sample 1 (biol rep 1)
Column name in RSEM_RawCounts.txt: A549n1_6h1


title: IP_P7_VDJ

description: Library name: IP_P7_VDJ

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples
Library strategy: TCR-Seq


title: d0-2

description: Library name: Sample 11


title: seedlings_T1_col-0_ZT-0.5_R1

description: Library name: C41


title: iPSC-aCMs + VAT EVs #4

city: Boston

first: Worawan

middle: B

last: Limpitikul

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

description: Library name: atrial_V68

data_processing:
Adapter sequences were trimmed from sequencing reads using Cutadapt (v4.8). Next, Quality assessment of both raw and adaptor-trimmed reads was carried out with FastQC (v0.12.1) (www.bioinformatics.babraham.ac.uk/projects/fastqc). Subsequently, the trimmed reads were aligned to the Gencode GRCh38.p13 reference genome using STAR (v2.7.11a). STAR was supplied with Gencode v38 gene annotations to enhance mapping precision, and gene-level read counts were obtained using featureCounts (v2.0.6)
Assembly: GRCh38.p13
Supplementary files format and content: csv files including cpm for each gene in each sample

source_name: ipsc-derived atrial myocytes

extract_protocol:
per manufacturer's protocol - miRNeasy Micro Kit (Qiagen, cat. no. 217084)
per manufacturer's protocol - SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio USA, Inc., cat. no. 634413)

value: ipsc-derived atrial myocytes

value: human iPSCs

value: atrial myocytes

value: wild type

value: VAT EVs


title: IP_P7_GEX

description: Library name: IP_P7_GEX


title: seedlings_C2_col-0_ZT3_R2

description: Library name: C38


title: seedlings_T1_col-0_ZT0.5_R2

description: Library name: C53


title: d0-1

description: Library name: Sample 10


title: iPSC-aCMs + VAT EVs #3

description: Library name: atrial_V67


title: IP_P5_VDJ

description: Library name: IP_P5_VDJ


title: seedlings_C2_col-0_ZT2.5_R2

description: Library name: C37


title: iPSC-aCMs + VAT EVs #2

description: Library name: atrial_V64


title: c0.1-3

description: Library name: Sample 9

value: Potassium peroxymonosulfate stress


title: IP_P5_GEX

description: Library name: IP_P5_GEX


title: seedlings_C2_col-0_ZT2_R2

description: Library name: C36


title: c0.1-2

description: Library name: Sample 8


title: iPSC-aCMs + VAT EVs #1

description: Library name: atrial_V61


title: seedlings_C2_col-0_ZT1.5_R2

description: Library name: C35


title: iPSC-aCMs + iPSC-aCM EVs #3

description: Library name: atrial_ctrl_3

value: iPSC-aCM EVs


title: IP_P2_VDJ

description: Library name: IP_P2_VDJ


title: c0.1-1

description: Library name: Sample 7


title: IP_P2_GEX

description: Library name: IP_P2_GEX


title: seedlings_C2_col-0_ZT1_R2

description: Library name: C34


title: b0.2-3

description: Library name: Sample 6


title: IP_P1_VDJ

description: Library name: IP_P1_VDJ


title: seedlings_C2_col-0_ZT0.5_R2

description: Library name: C33


title: seedlings_T1_col-0_ZT3_R1

description: Library name: C48


title: iPSC-aCMs + iPSC-aCM EVs #2

description: Library name: atrial_ctrl_2


title: iPSC-aCMs + iPSC-aCM EVs #1

description: Library name: atrial_ctrl_1


title: b0.2-2

description: Library name: Sample 5


title: IP_P1_GEX

description: Library name: IP_P1_GEX


title: seedlings_C2_col-0_ZT0_R2

description: Library name: C32


title: macrophages + VAT EVs #3

description: Library name: THP_V61

source_name: macrophages

value: macrophages

value: THP1 cell line


title: CSF_P18D7_VDJ

description: Library name: CSF_P18D7_VDJ

source_name: Cerebrospinal Fluid

value: Cerebrospinal Fluid

value: Immune cells

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: seedlings_C2_col-0_ZT-0.5_R2

description: Library name: C31

value: seedling


title: b0.2-1

description: Library name: Sample 4


title: CSF_P18D0_VDJ

description: Library name: CSF_P18D0_VDJ

value: Primary cells

value: Normal

value: Pre-treatment


title: a0.5-3

description: Library name: Sample 3

value: Whole cell

value: Chlorella pyrenoidosa cell


title: seedlings_C2_col-0_ZT3_R1

description: Library name: C28


title: macrophages + macrophage EVs #4

description: Library name: THP_ctrl_4

value: macrophage EVs


title: a0.5-2

description: Library name: Sample 2


title: seedlings_C2_col-0_ZT2.5_R3

description: Library name: C27


title: macrophages + macrophage EVs #3

description: Library name: THP_ctrl_3


title: CSF_P18D7_GEX

description: Library name: CSF_P18D7_GEX


title: a0.5-1

description: Library name: Sample 1


title: CSF_P18D0_GEX

description: Library name: CSF_P18D0_GEX


title: macrophages + VAT EVs #2

description: Library name: THP_V63


title: seedlings_C2_col-0_ZT2_R1

description: Library name: C26


title: d0-2

description: Library name: Sample 12

value: control


title: CSF_P17D7_VDJ

description: Library name: CSF_P17D7_VDJ


title: macrophages + VAT EVs #1

description: Library name: THP_V58

value: wild type


title: seedlings_C2_col-0_ZT1.5_R1

description: Library name: C25


title: d0-1

description: Library name: Sample 11


title: macrophages + macrophage EVs #2

description: Library name: THP_ctrl_2


title: seedlings_C2_col-0_ZT1_R1

description: Library name: C24


title: CSF_P17D0_VDJ

description: Library name: CSF_P17D0_VDJ


title: macrophages + macrophage EVs #1

description: Library name: THP_ctrl_1


title: CSF_P17D7_GEX

description: Library name: CSF_P17D7_GEX


title: seedlings_C2_col-0_ZT0.5_R1

description: Library name: C23


title: a0.5-122

description: Library name: Sample 10


title: a0.5-121

description: Library name: Sample 9


title: iPSC-CFs  + VAT EVs #4

description: Library name: fib_V64

source_name: ipsc-derived cardiac fibroblasts

value: ipsc-derived cardiac fibroblasts

value: human iPSCs

value: cardiac fibroblasts

value: VAT EVs


title: CSF_P17D0_GEX

description: Library name: CSF_P17D0_GEX


title: a0.5-92

description: Library name: Sample 8

value: Potassium peroxymonosulfate stress


title: seedlings_C2_col-0_ZT0_R1

description: Library name: C22


title: iPSC-CFs  + iPSC-CF EVs #4

description: Library name: fib_ctrl_4

value: iPSC-CF EVs


title: a0.5-91

description: Library name: Sample 7


title: seedlings_C2_col-0_ZT-0.5_R1

description: Library name: C21


title: iPSC-CFs  + iPSC-CF EVs #3

description: Library name: fib_ctrl_3


title: CSF_P16D7_VDJ

description: Library name: CSF_P16D7_VDJ

value: Cerebrospinal Fluid

value: Immune cells


title: CSF_P16D0_VDJ

description: Library name: CSF_P16D0_VDJ


title: seedlings_C1_col-0_ZT3_R2

description: Library name: C18

value: seedling


title: iPSC-CFs  + VAT EVs #3

description: Library name: fib_V68


title: a0.5-62

description: Library name: Sample 6


title: CSF_P16D7_GEX

description: Library name: CSF_P16D7_GEX

value: Primary cells

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: seedlings_C1_col-0_ZT2.5_R2

description: Library name: C17


title: iPSC-CFs  + VAT EVs #2

description: Library name: fib_V67


title: CSF_P16D0_GEX

description: Library name: CSF_P16D0_GEX

value: Normal

value: Pre-treatment


title: a0.5-61

description: Library name: Sample 5

value: Whole cell

value: Chlorella pyrenoidosa cell


title: seedlings_C1_col-0_ZT2_R2

description: Library name: C16


title: a0.5-32

description: Library name: Sample 4


title: iPSC-CFs  + VAT EVs #1

description: Library name: fib_V63


title: a0.5-31

description: Library name: Sample 3


title: CSF_P15D7_VDJ

description: Library name: CSF_P15D7_VDJ


title: iPSC-CFs  + iPSC-CF EVs #2

description: Library name: fib_ctrl_2


title: CSF_P15D0_VDJ

description: Library name: CSF_P15D0_VDJ


title: seedlings_T2_col-0_ZT1.5_R1

description: Library name: C65


title: seedlings_C1_col-0_ZT1.5_R2

description: Library name: C15


title: seedlings_C1_col-0_ZT1_R2

description: Library name: C14


title: iPSC-CFs  + iPSC-CF EVs #1

description: Library name: fib_ctrl_1


title: CSF_P15D7_GEX

description: Library name: CSF_P15D7_GEX


title: a0.5-02

description: Library name: Sample 2


title: human PBNK cells, Day0, replicate 3

city: Shanghai

first: Hongye

last: Wang

address: 1239 Siping Road, Yangpu District, Shanghai

institute: Tongji University

description:
Library name: Sample 3
Column name in raw_counts.csv: P-3

data_processing:
The initial paired-end reads underwent trimming and quality control using Trimmomatic, applying the parameters (SLIDINGWINDOW:4:15 MINLEN:75).
The resulting clean reads were individually aligned to the reference genome in orientation mode using hisat2 software with default settings. The quality of these data was assessed using qualimap_v2.21.
Clean reads were aligned to the ribosome database of human genome (hg38) using the alignment tool bowtie2 to evaluate the proportion of rRNA in the sample. Using featurecount to count each gene reads.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each gene was calculated using the fragments per kilobase of exon per million mapped reads (FRKM) method.
DEGs between PBNK and ExNK, Scramble and MS177, Scramble and Taz/GSK126 samples were analyzed with R statistical package edgeR and genes with an adjusted p-adjust < 0.05 were identified as DEGs.
Assembly: hg38
Supplementary files format and content: csv files include raw counts for each sample

source_name: human peripheral blood

growth_protocol: PBNK cells are freshly isolated from human peripheral blood monocyte cells (PBMC) using the NK Cell Isolation Kit (Miltenyi) according to the manufacturer's instructions. Cell purity, defined as the percentage of CD56⁺CD3⁻ cells, was determined by flow cytometry. Only preparations with a purity exceeding 90% were used for mRNA-seq.  Freshly purified PBNK were pre-activated with rhIL-12 (10ng/mL), rhIL-15 (100ng/mL), and rhIL-18 (50ng/mL) for 16- 24 hours to generate cytokine induced memory-like NK cells (CIML NK) , then harvested, washed, and allowed to differentiate for about 3-5 days supported with low-dose rhIL-15 (1 ng/ml). mExNK cells are NK cells that expanded with our protocol. Briefly, CD3-depleted PBMCs (dT-PBMC, with a residual T cell percentage ≤1%) were isolated from the PBMCs using Dynabeads™ CD3 (Thermo) in accordance with the manufacturer's protocol. Then dT-PBMCs were placed in anti-CD16a antibody (T&L) immobilization plate containing HIPP-T009 medium (Bioengine) supplemented with 5% UltraGRO™-Advanced Serum Replacement (Helios), 500U/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L), 50ng/mL rhIL-18 (T&L) and 4µM ADAM inhibitor (MCE) at 37℃ in a humidified atmosphere containing 5% CO2. After 2 days, fresh medium with 500U/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L) and 1μg/mL Urebumab (MCE) were added. From day 4, medium containing 500IU/mL rhIL-2 (PeproTech), 50ng/mL rhIL-15 (T&L) and 50ng/mL rhIL-21 (T&L) was replenished as necessary during the NK expansion process. After 14 days, expanded memory-like NK cells were tested, only expansion with the viability≥80%，purity≥97% were collected for preparation of mRNA-seq. cExNK cells s are NK cells that expanded with NK cell Activation/Expansion Kit (Miltenyi) by using the NKp46/CD2 coupling microbeads as described per manufacturer’s instructions. The expansion medium was HIPP-T009 medium (Bioengine) supplemented with 5% UltraGRO™-Advanced Serum Replacement (Helios), 500U/mL rhIL-2 (PeproTech). After 14 days, this conventional expanded NK cells (cExNK) were  collected for preparation of mRNA-seq.

extract_protocol:
Total RNA was extracted by TRIzol Reagent (Thermo)
Total RNA was constructed library using using VAHTS Universal V10 RNA-seq Library Prep Kit for MGI (Vazyme, NRM606). The libraries were size-selected for cDNA fragments of 200–300 bp on 2% Low Range Ultra Agarose and then subjected to PCR amplification using Phusion DNA polymerase (NEB) for 15 PCR cycles. Following quantification using TBS380, the paired-end libraries were sequenced

treatment_protocol: No treatment

value: human peripheral blood

value: natural killer cells

value: WT

value: NO treatment


title: a0.5-01

description: Library name: Sample 1


title: seedlings_C1_col-0_ZT0.5_R2

description: Library name: C13


title: CSF_P15D0_GEX

description: Library name: CSF_P15D0_GEX


title: seedlings_C1_col-0_ZT0_R2

description: Library name: C12


title: human PBNK cells, Day0, replicate 2

description:
Library name: Sample 2
Column name in raw_counts.csv: P-2


title: seedlings_C1_col-0_ZT-0.5_R2

description: Library name: C11


title: CSF_P14D7_VDJ

description: Library name: CSF_P14D7_VDJ


title: human PBNK cells, Day0, replicate 1

description:
Library name: Sample 1
Column name in raw_counts.csv: P-1


title: Antiviral drug&HIV&MCAO-1

city: Shenzhen

first: Fan

last: Bu

address: 1 Fuhua Road

institute: Shenzhen Traditional Chinese Medicine Hospital

description: Library name: N+M+D-1A

data_processing:
BGISEQ platform, Data filter in SOAPnuke: v2.3 -l 20 -q 0.4 -n 0.01, Read alignment software: HISAT2: v2.0.4 --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8
Assembly: NCBI.GCF_000001635.26_GRCm38
Supplementary files format and content: File includes FPKM value, log2 value and Q value of the genes that were regulated by either Middle Cerebral Artery Occlusion (M) or HIV infection (H) in mice.

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg total RNA was used for constructing sequencing libraries
RNA libraries for RNA seq were prepared following the manufacturer's protocols of DNBSEQ Transcriptom

value: Brain


title: CSF_P14D0_VDJ

description: Library name: CSF_P14D0_VDJ


title: Antiviral drug&HIV&MCAO-2

description: Library name: N+M+D-2A


title: HIV&MCAO-2

description: Library name: N+M-2A


title: seedlings_C1_col-0_ZT3_R1

description: Library name: C08


title: CSF_P14D7_GEX

description: Library name: CSF_P14D7_GEX


title: Placental organoid knockdown 3

city: Edmonton

first: Meghan

last: Riddell

state: AB

country: Canada

institute: University of Alberta

description: Library name: Bulk_seq_sample_6

data_processing:
Bulk seq libraries were quality processed and trimmed utilizing the FASTQC pipeline. Trimmed sequenced were mapped to GRCh38/hg38 utilizing STAR v2.7.11
Data was extracted in Ubuntu utilizing FeatureCounts. Data was analyzed utilizing the DESeq2 package in R.
Demultiplexing, barcode processing, gene counting and aggregatiosn were made utilizing CellRanger 9.0.1 in Ubuntu.
Assembly: hg38
Supplementary files format and content: tab delimited text including raw counts for each sample
Supplementary files format and content: tab delimited values and matrix files

growth_protocol: Both the CT27 and CT 29 lines were maintained on 5 µg/mL collagen IV coated plates and using human TSC culture medium in a humidified incubator at 37 degrees and 5% CO2. Organoids were generated using a rotatory cell culture system.

extract_protocol:
Placental organoids were pelleted and resuspended in trizol before being mechanically dissociated utilizing a tissue lyser. RNA was extracted by utilizing Invitrogen PureLink RNA Mini Kit.
CT27 and CT29 cell lines were flash-frozen and the nuclei for both cell lines were collected using the 10X Chromium Nuclei Isolation Kit with RNAse inhibitor following the manufacturer's intructions.
Bulk seq libraries were contructed using the Illumina Stranded mRNA Prep Kit.
Single nuclei libraries were prepared using the 10X GEM-X Universal 3' Gene expression v4 4-plex according to manufacturer's instructions.

treatment_protocol: CT29 knockdowns were achieved utilizing PRKCZ-targetting siRNA that was transfected into the cell line using Opti-MEM I Reduced Serum Medium and Lipofectamine LTX Reagent with PLUS reagent.

value: Trophoblast stem cells

value: PRKCZ knockdown


title: Placental organoid knockdown 2

description: Library name: Bulk_seq_sample_5


title: CSF_P14D0_GEX

description: Library name: CSF_P14D0_GEX


title: seedlings_C1_col-0_ZT2.5_R1

description: Library name: C07


title: MCAO-2

description: Library name: M-2A


title: HIV&MCAO-1

description: Library name: N+M-1A


title: seedlings_C1_col-0_ZT2_R1

description: Library name: C06


title: Placental organoid knockdown 1

description: Library name: Bulk_seq_sample_4


title: seedlings_C1_col-0_ZT1.5_R1

description: Library name: C05


title: CSF_P13D7_VDJ

description: Library name: CSF_P13D7_VDJ


title: MCAO-1

description: Library name: M-1A


title: Placental organoid control 3

description: Library name: Bulk_seq_sample_3

value: Control


title: CSF_P13D0_VDJ

description: Library name: CSF_P13D0_VDJ

value: Cerebrospinal Fluid


title: seedlings_C1_col-0_ZT1_R1

description: Library name: C04


title: Sham operation-2

description: Library name: S-2A


title: seedlings_C1_col-0_ZT0.5_R1

description: Library name: C03


title: Sham operation-1

description: Library name: S-1A


title: CSF_P13D7_GEX

description: Library name: CSF_P13D7_GEX

value: Immune cells


title: Placental organoid control 2

description: Library name: Bulk_seq_sample_2


title: Placental organoid control 1

description: Library name: Bulk_seq_sample_1


title: CSF_P13D0_GEX

description: Library name: CSF_P13D0_GEX


title: seedlings_C1_col-0_ZT0_R1

description: Library name: C02

value: seedling


title: Hi-C sequencing of N2-amanitin replicate rep2

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

library_source: genomic

data_processing:
Hi-C reads were aligned to the C. elegans reference genome WBcel235 via BWA mem v0.7.17.
3D contact matrices were constructed using hicBuildMatrix (HiCExplorer) where reads were compiled into raw matrices.
Matrices were filtered to exclude interactions involving regions listed in the ce11-blacklist.v2.bed file.
Matrices were balanced using Knight-Ruiz (KR) normalization to correct known biases of Hi-C data.
Corrected matrices were normalized using hicNormalize to compare read counts between different genomic regions or samples.
WBcel235
Processed data files are in HDF5 format and contain the normalized contact matrices.
Assembly: ce11/WBcel235
Supplementary files format and content: contact_map.h5, pca1.bw, tad_score.bm
Supplementary files format and content: Modified contact_map.g2i.h5 to enable its use with R.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: Embryo

extract_protocol:
Crosslinking of C. elegans embryos and nuclei preparation were done as described by Crane et al. (2015). Frozen embryos were thawed on ice and crosslinked in 50 mL of 2% (v/v) formaldehyde in PBS for 30 minutes at room temperature on a nutator. The crosslinked embryos were washed, dounced, and nuclei were isolated by centrifugation and analyzed for the presence of DAPI-stained nuclei under a fluorescence microscope.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following the manufacturer's protocol. Libraries were sequenced on NovaSeq 6000 PE150 S4 flowcells.

treatment_protocol: C. elegans samples were cultivated on nematode growth medium (NGM) plates seeded with E. coli OP50-1. NGM plates supplemented with ten times excess peptone were used to grow worms for Hi-C and ChIP-seq experiments.

value: Embryo


title: DMD19 iso iPSCs, untreated, biol rep 3

city: Irvine

first: Asuka

last: Eguchi

state: CA

address: 845 Health Sciences Road

department: Physiology & Biophysics

institute: University of California, Irvine

description:
Library name: Iso_iPSC_3
Column name in Transcripts_Raw_Counts_Matrix = Control_iPSC_3

data_processing:
Sequencing reads were quasi-mapped then counted to human GRCh38.p14 using Salmon (Version 1.8.0) with default settings for gene-level and transcript-level quantifications.
Differential gene expression analysis was performed on raw counts using the R package DESeq2. Genes and transcripts with more than 100 raw counts were considered as expressed. Transcript level quantifications were used for downstream analysis.
Assembly: GRCh38.p14
Supplementary files format and content: A raw counts matrix for the transcript-level quantifications is provided in an excel spreadsheet format. A TPM matrix for the gene level quantifications is also provided.
Supplementary files format and content: Salmon quantification files were provided. Each file contains one column with the Transcript Name, Gene Length, Effective Length, TPM, and Raw Counts

source_name: DMD19 iso

growth_protocol: iPSCs were seeded onto matrigel and cultured in Nutristem. For cardiomyocyte differentiation, iPSCs that were 70-90% confluent were cultured in RPMI 1640 supplemented with IX B27 minus insulin and 4 to 6 µm CHIR-99021. Two days later cells were refreshed with RPMI 1640 supplemented with 1X B27 minus insulin and 5 µm IWR. Another two days later cells were refreshed with RPMI 1640 supplemented with 1X B27 and maintained for 4 days with media changes every two days. Following treatment, iPSC-CMs were refreshed every two days with RPMI 1640 minus glucose supplemented with 1X B27 and 4 mM lactate.

extract_protocol:
iPSC-CMs were collected with Accutase:TrypLE on Day 30 of differentiation and flash frozen. RNA was extracted from cells using and purified using the RNeasy Micro Kit (Qiagen 74104).
Total RNA was sent to Novogene for quality control, library preparation, and bulk RNA-sequencing with poly-A mRNA selection.

treatment_protocol: On Day 10 of differentiation, iPSC-CMs were transduced with an empty vector lentiviral control or microDYS1, microDYS2, microDYS3, or miniDYS with 8 µg/mL polybrene.

value: DMD19 iso

value: induced pluripotent stem cells


title: CSF_P12D7_VDJ

description: Library name: CSF_P12D7_VDJ

value: Primary cells

value: Normal

value: 1e7 bivalent CAR T cells (EGFR, IL13RA2)


title: seedlings_C1_col-0_ZT-0.5_R1

description: Library name: C01


title: Hi-C sequencing of N2-amanitin replicate rep1


title: DMD19 iso iPSCs, untreated, biol rep 2

description:
Library name: Iso_iPSC_2
Column name in Transcripts_Raw_Counts_Matrix = Control_iPSC_2


title: CSF_P12D0_VDJ

description: Library name: CSF_P12D0_VDJ

value: Pre-treatment


title: DMD19 iso iPSCs, untreated, biol rep 1

description:
Library name: Iso_iPSC_1
Column name in Transcripts_Raw_Counts_Matrix = Control_iPSC_1


title: NS2

first: Hongrui

last: Chen

address: 639 Zhizaoju Road, Shanghai 200011, P.R.China.

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

description: Library name: 11

data_processing:
fastp  removed adapters and low-quality bases
Assembly: EC;SA
Supplementary files format and content: tab-delimited text file includes counts
Supplementary files format and content: tab-delimited text file includes tpm

organism: Staphylococcus aureus

source_name: Group 3:  S. aureus treated with AuPt@ZIF-8 + H₂O₂ + NIR

extract_protocol:
Total RNA was extracted. RNA was purified per manufacturer’s instructions and treated with RNase-free DNase I. RNA integrity was assessed on Agilent 2100 Bioanalyzer (RIN ≥ 8.5); concentrations were measured with Qubit RNA HS Assay
Ribosomal RNA was depleted. Strand-specific libraries were prepared: fragmentation at 94 °C for 8 min, adaptor ligation, and 12 PCR cycles. Libraries (~280 bp mean insert) were quantified by qPCR and profiled on Bioanalyzer. Sequencing was performed  with paired-end 150 bp reads.

value: cell


title: CSF_P12D7_GEX

description: Library name: CSF_P12D7_GEX


title: Hi-C sequencing of N2 replicate rep4


title: Hi-C sequencing of N2 replicate rep3


title: DMD19 Day 30 iPSC-CMs treated with miniDYS, biol rep 4

description:
Library name: DMD_miniDYS_4
Column name in Transcripts_Raw_Counts_Matrix = DMD_miniDYS_4

value: cardiomyocytes

value: DMD

value: miniDYS


title: NS3

description: Library name: 12

value: S. aureus treated with AuPt@ZIF-8 + H₂O₂ + NIR


title: CSF_P12D0_GEX

description: Library name: CSF_P12D0_GEX


title: CSF_P11D7_VDJ

description: Library name: CSF_P11D7_VDJ


title: Hi-C sequencing of N2 replicate rep2


title: NS1

description: Library name: 10


title: DMD19 Day 30 iPSC-CMs treated with miniDYS, biol rep 3

description:
Library name: DMD_miniDYS_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_miniDYS_3


title: CS3

description: Library name: 9

source_name: Group 4: untreated S. aureus

value: untreated S. aureus


title: Hi-C sequencing of N2 replicate rep1


title: DMD19 Day 30 iPSC-CMs treated with miniDYS, biol rep 2

description:
Library name: DMD_miniDYS_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_miniDYS_2


title: CSF_P11D0_VDJ

description: Library name: CSF_P11D0_VDJ


title: DMD19 Day 30 iPSC-CMs treated with miniDYS, biol rep 1

description:
Library name: DMD_miniDYS_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_miniDYS_1


title: CS1

description: Library name: 7


title: Hi-C sequencing of met2-set25-set32 replicate rep3


title: CS2

description: Library name: 8


title: DMD19 Day 30 iPSC-CMs treated with microDYS3, biol rep 5

description:
Library name: DMD_microDYS3_5
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS3_5


title: seedlings_T1_col-0_ZT0_R1

description: Library name: C42


title: CSF_P11D0_GEX

description: Library name: CSF_P11D0_GEX


title: AR0382 ATACseq replicate 1

city: Ann Arbor

first: Ajay

last: Larkin

state: MI

address: 1150 W Medical Center Dr

department: Microbiology & Immunology

institute: University of Michigan

description: Library name: AR0382_ATACseq_1

data_processing:
quality control with FastQC
alignment with BWA
bedgraph coverage files were created using Deeptools bamcoverage
Assembly: B8441.v3
Supplementary files format and content: bedgraph files showing binned ATACseq read coverage

organism: Candidozyma auris

source_name: yeast cell

extract_protocol:
Logarithmically-growing cells were harvested via centrifugation. Pellet was incubated in buffer 1 (100mM Tris pH 9.4, 10mM DTT) at 30°C for 5 minutes, then washed and digested in buffer 2 (DPBS, 1 M sorbitol, 1.5 U zymolase [Zymo E100])).
Tagmentation of spheroplasts and library construction were performed according to the ActiveMotif ATAC-seq kit (#53150).

tag: strain

value: yeast cell


title: Hi-C sequencing of met2-set25-set32 replicate rep1


title: Hi-C sequencing of lin61 replicate rep2


title: DMD19 Day 30 iPSC-CMs treated with microDYS3, biol rep 4

description:
Library name: DMD_microDYS3_4
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS3_4


title: Hi-C sequencing of lin61 replicate rep1


title: CSF_P10D7_VDJ

description: Library name: CSF_P10D7_VDJ

value: Cerebrospinal Fluid


title: DMD19 Day 30 iPSC-CMs treated with microDYS3, biol rep 3

description:
Library name: DMD_microDYS3_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS3_3


title: CSF_P10D0_R2_VDJ

description: Library name: CSF_P10D0_R2_VDJ

value: Immune cells


title: OP9 cells, Empty vector, RNAseq,batch2, rep3

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

description:
Library name: EV_batch2_rep3
EV-3_kallisto

data_processing:
Transcript abundances were quantified using the kallisto (version 0.48.0) under default settings. The transcript-level abundance estimates results were then imported into the R package tximport to summarize the gene-level abundance estimates for downstream analysis.
Assembly: GENCODE.vM29
Supplementary files format and content: xlsx file include TPM values for each Sample

growth_protocol: OP9 mesenchymal stem cells were maintained in MEMα supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Ultrapure RNA Kit (Omega, R6834-02), 1 ug of total RNA was used for the construction of sequencing libraries
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template   to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the MGI DNBSEQ-T7 or Illumina Novaseq X Plus.The total RNA of OP9 cells was extracted using Ultrapure RNA Kit (CW BIO, CW0581M) and sent to BGI for library preparation and sequencing by MGISEQ2000.

treatment_protocol: OP9 cells were plated, and rosiglitazone was added to the medium at a concentration of 1 μM when the cells reached 100% confluence. This treatment was continued for 10 days.

value: mesenchymal stem cell

value: WT

value: adipogenic differentiation


title: Hi-C sequencing of I158A replicate rep2

value: Embryo


title: Hi-C sequencing of I158A replicate rep1


title: CSF_P10D0_R1_VDJ

description: Library name: CSF_P10D0_R1_VDJ

value: Primary cells


title: OP9 cells, Empty vector, RNAseq,batch2, rep2

description:
Library name: EV_batch2_rep2
EV-2_kallisto


title: DMD19 Day 30 iPSC-CMs treated with microDYS3, biol rep 2

description:
Library name: DMD_microDYS3_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS3_2


title: CSF_P10D7_GEX

description: Library name: CSF_P10D7_GEX

value: Normal


title: DMD19 Day 30 iPSC-CMs treated with microDYS3, biol rep 1

description:
Library name: DMD_microDYS3_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS3_1


title: OP9 cells, Empty vector, RNAseq,batch2, rep1

description:
Library name: EV_batch2_rep1
EV-1_kallisto


title: CSF_P11D7_GEX

description: Library name: CSF_P11D7_GEX

value: 1e7 bivalent CAR T cells (EGFR, IL13RA2)


title: DMD19 Day 30 iPSC-CMs treated with microDYS2, biol rep 5

description:
Library name: DMD_microDYS2_5
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS2_5


title: Hep3B_Wildtype_rep1_Mock

city: Chicago

first: Daniel

last: Arango

state: IL

address: 303 E Superior St, Office 7-119

institute: Northwestern University

description: Library name: M1

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
The UMI was extracted using UMI-tools/1.1.5.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode.
All alignments were deduplicated using UMI-tools and nucleotide counts of aligned reads were extracted via samtools/1.6 mpileup. Read counts were extracted with https://github.com/IARCbioinfo/mpileup2readcounts.
We appended strand information to each site. We then filtered: 1) read depth per position must be >=30 2) dominant mismatch nucleotide per position must have at least 5 reads and a mismatch frequency of 0.001 or 0.01. We then identified significantly decreased sites in each sample vs NAT10-WT. Statistics and plots were performed in R/.
Assembly: GRCh38
Supplementary files format and content: BED files containing raw nucleotide counts per position

source_name: Liver

growth_protocol: HEP3B cells were maintained in DMEM supplemented with 10% fetal bovine albumin (FBS) and 1% Penicillin/Streptomycin. All cells were grown in an incubator condition of 37oC and 5% CO2 and passaged every 3 days.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Total RNA was dephosphorylated followed by a 3' adapter ligation. The 3' adapter contains a spacer that impedes the self-ligation of RNA. The ligated RNA was fragmented, treated with NaCNBH3, dephosphorylated, and repurified. Reverse transcription was performed using the Induro enzyme in a dNTP cocktail contianing 2-amino-dATP. cDNA was then ligated to an adapter containing unique molecular identifiers (UMI) of ten randomized nucleotides.Final libraries were PCR amplified using Q5® High-Fidelity 2X Master Mix (NEB) and NEBNext® Multiplex Oligos for Illumina®. The primers aligned perfectly to the 5’ adapter and the second 3’ adapter. Each sample was assigned a different indexed primer.

treatment_protocol: NAT10-FKBP cells were transduced with single mutants in the Helicase domain (E389L. K290A) or the acetyltransferase domain (G641E, H537A), NAT10-WT, or a control plasmid for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1 for 24 hrs.

value: Liver

value: Hepatocellular carcinoma

value: Wildtype

value: Mock


title: Hi-C sequencing of hpl2-lin61 replicate rep3


title: OP9 cells, Drosha KO, RNAseq,batch2, rep3

description:
Library name: Drosha_KO_batch2_rep3
Drosha_g1-3_kallisto

value: Drosha KO


title: CSF_P10D0_R2_GEX

description: Library name: CSF_P10D0_R2_GEX

value: Pre-treatment


title: Hi-C sequencing of hpl2-lin61 replicate rep2


title: DMD19 Day 30 iPSC-CMs treated with microDYS2, biol rep 4

description:
Library name: DMD_microDYS2_4
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS2_4

value: cardiomyocytes

value: DMD


title: CSF_P10D0_R1_GEX

description: Library name: CSF_P10D0_R1_GEX

value: Cerebrospinal Fluid


title: OP9 cells, Drosha KO, RNAseq,batch2, rep2

description:
Library name: Drosha_KO_batch2_rep2
Drosha_g1-2_kallisto


title: Hi-C sequencing of hpl2-lin61 replicate rep1


title: CSF_P9D7_VDJ

description: Library name: CSF_P9D7_VDJ

value: Immune cells

value: 2.5e7 bivalent CAR T cells (EGFR, IL13RA2)


title: DMD19 Day 30 iPSC-CMs treated with microDYS2, biol rep 3

description:
Library name: DMD_microDYS2_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS2_3


title: C. auris NAT insert mutagenesis library

description: Library name: Cauris_NAT_insert_lib

data_processing:
quality control with FastQC
alignment with BWA
processed with extractSoftClipped from SE-MEI
insert sites processed with bedtools
Assembly: B8441.v3
Supplementary files format and content: bed file indicating site of NAT cassette insertion

extract_protocol:
Cells were resuspended in buffer [2% (v/v) Triton X-100, 1% (w/v) SDS, 100 mM NaCl, 10 mM Tris-Cl, 1 mM EDTA] and beat-beat to lyse. DNA was extracted using phenol chloroform and ethanol preciptitation. Extracted DNA was treated with RNAse A.
Genomic DNA was digest the end of inserted NAT gene cassettes with MseI and ligated cut fragments to a custom U-linker. PCR [Q5 Hot-start, with USER to digest U-linker] was used to enrich NAT-U-linker fragments, followed by a second round of PCR to add Illumina-compatible barcoded sequences. Products were cleaned up via size-selection beads [Omega Bio-Tek Mag-Bind TotalPure SPRI beads] at each step.

value: yeast cell


title: OP9 cells, Drosha KO, RNAseq,batch2, rep1

description:
Library name: Drosha_KO_batch2_rep1
Drosha_g1-1_kallisto

value: mesenchymal stem cell

value: adipogenic differentiation


title: Hi-C sequencing of hpl2 replicate rep2

value: Embryo


title: CSF_P9D0_VDJ

description: Library name: CSF_P9D0_VDJ

value: Primary cells

value: Normal


title: OP9 cells,Empty vector,Small RNA-seq,rep3

description: Library name: OP9 cells, Empty vector-3, Day 10

data_processing:
Clean reads were aligned to the murine rRNA genome using Bowtie2 (v2.5.1), and unmapped sequences were retained for downstream analysis.
Filtered reads were subsequently mapped to the Mus musculus GRCm38 reference genome (GENCODE vM23) using the mapper.pl module from the miRDeep2 suite, with a minimum read length of 18 nucleotides (-l 18).
Known miRNAs were quantified via the quantifier.pl module after converting uracil to thymine in mature (mature.fa) and precursor (hairpin.fa) miRNA sequences from the miRBase database (v22.1).
Assembly: GRCm38
Supplementary files format and content: xlsx file include TPM values for each Sample

extract_protocol:
RNA was harvested using Ultrapure RNA Kit (Omega, R6834-02), 1 ug of total RNA was used for the construction of sequencing libraries
Small RNA enrichment and purification.Then ligate the 5-adenylated and 3-blocked adaptor to the 3' end of the small RNA fragment. Add Unique molecular identifiers (UMI) labeled Primer. 5' end adaptor ligation. First strand synthesis with Unique molecular identifiers (UMI) labeled Primer.   Second strand synthesis. Fragment selection. Library quality control. The double stranded PCR products were heat denatured and circularized by the  splint oligo sequence.   The single strand circle DNA (ssCir DNA) were formatted as the final library. Sequencing on DNBSEQ.

value: WT


title: DMD19 Day 30 iPSC-CMs treated with microDYS2, biol rep 2

description:
Library name: DMD_microDYS2_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS2_2


title: Hi-C sequencing of hpl2 replicate rep1


title: DMD19 Day 30 iPSC-CMs treated with microDYS2, biol rep 1

description:
Library name: DMD_microDYS2_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS2_1


title: OP9 cells,Empty vector,Small RNA-seq, rep1

description: Library name: OP9 cells, Empty vector-1, Day 10


title: CSF_P9D7_GEX

description: Library name: CSF_P9D7_GEX


title: OP9 cells,Empty vector,Small RNA-seq,rep2

description: Library name: OP9 cells, Empty vector-2, Day 10


title: DMD19 Day 30 iPSC-CMs treated with microDYS1, biol rep 5

description:
Library name: DMD_microDYS1_5
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS1_5


title: CSF_P9D0_GEX

description: Library name: CSF_P9D0_GEX


title: Hi-C sequencing of CEC4 replicate rep1


title: Input of condition met2-set25-set32, ID:FITKS

data_processing:
ChIP-seq reads were aligned to the C. elegans WBcel235 reference genome using BWA with default parameters.
Fragment length and quality assessments were performed using PyMASC.
MACS2 was employed for peak calling using -q 0.5 to lower the threshold of reported peaks. Peak calling results from different replicates within a given IP and condition were then filtered using ChIP-R to assess the irreproducible discovery rate (IDR).
ChIP-seq samples were normalized using their respective input controls with bamCompare (deepTools), applying specific parameters including --minMappingQuality 20, --binSize 10, --smoothLength 30, --extendReads, --scaleFactorsMethod readCount, --operation log2, and --pseudocount 1.
Assembly: WBcel235/ce11
Supplementary files format and content: macs2 peak calling filtered by chipr
Supplementary files format and content: Input normalised bigwig
Supplementary files format and content: Differential zscore bigwig

source_name: embryos

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) plates seeded with E. coli OP50-1 according to Lewis and Fleming (1995). NGM plates supplemented with ten times excess peptone were employed for growing worms destined for Hi-C and ChIP-seq experiments. The wild-type strain used was N2. The C. elegans strains utilized, along with their genotypes, are as follows: lin-61(tm2649) (Koester-Eiserfunke and Fischle, 2011), hpl-2(tm1489) (Schott et al., 2006), set-32(red11); met-2(n4256) set-25(n5021) (Kalinava et al., 2017), and cec-4(ok3124) (Gonzalez-Sandoval et al., 2015). The hpl-2(I158A) allele was created using a CRISPR/Cas9 approach; further details can be provided upon request. The genotypes of all C. elegans strains were routinely confirmed by single-worm PCR.

extract_protocol:
ChIP was conducted with slight adjustments following the method described by Ercan et al. (2007). Post-crosslinking, C. elegans embryos underwent a wash with 100 mM Tris-HCl, pH 7.5, followed by two washes with FA buffer (50 mM HEPES-KOH, pH 7.5; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 150 mM NaCl; 1x protease inhibitor (cOmplete™, Sigma, Germany)). Nuclei were sheared as for Hi-C and then centrifuged at 13,000 xg for 15 minutes at 4°C to gather extracts. Immunoprecipitations were arranged using extracts equivalent to 3 mg along with 3–5 μg of antibodies in a total volume of 500 μL FA buffer. Prior to antibody addition, 10% of the reactions were kept aside as input. After 16 hours of incubation at 65°C with agitation, complexes were recovered by adding 20 μL of Protein A/G beads (Pierce™ Protein A/G Magnetic Beads, USA) and washed twice with FA buffer supplemented to 1 M NaCl, followed by two washes with FA buffer supplemented to 500 mM NaCl. Beads were treated with 1% (w/v) SDS in TE containing 250 mM NaCl at 65°C for 30 minutes to elute the complexes. Samples and inputs were treated with 2 μL of 10 mg/mL Proteinase K for 1 hour at 55°C. Decrosslinking was carried out at 65°C overnight in a thermomixer. DNA purification was executed with a PCR clean-up kit (Macherey-Nagel™, Germany) and quantified using Qubit Fluorometric Quantification. Library preparation followed the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, USA) protocol. Libraries were sequenced on Novaseq 6000 PE150 S4 flow cells. Various antibodies were employed for ChIP experiments: anti-HPL-2 (Novus Biologicals 38630002), anti-LIN-61 (Novus Biologicals 29590002), anti-LEM-2 (Novus Biologicals 48540002), anti-H3K9me2 (Abcam ab1220), anti-H3K9me3 (VWR 309M3-B), anti-H3K4me1 (Abcam ab8895), anti-H3K4me3 (Active Motif 39159), anti-H3K27me3 (Abcam ab6002), and anti-H3K27ac (Active Motif Ab39133). All ChIP-seq experiments were conducted as biological independent triplicates.
Immunoprecipitation of C. elegans nuclear extracts utilized anti-LIN-61 (Novus Biologicals 29590002), anti-HPL-2 (Novus Biologicals 38630002), and anti-T7 (Abcam ab9138) antibodies. The antibodies were crosslinked to dynabeads M-280 sheep anti-rabbit IgG (Pierce, USA) overnight at 4°C on a nutator, following the manufacturer’s instructions. Unbound antibodies were removed by washing the beads with 1xPBS three times. Beads were then resuspended in 1 mL 0.2 M triethanolamine, pH 8.2, 20 mM DMP at room temperature for 60 minutes. Cross-linking was halted by adding 1 mL 50 mM Tris-HCL, pH 7.5, at room temperature for 60 minutes. After three washes with 1xPBS, 5 mg of total protein C. elegans extracts in 500 μL were added to the beads and incubated for 30 minutes at room temperature. Subsequently, beads underwent six washes with buffer D (each wash involving incubation with 1 mL buffer D for 5 minutes followed by centrifugation at 2000 xg for 1 minute at room temperature). Bound proteins were released from the beads in SDS-PAGE sample buffer by incubating at 95°C for 10 minutes. The proteins were resolved on SDS-PAGE and subjected to analysis by western blotting following standard procedures.

treatment_protocol: Crosslinking of C. elegans embryos and nuclei preparation followed the protocol outlined by Crane et al. (2015). Gravid adult worms were harvested and bleached to yield a late-stage embryo pellet of at least 1 or 4 mL for ChIP-seq or Hi-C experiments, respectively. The embryos underwent two washes in 1xPBS, were flash-frozen in liquid nitrogen, and stored at -80 °C. Thawed on ice, the embryos were then crosslinked in 50 mL of 2% (v/v) formaldehyde in PBS for 30 minutes at room temperature on a nutator. Subsequent to crosslinking, they were sequentially washed in 100 mM Tris-HCl, pH 7.5, twice in 1xPBS, and once in lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% (v/v) Igepal CA-630 (Sigma, Germany); 5 mM DTT; 0.5 mM EGTA; 1x protease inhibitor (cOmplete™, Sigma, Germany)). The embryos were then dounced 25 times with pestle A and 25 times with pestle B (PYREX® 7 mL Dounce Tissue Grinder, Corning, USA) while kept on ice. The resulting extract was centrifuged at 100 xg at 4 °C, and the supernatant containing nuclei was collected. This extraction process was repeated up to six times, with each supernatant checked for the presence of DAPI-stained nuclei under a fluorescence microscope. Supernatants containing pure nuclei were combined and centrifuged for 5 minutes at 2000 xg at 4 °C to collect material for further experimentation.

value: embryos

value: Input


title: OP9 cells,Drosha KO,Small RNA-seq,rep2

description: Library name: OP9 cells, Drosha KO-2, Day 10


title: Input of condition met2-set25-set32, ID:KGJEK


title: DMD19 Day 30 iPSC-CMs treated with microDYS1, biol rep 4

description:
Library name: DMD_microDYS1_4
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS1_4


title: 10434~IL15/IL7 +pep~Day 10~neg ctrl~pool_2

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: FIX10434-056
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the Fixed RNA Profiling capability (version 9.0.1), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

growth_protocol: VST culture and fixation: Culture was performed using GREX-10, 6 well plates (Wilson Wolf), largely following a previously published rapid expansion protocol (Lazarski 2021). Briefly, PBMC were thawed, pelleted at 400 xg and resuspended in 2% BSA/PBS for counting. Cells were pelleted once again and resuspended at 1.5x107 cells per mL in CTL culture media including 300ng/mL each of CMV derived pp65 and IE-1 peptide pools (Peptivator, Milltenyi) or vehicle control (water). CTL culture media contained 44% RPMI, 44% Clicks, 10% FBS, 1% PenStrep, 1x Glutamax. Cells were incubated/pulsed for 1h at 37C. Following peptide pulse, cells were distributed into GREX-10 6 well plates containing 30mL total volume CTL media. Media was supplemented with IL4 (400U/mL), IL7, and/or IL15 (10ng/mL) as indicated. On day 7 of culture, the upper 15mL of media was carefully removed from each well without disturbing cells and replaced with 15mL fresh CTL media including 2x cytokine addition. If applicable, treatment with metabolic inhibitors UK5099 (Sigma), TWS-119 (Selleck Chem.) or vehicle/DMSO, was initiated on day 1 of culture. Further addition of inhibitors was done at 1x concentration and occurred only during day 7 media exchange. Individual wells were harvested at indicated timepoints during VST culture. Upon harvest, cells were washed 1x with cold 0.4% BSA/PBS followed by 1x with cold PBS alone prior to pelleting and resuspension in cold 10x fixation buffer per the standard FLEX protocol. Cells were counted and fixed at a maximum of 1x107 per mL fixation buffer. Fixation occurred for 20-26 hours at 4C. After fixation, cells were pelleted at 850 xg and resuspended in 1mL ice cold quenching buffer per 10x FLEX guideline. 10x Enhancer and 50% glycerol were added, prior to storage at -80°C, per 10x FLEX guidelines.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell FLEX GEM Library and Gel Bead kit.
REFLEX (Library prep, pre-amp): Following GEM incubation, 125 μL of Recovery Agent was added to break the GEM emulsion. Mixtures were inverted 10x and incubated for 2 minutes at room temperature. 125 μL of recovery agent was then carefully removed from the bottom of each well. The remaining approximately 65 μL of recovered GEM sample was combined with a master mix containing 27 μL of Amp Mix (10X PN-2000047), 10 μL of Pre-Amp Primers B (10XPN-20000529), 1.5 μL of TruSeq1 [1 μM], and 3 μL of a pre-mixed TCR Variable Primer Pool (See Supplemental Note [REF]) [0.66 μM] for a total volume of 106.5 μL of master mix plus recovered GEM. Samples were inverted 10x to mix and placed in a thermal cycler with the following cycling conditions: 98C for 3 minutes; 8 cycles of 98C/20 seconds, 60C for 30 seconds, 72C for 2 minutes; 72C for 5 minutes, 4C infinite hold. Upon completion of the PCR, tubes were pulsed briefly on a minifuge to collect liquid. 90 μL was then transferred into a new 1.5 mL Eppendorf tube. A 1.8X SPRI bead cleanup was performed and sample was eluted into 100 μL of elution solution in accordance with 10X User Guide CG000673 Rev B.
REFLEX (library prep, re-amplification): Pre-amplified library eluates were split into two or three pools for preparation of gene expression libraries,TCR libraries, and ADT libraries (when applicable). Gene expression and ADT libraries were prepared using 20uL pre-amp product and following 10x guidelines for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev B). Linear PCR master mix for TCR libraries consisted of 20 μL 1X KAPA HiFi HotStart (Roche, KK260), 10 uL molecular biology grade water (Fisher, BP2819100), and 0.5 μL TruSeq2 primer at 123.4 nM per reaction. TCR libraries utilized 40 μL of pre-amp product total, divided into 4, 10 μL aliquots. Each 10 μL aliquot was combined with 30.5 μL master mix in a PCR strip tube and incubated with the following PCR program: 95C/3min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeat x4 for 5 total cycles, 72C/5min final extension, hold 4C. After the 5 cycle linear PCR was completed, 0.5 μL TruSeq1, at 123.4 nM per reaction, was spiked into each reaction and an exponential PCR was performed with the following conditions: 95C/3 min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeated x7 for 8 total cycles, 72C/5min final extension, hold 4C. Following exponential PCR, each of the four 41 μL reactions per library condition were repooled for a total volume of 164 μL. Samples were SPRI cleaned at 0.8X ratio, eluted in 50 μL aforementioned “elution solution ”.
REFLEX (Indexing TCR Libraries): PCR indexing master mix was prepared with 50 μL 1X Kapa HiFi HotStart and 10 μL molecular biology grade water per reaction. Indexing reactions combined 20 μL cleaned re-amplified product, 60 μL master mix, and 20 μL Dual Index TT Set A (10X Genomics, PN-1000215). Each library used a unique TT index well enabling later identification via sequencing. Samples were inverted to mix and briefly spun down. Thermocycler conditions used were as follows: 98C/45s activation [98C/20s denaturation, 54C/30s annealing, 72C/90s] repeated x12-15 for 13-16 total cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. A final SPRIselect bead clean up was performed at a 0.7X ratio with cleaned product eluted into 40 μL Buffer EB (Qiagen, Cat No. 19086).
REFLEX (Indexing GEX libraries): GEX library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 4.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TS Set A primers (PN-3000511). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
REFLEX (Indexing ADT libraries): ADT library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 5.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TN Set A primers for the ADT libraries (10X, PN 1000250). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
Sequencing: Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300 or NextSeq2000 P4 300 cycle flow cell, Read1:80 Read2:200. A read depth of 5000 reads per cell for TCR libraries or 10,000 reads per cell for GEX libraries was targeted. ADT or CITEseq libraries were targeted at 5000 reads per cell.

treatment_protocol: Cell Lines: Parental Jurkat T cells were originally purchased from ATCC and were transduced with pMW39 lentivirus (CXCR4 sgRNA) + pMW5 lentivirus (dCas9 ) by our group for use in other studies. No modifications were made to the native Jurkat TCR. The Raji CCL-86 cell line was purchased from ATCC.

value: Blood

value: PBMC

tag: subject id

tag: age at_blood_drawn

tag: Sex

value: Male

tag: ethnicity/race

value: Asian/Non-Hispanic Origin

tag: cmv stats

value: CMV+

tag: treatment time

tag: batch id

tag: pool id

value: PE

tag: batch pool

tag: probe barcode_id


title: DMD19 Day 30 iPSC-CMs treated with microDYS1, biol rep 3

description:
Library name: DMD_microDYS1_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS1_3

tag: cell line

value: cardiomyocytes

value: DMD


title: OP9 cells,Drosha KO,Small RNA-seq,rep1

description: Library name: OP9 cells, Drosha KO-1, Day 10

tag: cell type

value: Drosha KO


title: Input of condition met2-set25-set32, ID:KEOJF

tag: tissue

tag: genotype


title: 10434~IL15/IL7 +pep~Day 10~neg ctrl~pool_1

description:
Library name: FIX10434-052
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment


title: Input of condition met2-set25-set32, ID:OEJHD


title: 10434~IL15/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_1

description:
Library name: FIX10434-051
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: RNA-seq of heart_9

city: sichuan

first: Mantang

last: Jiang

address: west china hospital

institute: Sichuan University

description: Library name: MI+BPD_3

data_processing:
Raw reads were processed to remove adaptor sequences and low-quality reads, and clean reads were aligned to the mouse reference genome (mm10, Ensembl v100) using STAR.
Assembly: GRCm39 (mm39)
Supplementary files format and content: CSV filies including Reads count for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from left ventricular myocardial tissues (including the infarct core and peri-infarct regions) using TRIzol reagent (Invitrogen). RNA quality was assessed using an Agilent 2200 system, and samples with RNA integrity number (RIN) > 7.0 were used for library preparation.
RNA-seq libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s instructions. Library quality was validated using the Agilent 2200 system. Sequencing was performed on the DNBSEQ-T7 platform (150 bp paired-end) by NovelBio.

value: heart

value: MI+BPD


title: DMD19 Day 30 iPSC-CMs treated with microDYS1, biol rep 1

description:
Library name: DMD_microDYS1_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS1_1


title: DMD19 Day 30 iPSC-CMs treated with microDYS1, biol rep 2

description:
Library name: DMD_microDYS1_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_microDYS1_2


title: 10434~IL15/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_2

description:
Library name: FIX10434-055
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Input of condition met2-set25-set32, ID:KSIEH


title: RNA-seq of heart_8

description: Library name: MI+BPD_2


title: DMD19 iPSCs, untreated, biol rep 3

description:
Library name: DMD_iPSC_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_iPSC_3

value: induced pluripotent stem cells


title: RNA-seq of heart_7

description: Library name: MI+BPD_1


title: Input of condition met2-set25-set32, ID:AOCKQ


title: 10434~IL4/IL7 +pep~Day 10~neg ctrl~pool_2

description:
Library name: FIX10434-054
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: DMD19 iPSCs, untreated, biol rep 2

description:
Library name: DMD_iPSC_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_iPSC_2


title: 10434~IL4/IL7 +pep~Day 10~neg ctrl~pool_1

description:
Library name: FIX10434-050
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Input of condition lin61, ID:FKOZA


title: 10434~IL4/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_2

description:
Library name: FIX10434-053
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: DMD19 iPSCs, untreated, biol rep 1

description:
Library name: DMD_iPSC_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_iPSC_1


title: RNA-seq of heart_6

description: Library name: MI_3

value: MI


title: RNA-seq of heart_5

description: Library name: MI_2


title: Input of condition lin61, ID:SJFJG


title: 10434~IL4/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_1

description:
Library name: FIX10434-049
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: DMD19 Day 30 iPSC-CMs treated with empty vector control, biol rep 4

description:
Library name: DMD_Empty_4
Column name in Transcripts_Raw_Counts_Matrix = DMD_Empty_4

value: empty vector control


title: RNA-seq of heart_4

description: Library name: MI_1


title: DMD19 Day 30 iPSC-CMs treated with empty vector control, biol rep 3

description:
Library name: DMD_Empty_3
Column name in Transcripts_Raw_Counts_Matrix = DMD_Empty_3


title: 10435~IL15/IL7 +pep~Day 10~neg ctrl~pool_2

description:
Library name: FIX10435-078
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female

value: Other/ Non-Hispanic Origin


title: Input of condition lin61, ID:KDPEK

value: embryos

value: Input


title: RNA-seq of heart_3

description: Library name: Sham_3

value: Sham


title: Input of condition lin61, ID:JWITN


title: 10435~IL15/IL7 +pep~Day 10~neg ctrl~pool_1

description:
Library name: FIX10435-074
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC


title: DMD19 Day 30 iPSC-CMs treated with empty vector control, biol rep 2

description:
Library name: DMD_Empty_2
Column name in Transcripts_Raw_Counts_Matrix = DMD_Empty_2


title: RNA-seq of heart_2

description: Library name: Sham_2


title: Input of condition lin61, ID:DOTHA


title: 10435~IL15/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_2

description:
Library name: FIX10435-077
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: CMV+


title: RNA-seq of heart_1

description: Library name: Sham_1


title: Input of condition lin61, ID:ZJTUD


title: DMD19 iso Day 30 iPSC-CMs treated with empty vector control, biol rep 5

description:
Library name: Control_Empty_5
Column name in Transcripts_Raw_Counts_Matrix = Control_Empty_5

value: DMD19 iso

value: WT


title: DMD19 Day 30 iPSC-CMs treated with empty vector control, biol rep 1

description:
Library name: DMD_Empty_1
Column name in Transcripts_Raw_Counts_Matrix = DMD_Empty_1

value: cardiomyocytes

value: DMD


title: 10435~IL15/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_1

description:
Library name: FIX10435-073
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PE


title: Input of condition hpl2-lin61, ID:EEOQA


title: 10435~IL4/IL7 +pep~Day 10~neg ctrl~pool_2

description:
Library name: FIX10435-076
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Input of condition hpl2-lin61, ID:XIRNW


title: DMD19 iso Day 30 iPSC-CMs treated with empty vector control, biol rep 4

description:
Library name: Control_Empty_4
Column name in Transcripts_Raw_Counts_Matrix = Control_Empty_4


title: CD11c negative/low neutrophils_13

first: Koichi

last: Yuki

address: 300 Longwood Avenue

institute: Boston Children's Hospital

description:
Library name: Sample 39
Counts per gene written in each row

data_processing:
Raw sequencing reads underwent quality control and preprocessing, including adapter trimming and removal of low-quality bases using Trimmomatic (v0.36).
Processed reads were aligned to the human reference genome using STAR aligner (v2.5.2b), and only uniquely mapped reads within annotated exon regions were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: counts in txt file.

source_name: Neutrophils

growth_protocol: Not relevant

extract_protocol:
RNA was purified using trizol
Sequencing libraries were generated using the Illumina Nextera XT library preparation kit

treatment_protocol: Not relevant

value: Neutrophils

tag: cell surface_cd11c_expression

value: CD11c negative/low


title: CD11c high neutrophils_13

description:
Library name: Sample 40
Counts per gene written in each row

value: CD11c high


title: DMD19 iso Day 30 iPSC-CMs treated with empty vector control, biol rep 3

description:
Library name: Control_Empty_3
Column name in Transcripts_Raw_Counts_Matrix = Control_Empty_3

value: empty vector control


title: 10435~IL4/IL7 +pep~Day 10~neg ctrl~pool_1

description:
Library name: FIX10435-072
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Female


title: CD11c high neutrophils_12

description:
Library name: Sample 34
Counts per gene written in each row


title: 10435~IL4/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_2

description:
Library name: FIX10435-075
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Other/ Non-Hispanic Origin


title: DMD19 iso Day 30 iPSC-CMs treated with empty vector control, biol rep 2

description:
Library name: Control_Empty_2
Column name in Transcripts_Raw_Counts_Matrix = Control_Empty_2


title: Input of condition hpl2-lin61, ID:QORKA

value: embryos


title: CD11c negative/low neutrophils_12

description:
Library name: Sample 33
Counts per gene written in each row


title: Input of condition hpl2-lin61, ID:COLQA

value: Input


title: DMD19 iso Day 30 iPSC-CMs treated with empty vector control, biol rep 1

description:
Library name: Control_Empty_1
Column name in Transcripts_Raw_Counts_Matrix = Control_Empty_1


title: 10435~IL4/IL7 +pep~Day 10~pp65 pos~NLVPMVATV_1

description:
Library name: FIX10435-071
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: CD11c high neutrophils_11

description:
Library name: Sample 32
Counts per gene written in each row


title: Input of condition hpl2, ID:CITNR


title: (KT10435) BW2164TWS-119 1uM -pep

description:
Library name: FIX10435-037
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PD


title: CD11c negative/low neutrophils_11

description:
Library name: Sample 31
Counts per gene written in each row


title: human BMMSCs (control)

city: UC Irvine

first: Ronke

middle: Mojoyinola

last: Olabisi

state: California

address: 3105 Natural Sciences II

department: Biomedical Engineering

institute: UC Irvine

description:
Library name: mixed_all_human
PARSE EvercodeTM WT v2 100K Well, sample A1:A5, 8013L_media A6:A10, 8013L_ins A11:D12, unused

data_processing:
Parse Biosciences' split-pipe v1.0.3 was used process the Fastq files into cell matrices
Assembly: hg38
Supplementary files format and content: tab-delimited files and matrix files

source_name: bone marrow

extract_protocol:
After 3 days of incubation with insulin, plated cells were detached using trypsin/EDTA (0.05%) and counted using the automated cell counter Countess (Thermo). Cells were centrifuged at 200 x g for 10 min, the supernatant was discarded, and cells were resuspended in 750 μL of Cell Prefixation Buffer (Parse Biosciences). Samples were then fixed using the Parse Biosciences Cell Fixation (v1 or v2) kit.
The fixed cells were then processed using the Parse Biosciences WT v1 kit.

treatment_protocol: incubated with 0.1 ng/mL recombinant human insulin

value: bone marrow

value: primary

value: mesenchymal stem cell


title: Input of condition hpl2, ID:FKLRS


title: HEP3B, NAT10-K290V, IP, Rep 2

description: Library name: SL20

data_processing:
Raw reads were pre-processed to remove low quality bases, adapter sequences, and a stretch of at least 10 consecutive guanine nucleotides at the 3’ end using cutadapt/4.2.
The UMI was extracted using UMI-tools/1.1.5.
Reads were aligned to the human genome using STAR/2.7.9a in local alignment mode.
All alignments were deduplicated using UMI-tools and R1 was extracted using samtools/1.6.
Alignments were converted to bigwig files normalized by RPKM using Deeptools/3.5.1. Bigwig files were visualized using Integrative Genomics Viewer/2.19.1.
Assembly: GRCh38
Supplementary files format and content: Bigwig files with R1 extracted, normalized by RPKM.

extract_protocol:
For cellular lysis, pellets were resuspended in 1 mL cold lysis buffer [50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% (vol/vol) Igepal CA-630, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate, and 5.5 µL 200× protease inhibitor cocktail III], Lysates were sonicated in a Bioruptor sonicator (30s on/30s off at 4°C for 5 min). 5 µL Turbo DNase and 10 µL diluted RNase I (1:25 dilution in iced cold 1× PBS) were added to each lysate and then immediately incubated in a Thermomixer at 37°C and 1,200 rpm for 5 min. RNAse digestion was stopped by adding 11 µL murine RNase inhibitor. Lysis were cleared by centrifugation at 15000 ×g, 4°C for 15 min and 1 mL of each supernatant was collected for further use.
NAT10 was immunoprecipitated with anti-NAT10 antibody (10 µg per sample, rabbit polyclonal) conjugated to M-280 sheep anti-rabbit IgG magnetic beads. To identify the NAT10 bound RNAs, a 3’ Illumina adapter was ligated on-beads followed by separation of the complexes via SDS-PAGE. The NAT10-RNA complexes were excised out of the membranes, followed by proteinase K digestion and RNA isolation using the RNA Clean and Concentrator Kit (Zymo Research, R1018). Reverse transcription was performed using a specific primer aligning to the 3’ Illumina adapter. Following cDNA purification, the other Illumina adapter, which contained a ten nucleotide UMI, was ligated to the 3’ end of the cDNA. Final libraries were generated by performing PCR using Q5® High-Fidelity 2X Master Mix (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs) as primers. Libraries were gel purified and quality was verified on a TapeStation 4200 System (Agilent) before sequencing.  To process size-matched input (SMInput) samples, an aliquot of cell lysates was collected before the immunoprecipitation was carried out. Inputs were separated using SDS-PAGE and a region that matches NAT10’s molecular weight was excised out of the membranes, followed by proteinase K digestion and RNA isolation using the RNA Clean and Concentrator Kit (Zymo Research, R1018). A 3’ Illumina adapter was ligated followed reverse transcription using a specific primer aligning to the 3’ Illumina adapter. Following cDNA purification, the other Illumina adapter, which contained a ten nucleotide UMI, was ligated to the 3’ end of the cDNA. Final libraries were generated by performing PCR using Q5® High-Fidelity 2X Master Mix (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs) as primers. Libraries were gel purified, and quality was verified on a TapeStation 4200 System (Agilent) before sequencing.

treatment_protocol: HEP3B cells expressing NAT10-FKBP  were transduced with single mutants in the Helicase domain (K290A or E389L) or vector control (YFP) for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1. Cell were crosslinked at 400,000 µJ/cm2 UV254nm . Cells were scraped out and washed by centrifugation at 300 ×g with cold PBS twice. Pellets were flash-frozen in liquid nitrogen and stored at -80°C until further use.

value: Liver

value: Hepatocellular Carcinoma

value: IP

tag: batch

value: Replicate 2


title: (KT10435) BW2164TWS-119 5uM -pep

description:
Library name: FIX10435-036
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

tag: subject id

value: CMV+


title: Input of condition hpl2, ID:OTMPR


title: HEP3B, NAT10-E389L, IP, Rep 2

description: Library name: SL19


title: CD11c high neutrophils_10

description:
Library name: Sample 26
Counts per gene written in each row

value: Neutrophils

value: CD11c high


title: (KT10435) BW2164TWS-119 10uM -pep

description:
Library name: FIX10435-035
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: age at_blood_drawn

value: Female


title: Input of condition hpl2, ID:XOTLD


title: CD11c negative/low neutrophils_10

description:
Library name: Sample 25
Counts per gene written in each row

value: CD11c negative/low


title: (KT10435) BW2164TWS-119 1uM +pep

description:
Library name: FIX10435-034
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: Sex

value: Other/ Non-Hispanic Origin


title: HEP3B, YFP, IP, Rep 2

description: Library name: SL18

value: YFP


title: CD11c high neutrophils_9

description:
Library name: Sample 24
Counts per gene written in each row


title: Input of condition hpl2, ID:OTLCJ

value: embryos

value: Input


title: HEP3B, NAT10-WT, IP, Rep 2

description: Library name: SL17


title: CD11c negative/low neutrophils_9

description:
Library name: Sample 23
Counts per gene written in each row


title: (KT10435) BW2164TWS-119 5uM +pep

description:
Library name: FIX10435-033
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: ethnicity/race

value: PD


title: Input of condition CEC4, ID:COTNQ


title: HEP3B, Control, IP, Rep 2

description: Library name: SL16

value: Parental


title: (KT10435) BW2164TWS-119 10uM +pep

description:
Library name: FIX10435-032
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: cmv stats


title: CD11c high neutrophils_8

description:
Library name: Sample 22
Counts per gene written in each row


title: Input of condition CEC4, ID:CITNQ


title: HEP3B, NAT10-K290V, Input, Rep 2

description: Library name: SL15

value: Liver


title: CD11c negative/low neutrophils_8

description:
Library name: Sample 21
Counts per gene written in each row


title: Input of condition CEC4, ID:CSOTN


title: (KT10435) BW2164UK5099 50uM late -p

description:
Library name: FIX10435-029
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment time

value: PC


title: (KT10435) BW2164Day 0

description:
Library name: FIX10435-031
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch id


title: HEP3B, NAT10-E389L, Input, Rep 2

description: Library name: SL14

value: Hepatocellular Carcinoma


title: CD11c high neutrophils_7

description:
Library name: Sample 20
Counts per gene written in each row


title: Input of condition CEC4, ID:XOMTP


title: HEP3B, YFP, Input, Rep 2

description: Library name: SL13

value: Replicate 2


title: (KT10435) BW2164UK5099 50uM late +p

description:
Library name: FIX10435-028
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

tag: pool id


title: CD11c negative/low neutrophils_7

description:
Library name: Sample 19
Counts per gene written in each row


title: Input of condition CEC4, ID:WSITN


title: HEP3B, NAT10-WT, Input, Rep 2

description: Library name: SL12


title: (KT10435) BW2164UK5099 12.5uM -pep-34

description:
Library name: FIX10435-027
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: PBMC

tag: batch pool


title: HEP3B, Control, Input, Rep 2

description: Library name: SL11


title: Input of condition CEC4, ID:VJUTG


title: CD11c high neutrophils_6

description:
Library name: Sample 18
Counts per gene written in each row


title: (KT10435) BW2164UK5099 25uM -pep-33

description:
Library name: FIX10435-026
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: CMV+

tag: probe barcode_id


title: HEP3B, NAT10-K290V, IP, Rep 1

description: Library name: SL10

tag: cell line

value: IP

value: Replicate 1


title: CD11c high neutrophils_5

description:
Library name: Sample 16
Counts per gene written in each row

tag: cell type

value: Neutrophils

value: CD11c high


title: (KT10435) BW2164UK5099 50uM -pep-32

description:
Library name: FIX10435-025
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: tissue

value: Female

value: Other/ Non-Hispanic Origin


title: HEP3B, NAT10-E389L, IP, Rep 1

description: Library name: SL9

tag: genotype


title: Input of condition I158A, ID:CRTSA

value: embryos

tag: treatment


title: CD11c negative/low neutrophils_6

description:
Library name: Sample 17
Counts per gene written in each row

tag: cell surface_cd11c_expression

value: CD11c negative/low


title: Input of condition I158A, ID:ETGCA

value: Input


title: Input of condition I158A, ID:VTRSQ


title: CD11c negative/low neutrophils_5

description:
Library name: Sample 15
Counts per gene written in each row


title: (KT10435) BW2164UK5099 12.5uM +pep-31

description:
Library name: FIX10435-024
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: (KT10435) BW2164UK5099 25uM +pep-30

description:
Library name: FIX10435-023
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture


title: Input of condition I158A, ID:STGOI


title: HEP3B, NAT10-WT, IP, Rep 1

description: Library name: SL7

tag: batch


title: CD11c high neutrophils_4

description:
Library name: Sample 14
Counts per gene written in each row


title: HEP3B, Control, IP, Rep 1

description: Library name: SL6

value: Parental


title: CD11c negative/low neutrophils_4

description:
Library name: Sample 13
Counts per gene written in each row


title: (KT10435) BW2164UK5099 50uM +pep-29

description:
Library name: FIX10435-022
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: subject id


title: (KT10435) BW2164DMSO -pep-28

description:
Library name: FIX10435-021
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: age at_blood_drawn


title: HEP3B, NAT10-K290V, Input, Rep 1

description: Library name: SL5

value: Liver


title: Input of condition I158A, ID:TGEZB


title: Input of condition I158A, ID:QTGCE


title: CD11c high neutrophils_3

description:
Library name: Sample 8
Counts per gene written in each row


title: HEP3B, NAT10-E389L, Input, Rep 1

description: Library name: SL4


title: (KT10435) BW2164Std -pep-27

description:
Library name: FIX10435-020
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: Sex

value: PC


title: Input of condition N2, ID:FRTGE


title: CD11c negative/low neutrophils_3

description:
Library name: Sample 7
Counts per gene written in each row


title: HEP3B, NAT10-WT, Input, Rep 1

description: Library name: SL2

value: Hepatocellular Carcinoma


title: (KT10435) BW2164Std -pep-26

description:
Library name: FIX10435-019
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: ethnicity/race


title: Input of condition N2, ID:KFRED


title: HEP3B, Control, Input, Rep 1

description: Library name: SL1


title: CD11c negative/low neutrophils_2

description:
Library name: Sample 3
Counts per gene written in each row


title: (KT10435) BW2164DMSO +pep-25

description:
Library name: FIX10435-018
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: cmv stats


title: (KT10435) BW2164Std +pep-24

description:
Library name: FIX10435-017
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: treatment time


title: Input of condition N2, ID:SJEPO


title: (KT10435) BW2164Std +pep-23

description:
Library name: FIX10435-016
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: batch id


title: Input of condition N2, ID:JEOSM


title: HEP3B, Control, Rep 2

description: Library name: P52

data_processing:
Raw reads were pre-processed to remove low-quality bases, adapter sequences from the first and second 3' adapter ligation steps, and possible stretches of at least 10 consecutive guanine (G) nucleotides at the 3' end using cutadapt/v4.257. It was necessary to remove long stretches of G's due to the sequencing instrument reporting high-quality Gs in the absence of signal towards the end of the read.
Reads were aligned to the RNA45SN5 sequence (NT_167214.1), previously split into multiple references corresponding to each cleavage site ("5ETS", "A0", "A1", "18S", "E", "A2", "B1", "5_8S", "ITS2", "28S", "3ETS") using Bowtie2/v2.5.458. All alignment files were sorted and indexed using samtools/v1.653.
The first-in-pair (R1) read was extracted using samtools to obtain reads containing information about the 5’-end of the sequence. These alignments were converted to bigwig files normalized by reads per kilobase per million mapped reads (RPKM) using Deeptools/v3.5.159. Bigwig files were visualized using Integrative Genomics Viewer (IGV)/v2.19.160. RPKM values with a window of 50 nt from the start sites of each cleavage site ("5ETS", "A0", "A1", "18S", "E", "A2", "B1", "5_8S", "ITS2", "28S", "3ETS") were extracted from Bigwig files using the rtracklayer package in R. The mean RPKM values of the 50 nt window were computed and compared across samples.
Assembly: RNA45SN5 (NT_167214.1)
Supplementary files format and content: Bigwig files containing the extracted R1, normalized by RPKM.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (ThermoFisher Scientific) according to the manufacturer's protocol. Total RNA was then DNase treated with DNase I (NEB) and reconstituted in nuclease-free water.
Total RNA was dephosphorylated followed by a 3' adapter ligation. The 3' adapter contains a spacer that impedes the self-ligation of RNA. The ligated RNA mixture was 5' re-phosphorylated followed by ligation of a 5' RNA adaptor containing a Unique Molecular Identifier (UMI) of ten randomized nucleotides. Ligated RNA was then fragmented to obtain fragments of ~200 nt from the 5’end of the molecule. Fragmented RNA was ligated to another 3’ RNA adapter. Final libraries were PCR amplified using Q5® High-Fidelity 2X Master Mix (NEB) and NEBNext® Multiplex Oligos for Illumina®. The primers aligned perfectly to the 5’ adapter and the second 3’ adapter. Each sample was assigned a different indexed primer.

treatment_protocol: NAT10-FKBP cells were transduced with single mutants in the Helicase domain (E389L) for 24 h, released from transduction by replacing with fresh DMEM for 24 h, and then selected using 5 µg/ml Blasticidin-S HCl for 5 days. Blasticidin selected transduced cells with parental control and NAT10-FKBP cells were then treated with 100 nM dTAGV1 for 24 hrs.

value: 100 nM dTAGV1 (24 hours)

value: Replicate 2


title: HEP3B, Control, Rep 1

description: Library name: P51


title: CD11c negative/low neutrophils_1

description:
Library name: Sample 1
Counts per gene written in each row


title: CD11c high neutrophils_1

description:
Library name: Sample 2
Counts per gene written in each row


title: CD11c high neutrophils_2

description:
Library name: Sample 4
Counts per gene written in each row


title: Input of condition N2, ID:QFCZI


title: HEP3B, E389L, Rep 2

description: Library name: H52


title: (KT10434) BW3446TWS-119 10uM late -p-22

description:
Library name: FIX10434-037
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC

value: Male

value: Asian/Non-Hispanic Origin

tag: pool id

value: PB


title: UK-Not Stretched (-peristalsis)

city: Los Angeles

first: Shannon

last: Mumenthaler

address: 12414 Exposition Blvd

department: Translational Research

institute: Ellison Medical Institute

description:
Library name: Sample 10
Column name in bulk_RNA_normalized_counts.csv: EITB.000UK.Chip.NoStretch

data_processing:
Fastp was used for read quality evaluation and STAR was used for read alignment against GENCODE v39 annotation (GRCh38).  MutliQC was used to summarize sample statistics.  High-quality samples were selected based on duplication and alignment rate as well as PCA and correlation to remove outliers.
Assembly: GRCh38
Supplementary files format and content: gene count matrix as a CSV file

source_name: Colon Epithelial Organoid

extract_protocol:
Cells were lysed directly on chip using Lysis Buffer and RNA was isolated using the PureLink RNA Mini Kit
Sequencing libraries were generated by SMARTer Stranded Total RNAseq Kit - Pico Input Mammalian V3 (Takara Bio)

value: Colon Epithelial Organoid

value: (-peristalsis)


title: ChIP-seq of lin61 in condition N2, rep2

description:
rep2
lin61_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_N2_merged.bwa_aln.rmdup.bamCompare.bw


title: (KT10434) BW3446TWS-119 1uM -pep-18

description:
Library name: FIX10434-033
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: CMV+

tag: batch pool


title: HEP3B, E389L, Rep 1

description: Library name: H51

value: Replicate 1


title: UK-Stretched (+peristalsis)

description:
Library name: Sample 9
Column name in bulk_RNA_normalized_counts.csv: EITB.000UK.Chip.Stretch

value: (+peristalsis)


title: (KT10434) BW3446TWS-119 5uM -pep-17

description:
Library name: FIX10434-032
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: probe barcode_id


title: ChIP-seq of lin61 in condition N2, rep1

description:
rep1
lin61_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
lin61_N2_merged.bwa_aln.rmdup.bamCompare.bw

value: embryos


title: V8-Not Stretched (-peristalsis)

description:
Library name: Sample 8
Column name in bulk_RNA_normalized_counts.csv: EITB.000V8.Chip.NoStretch


title: THP-1-derived macrophage cells,  siDUSP6_3

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

description:
Library name: siDUSP6_3
RNA-seq

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS. Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: GRCh38
Supplementary files format and content: gene.TPM.matrix.xlsx

source_name: cell line

growth_protocol: THP-1-derived macrophage cells were maintained in RPMI 1640 medium supplemented with FBS in humidified atmosphere wwith 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen, USA).
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: THP-1-derived macrophage cells were transfected with NC siRNA or DUSP6 siRNA, respectively.

value: cell line

tag: cell line

value: THP-1-derived macrophage cells

value: macrophage

value: DUSP6 knockdown

value: transfectIion with DUSP8 siRNA

tag: time


title: ChIP-seq of LEM2 in condition N2, rep3

description:
rep3
LEM2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_N2_merged.bwa_aln.rmdup.bamCompare.bw

tag: tissue


title: (KT10434) BW3446TWS-119 10uM -pep-16

description:
Library name: FIX10434-031
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

tag: cell type


title: ChIP-seq of LEM2 in condition N2, rep2

description:
rep2
LEM2_N2.bwa_aln.rmdup._peaks.narrowPeak_optimal.bed
LEM2_N2_merged.bwa_aln.rmdup.bamCompare.bw

tag: genotype

tag: treatment


title: THP-1-derived macrophage cells,  siDUSP6_2

description:
Library name: siDUSP6_2
RNA-seq

value: transfectIion with DUSP7 siRNA


title: V8-Stretched (+peristalsis)

description:
Library name: Sample 7
Column name in bulk_RNA_normalized_counts.csv: EITB.000V8.Chip.Stretch


title: THP-1-derived macrophage cells,  siDUSP6_1

description:
Library name: siDUSP6_1
RNA-seq

value: transfectIion with DUSP6 siRNA


title: (KT10434) BW3446TWS-119 1uM +pep-15

description:
Library name: FIX10434-030
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

value: Blood

value: PBMC


title: US-Not Stretched (-peristalsis)

description:
Library name: Sample 6
Column name in bulk_RNA_normalized_counts.csv: EITB.000US.Chip.NoStretch