title: Post_treatment _5

city: Fuzhou

first: Aling

last: Shen

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

description:
Library name: Sample 10
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks

data_processing:
Raw sequencing reads were filtered to remove low-quality reads, adapter sequences, and reads outside the 18-35nt length range using FastQC and Trimmomatic.
miRNA expression levels were calculated using TPM (Transcripts Per Million) values, and novel miRNAs were predicted using miRDeep2.
Differentially expressed miRNAs were identified using DESeq2 (|log2FoldChange| ≥ 1, p-adj < 0.05), followed by target prediction and pathway analysis.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

source_name: Gastric tissue

extract_protocol:
Total RNA was extracted and quality controlled using NanoDrop and Agilent 2100 Bioanalyzer to assess RNA integrity, requiring RIN value ≥8 and 28S:18S ratio ≥1.5:1. Small RNA library was constructed using 1-10μg total RNA, including 3' adapter ligation, 5' adapter ligation, reverse transcription, and PCR amplification. The PCR products were separated by 6% polyacrylamide gel electrophoresis, and target fragments of 145-160bp were excised and recovered. Library quality control and quantification were performed using Bioanalyzer and qPCR, and the library concentration was adjusted to 2nM. Finally, cluster generation and sequencing were performed on the HiSeq 2500 platform, with sequencing quality assessed by First Base Report.
Small RNA libraries were constructed using the Illumina platform. Library construction was performed using 1-10μg of quality-controlled total RNA (RIN≥8), including 3' adapter ligation, 5' adapter ligation, reverse transcription, and PCR amplification. The PCR products were separated by gel electrophoresis, and 145-160bp target fragments were recovered. After quality control and quantification, the library concentration was adjusted to 2nM for sequencing on the HiSeq 2500 platform.

value: Gastric tissue

value: after JPQHSYY treatment


title: Pt11, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

status: Public on Mar 01 2025

type: SRA

city: Philadelphia

first: Michael

last: Klichinsky

state: Pennsylvania

address: 3675 Market Street Ste. 401

country: USA

institute: Carisma Therapeutics

description: Library name: Pt11_PD_Week4_Tumor

library_source: transcriptomic

data_processing:
Data processing was performed by Adaptive Biotechnologies according to their pipeline
Assembly: MM10
Supplementary files format and content: tab-delimited text file with TCR sequences, counts, frequencies, and VDJ gene predictions
Library strategy: TCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Extraction performed by Adaptive Biotechnologies
Library construction performed by Adaptive Biotechnologies

tag: tissue

value: Tumor

tag: treatment

value: CT-0508 CAR Macrophages


title: 19577X95 UU20 Washed Plts

city: Salt Lake City

first: Matthew

middle: T

last: Rondina

state: Utah

department: Hematology

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
The output files were summarized using MultiQC to check for sample outliers and plot alignment statistics
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCh38
Supplementary files format and content: featureCount ouput files combined into a single tab-delimited raw count matrix

source_name: Blood

extract_protocol:
RNA from with Washed Platelets or Leukocyte-depletion using CD45 beads, or PALL-filtered platelets, were isolated using the standard TRIzol® protocol (ThermoFisher #15596018) with the addition of 20 µg glycogen (Sigma #10901393001) at the isopropanol precipitation step.  Following a 75% ethanol wash, RNA pellets were allowed to air dry. RNA pellets were next suspended in nuclease-free water. Any potential contaminating DNA was digested 25 minutes at 37°C using Turbo DNA Free Kit (ThermoFisher AM1907) and the final RNA was cleaned and eluted in 26 µl nuclease-free water using Zymo RNA Clean & Concentrate kit (Zymo R1017) following the product instructions.
Intact poly(A) RNA was purified from total RNA samples (150 ng) with oligo(dT) magnetic beads. RNA concentration was evaluated using a Nanodrop (ThermoFisher Scientific; Illkirch, France). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102) with PolyA Selection. The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 5 nM and equal volumes were pooled in preparation for sequencing. RNA was sequenced by an Illumina NovaSeq sequencer using the NovaSeq 6000 using v1.5 reagents and S4 flow cell to produceKit 1 150x150 bp (paired end reads).

value: Blood

tag: cell type

value: platelets

tag: isolation technique

value: Washed Platelet Isolation


title: 19577X94 UU19 Bead

value: Leukocyte-bead depletion Isolation


title: 19577X93 UU19 Washed Plts


title: FcgRIIB-/- scRNA 2

last: Gonzalez

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description: FACS sorted live cells CD3- B220+CD19+ (90% IgD- and 10% IgD+

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on an Illumina HiSeq sequencer. Data was then processed through the Cellranger pipeline (10x Genomics). Demultiplexing and alignments were performed against the mm10 transcriptome. Analysis was performed via Seurat package (v. 4.99) within R. Cells expressing less than 200 or more than 4000 unique genes were excluded from further analysis. Cells with >10% mitochondrial genes expression were also excluded. Log normalization and scaling of features was completed before principal component dimensionality reduction, clustering, and visualization via UMAP. Pseudotime analysis was performed using the Monocle3 package in R. A wilcoxon rank sum test with a Bonferroni multiple testing correction was used to identify differentially expressed genes between FcgRIIB-/- and FcgRIIB-/-IRF7-/- groups.
Assembly: mm10
Supplementary files format and content: Processed data files for each sample consist of a barcode ID file, feature ID file, and count matrix file as produced from the Cellranger Pipeline (10x Genomics). An additional processed data file set includes the resulting filtered_contig_annotations.csv file for each library which contains the "annotations of each high-confidence cellular contig" (10x Genomics)

molecule: polyA RNA

organism: Mus musculus

source_name: spleen

extract_protocol:
Murine spleens processing the tissue into a single cell suspension followed by RBC lysis using Tris-Ammonium Chloride. CD3-B220+CD19+IgD- and CD3-B220+CD19+IgD+ cells were sorted from each animal and mixed at a ratio of 9:1 (IgD-: IgD+) prior to library preparation.
Libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2 per manufacturer’s instructions.

value: spleen

tag: age

value: 3 month old

tag: genotype

value: FcgRIIB-/-

tag: Sex

value: female

value: B cells


title: Post_treatment _4

state: Fujian

country: China

description:
Library name: Sample 9
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: Post_treatment _3

description:
Library name: Sample 8
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: Pt11, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt11_PD_Day15_Blood


title: Pt11, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt11_PD_Day8_Tumor


title: FcgRIIB-/- scRNA 1


title: Post_treatment _2

description:
Library name: Sample 7
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks


title: Pt11, Progressive Disease, Screening, Tumor, TCR-seq

description: Library name: Pt11_PD_Screening_Tumor

value: Screening


title: SCN, control2, 22hours, rep2

city: Didcot

first: Akanksha

last: Bafna

address: Harwell Campus

country: United Kingdom

institute: MRC HARWELL

data_processing:
Paired-end FASTQ files were quality assessed (Phred<20 removed) with FastQC
Illumina adapters were trimmed with TrimGalore (v0.4.3)
Reads were aligned to mm10 genome assembly using STAR (v2.7.8a) with MAPQ value for unique mappers set to 60.
Binary alignment map (BAM) files were used to generate read counts per gene by FeatureCounts via Samtools
Limma-voom method (Liu et al. 2015) from the Bioconductor package-limma (v3.48.0) was adopted to quantify differential gene expression and normalised logarithmic CPM values were generated
Assembly: mm10
Supplementary files format and content: tam-delimited text file contains normalized counts (CPM) for each sample

source_name: suprachiasmatic nucleus

growth_protocol: Mice from control (Cre-neg and Pre-tam) and Zfhx3 knock out (Post-tam) cohorts were used for SCN tissue collection (Bafna, Lau, et al., 2023) at 6 distinct time-points starting from ZT2 at every 4 hours.

extract_protocol:
Total RNA from each sample replicate was extracted using RNeasy Micro Kit (QIAGEN, #74004) following the protocol for microdissected cryosections as per manufacturer’s guidelines and stored at -80°C.
PolyA RNA-Seq libraries were prepared by Oxford Genomics Centre, University of Oxford using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, #E7760) and sequenced on NovaSeq6000_150PE (150 bp paired-end directional reads: ~40 million reads/sample) platform.

value: suprachiasmatic nucleus

tag: time

value: 22 hours

value: tamoxifen undosed


title: Post_treatment _1

description:
Library name: Sample 6
Gastric tissue of reg patients afterJPQHSYY treatment for 8-12 weeks

value: Gastric tissue


title: 19577X91 PG08 B Washed Plts


title: Pt11, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt11_PD_Screening_Blood


title: Pre_treatment_5

description:
Library name: Sample 5
Gastric tissue of reg patients

value: before JPQHSYY treatment


title: 19577X90 PG07 C Bead


title: SCN, control2, 18hours, rep1

value: 18 hours


title: Pt11, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt11_PD_Week4_Blood

value: CT-0508 CAR Macrophages


title: 19577X89 PG07 B Washed Plts

value: Blood


title: Pre_treatment_4

description:
Library name: Sample 4
Gastric tissue of reg patients


title: Pre_treatment_3

description:
Library name: Sample 3
Gastric tissue of reg patients


title: SCN, control2, 22hours, rep1


title: SCN, control2, 14hours, rep3

value: 14 hours


title: 19577X92 PG08 C Bead

value: platelets


title: 19577X88 UD08 Bead

value: Leukocyte-bead depletion Isolation


title: Pt7, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt7_PD_Week4_Blood


title: Pt7, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt7_PD_Week4_Tumor

value: Tumor


title: SCN, control2, 14hours, rep2


title: Pt7, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt7_PD_Day15_Blood


title: Pre_treatment_2

description:
Library name: Sample 2
Gastric tissue of reg patients


title: SCN, control2, 14hours, rep1


title: Pre_treatment_1

description:
Library name: Sample 1
Gastric tissue of reg patients


title: 19577X86 UD07 Bead


title: Pt7, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt7_PD_Day8_Tumor


title: 19577X85 UD07 Washed Plts

value: Washed Platelet Isolation


title: SCN, control2, 10hours, rep3

value: 10 hours


title: AC16 cells，PA_3

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing:
Use fastqc software for quality control(default parameters)
Use fastp for data cleaning, including removing sequencing reads that contain adapters and too many low-quality bases(parameters- length_required 20 compression 4 q 20 n 7)
Use hisat2 to align clean reads to the ucsc hg19 genome (parameters- default)
Predicting novel transcripts using the stringtie toolbox(parameters- default）
Use rsem software to estimate transcripts, gene-level expression, and then extract raw counts and normalized expression FPKM from the results(parameters- default）
Assembly: ucsc hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

tag: cell line

value: human cardiomyocytes cells

value: WT

value: Palmitelaidic Acid


title: Pt7, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt7_PD_Screening_Blood

value: Screening


title: Pt7, Progressive Disease, Screening, Tumor, TCR-seq

description: Library name: Pt7_PD_Screening_Tumor


title: SCN, control2, 10hours, rep2

value: suprachiasmatic nucleus


title: Pt12, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt12_PD_Week4_Tumor


title: SCN, control2, 10hours, rep1

value: tamoxifen undosed


title: SCN, control2, 6hours, rep2

value: 6 hours


title: AC16 cells，PA_1


title: 19577X83 C09 Bead


title: 19577X84 C09 Filter

value: PALL-Filtration Isolation


title: Pt12, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt12_PD_Week4_Blood


title: 19577X82 C09 Washed Plts


title: AC16 cells，control_3

value: Ethanol


title: SCN, control2, 6hours, rep1


title: AC16 cells，control_2


title: 19577X87 UD08 Washed Plts


title: 19577X81 C08 Filter


title: AC16 cells，PA_2


title: Pt12, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt12_PD_Day15_Blood

value: CT-0508 CAR Macrophages


title: SCN, control2, 2hours, rep2

value: 2 hours


title: AC16 cells，control_1


title: Pt12, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt12_PD_Day8_Tumor


title: SCN, control2, 2hours, rep1


title: 19577X80 C08 Bead

value: Blood


title: Pt10, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt10_PD_Day15_Blood


title: Pt10, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt10_PD_Week4_Tumor


title: 19577X76 UU17 Bead

value: platelets


title: Pt12, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt12_PD_Screening_Blood


title: 19577X79 C08 Washed Plts


title: 19577X78 UU18 Bead

value: Leukocyte-bead depletion Isolation


title: SCN, mutant, 18hours, rep4

value: 18 hours

value: tamoxifen dosed


title: M030192_10 Peripheral Choroid

first: Mingyao

last: Li

state: PA

address: 423 Guardian Drive

institute: Univerrsity of Pennsylvania

data_processing:
For each sample a cell by gene count matrix is provided
Assembly: HG38
Supplementary files format and content: 10X Genomics sparse data matrix

source_name: Choroid

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina and RPE /choroid was carefully removed under a dissecting microscope and both tissue layers were dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.

value: Peripheral Choroid


title: SCN, mutant, 22hours, rep1

value: 22 hours


title: Pt10, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt10_PD_Week4_Blood


title: SCN, mutant, 22hours, rep3


title: SCN, control2, 14hours, rep4

value: 14 hours


title: 19577X74 UU16 Bead


title: SCN, mutant, 22hours, rep4


title: M030192_12 Peripheral Retina

source_name: Retina

value: Peripheral Retina


title: 19577X75 UU17 Washed Plts

value: Washed Platelet Isolation


title: M030192_11 Peripheral Retina


title: SCN, mutant, 22hours, rep2

value: suprachiasmatic nucleus


title: 19577X77 UU18 Washed Plts


title: Pt10, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt10_PD_Screening_Blood

value: Screening


title: M030192_12 Macula Retina

value: Macula Retina


title: Pt10, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt10_PD_Day8_Tumor

value: Tumor


title: SCN, mutant, 18hours, rep3


title: M030192_10 Peripheral Retina


title: M030192_10 Macula Retina


title: M030192_11 Macula Retina


title: 19577X73 UU16 Washed Plts


title: Pt2, Stable Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt2_SD_Week4_Tumor


title: SCN, mutant, 18hours, rep2


title: 19577X72 UU15 Bead


title: Pt2, Stable Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt2_SD_Week4_Blood


title: M030192_10 Macula Choroid

value: Macula Choroid


title: SCN, mutant, 18hours, rep1


title: SCN, mutant, 14hours, rep4


title: 19577X70 PG06 C Bead


title: M030192_9 Macula Retina


title: SCN, mutant, 14hours, rep3


title: M030192_8 Peripheral Retina


title: SCN, mutant, 14hours, rep1


title: SCN, mutant, 14hours, rep2


title: M030192_9 Peripheral Retina


title: Pt2, Stable Disease, Screening, Blood, TCR-seq

description: Library name: Pt2_SD_Screening_Blood


title: 19577X67 PG05 B Washed Plts


title: Pt2, Stable Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt2_SD_Day8_Tumor

value: CT-0508 CAR Macrophages


title: 19577X68 PG05 C Bead


title: Pt9, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt9_PD_Week4_Tumor


title: 19577X69 PG06 B Washed Plts


title: Pt2, Stable Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt2_SD_Day15_Blood


title: M030192_8 Peripheral Choroid


title: M030192_8 Macula Retina


title: Pt9, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt9_PD_Day15_Blood


title: 19577X71 UU15 Washed Plts


title: M030192_8 Macula Choroid


title: SCN, mutant, 10hours, rep4

value: 10 hours


title: 19577X66 UD06 Bead

value: Blood


title: Pt9, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt9_PD_Day8_Tumor


title: SCN, mutant, 10hours, rep3


title: M030192_7 Peripheral Retina


title: 19577X65 UD06 Washed Plts

value: platelets


title: Pt9, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt9_PD_Screening_Blood


title: M030192_7 Macula Retina


title: SCN, mutant, 10hours, rep2


title: Pt14, Response Not Evalutated, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt14_NE_Day8_Tumor


title: SCN, mutant, 10hours, rep1


title: Pt14, Response Not Evalutated, Screening, Tumor, TCR-seq

description: Library name: Pt14_NE_Screening_Tumor


title: M030192_6 Peripheral Retina


title: Pt3, Stable Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt3_SD_Week4_Tumor


title: SCN, mutant, 6hours, rep3

value: 6 hours


title: SCN, mutant, 6hours, rep4


title: 19577X63 UD05 Washed Plts


title: SCN, mutant, 6hours, rep2


title: M030192_5 Hashing

source_name: Retina, Choroid

value: Hashing


title: M030192_6 Macula Retina


title: SCN, mutant, 6hours, rep1

value: tamoxifen dosed


title: M030192_4 Peripheral Retina


title: 19577X59 C06 Filter

value: PALL-Filtration Isolation


title: M030192_4 Peripheral Choroid

value: Peripheral Choroid


title: SCN, mutant, 2hours, rep4

value: 2 hours


title: Pt3, Stable Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt3_SD_Week4_Blood


title: 19577X62 C07 Filter


title: 19577X58 C06 Bead

value: Leukocyte-bead depletion Isolation


title: M030192_4 Macula Retina


title: 19577X64 UD05 Bead


title: Pt14, Response Not Evalutated, Screening, Blood, TCR-seq

description: Library name: Pt14_NE_Screening_Blood


title: Pt3, Stable Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt3_SD_Day8_Tumor


title: 19577X61 C07 Bead


title: SCN, mutant, 2hours, rep3


title: Pt3, Stable Disease, Screening, Tumor, TCR-seq

description: Library name: Pt3_SD_Screening_Tumor


title: M030192_4 Macula Choroid


title: 19577X57 C06 Washed Plts

value: Washed Platelet Isolation


title: SCN, mutant, 2hours, rep2

value: suprachiasmatic nucleus


title: 19577X56 UU14 Bead


title: M030192_3 Peripheral Retina

value: Peripheral Retina


title: Pt3, Stable Disease, Screening, Blood, TCR-seq

description: Library name: Pt3_SD_Screening_Blood

value: Screening


title: SCN, mutant, 2hours, rep1


title: Pt8, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt8_PD_Week4_Tumor

value: Tumor


title: M030192_3 Peripheral Choroid


title: 19577X55 UU14 Washed Plts


title: 19577X54 UU13 Bead


title: 19577X60 C07 Washed Plts


title: Pt8, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt8_PD_Week4_Blood


title: SCN, control1, 22hours, rep3

value: 22 hours


title: Pt3, Stable Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt3_SD_Day15_Blood

value: CT-0508 CAR Macrophages


title: Pt8, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt8_PD_Day15_Blood


title: 19577X53 UU13 Washed Plts


title: M030192_3 Macula Choroid

source_name: Chorod

value: Macula Choroid


title: SCN, control1, 22hours, rep2


title: 19577X52 UU12 Bead

value: Blood


title: Pt8, Progressive Disease, Screening, Tumor, TCR-seq

description: Library name: Pt8_PD_Screening_Tumor


title: Pt8, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt8_PD_Day8_Tumor


title: 19577X51 UU12 Washed Plts

value: platelets


title: M030192_2 Peripheral Retina


title: SCN, control1, 22hours, rep1


title: M030192_2 Macula Retina

value: Macula Retina


title: SCN, control1, 18hours, rep4

value: 18 hours


title: Pt8, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt8_PD_Screening_Blood


title: Pt5, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt5_PD_Week4_Tumor


title: 19577X49 UU11 Washed Plts


title: M030192_1 Peripheral Choroid


title: M030192_1 Peripheral Retina


title: SCN, control1, 18hours, rep3

value: tamoxifen dosed


title: Pt5, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt5_PD_Week4_Blood


title: M030192_3 Macula Retina


title: M030192_1 Macula Retina


title: 19577X48 UU10 Bead


title: SCN, control1, 18hours, rep2


title: 19577X50 UU11 Bead


title: SCN, control1, 22hours, rep4


title: Pt5, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt5_PD_Day15_Blood


title: 19577X47 UU10 Washed Plts


title: M030192_1 Macula Choroid


title: SCN, control1, 14hours, rep4

value: 14 hours


title: SCN, control1, 18hours, rep1


title: 19577X46 PG04 C Bead


title: CPB+Nitrite4

city: Sapporo

first: Sho

last: Ohno

address: South1 West 16 291

department: Anesthesiology

country: Japan

institute: Sapporo Medical University

description: Library name: Sample12

data_processing:
Base calls were generated in real-time on the NovaSeq6000 instrument (RTA 3.4.4). Bcl2fastq v2.19 Conversion Software (Illumina) was used to generate demultiplexed Fastq files. Sequencing was performed on a NovaSeq6000 (Illumina) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol.
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Cutadapt v1.18. (parameters : -q 20 --pair-filter=any --minimum-length 75 --max-n 0)
Trimmed reads were quantified in mapping-based mode using Salmon v.1.2.1, based on the Rattus norvegicus reference transcripts (mRatBN7.2, release 110) available via Ensembl. (parameter : -l ISR)
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
A comparison of gene expression was performed using R v3.5.1. The version of the major R pacakge used Tag Count Comparison (TCC) v1.22.0.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include TCC normalized count values for all samples. (genes.AllEntity.txt)
Supplementary files format and content: tab-delimited text files include raw count values for all samples. (Allsample_NumReads.genes.txt)

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Total RNA was extracted from rat kidney tissues using QIAzol Lysis reagent (QIAGEN, Valencia, CA, USA) according to the manufacturer’s protocol. To remove genomic DNA contamination, DNase treatment was performed using the TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA), following the manufacturer's instructions.

value: Kidney

value: CPB+Nitrite


title: Pt5, Progressive Disease, Screening, Tumor, TCR-seq

description: Library name: Pt5_PD_Screening_Tumor


title: SCN, control1, 14hours, rep3


title: Pt5, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt5_PD_Screening_Blood


title: 19577X44 PG03 C Bead

value: Leukocyte-bead depletion Isolation


title: 19577X45 PG04 B Washed Plts

value: Washed Platelet Isolation


title: Pt5, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt5_PD_Day8_Tumor


title: 19577X43 PG03 B Washed Plts


title: CPB+Nitrite1

description: Library name: Sample9


title: SCN, control1, 14hours, rep1

value: suprachiasmatic nucleus


title: CPB+Nitrite2

description: Library name: Sample10


title: Pt1, Stable Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt1_SD_Week4_Tumor


title: SCN, control1, 10hours, rep4

value: 10 hours


title: CPB4

description: Library name: Sample8

value: CPB


title: Pt1, Stable Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt1_SD_Week4_Blood


title: CPB+Nitrite3

description: Library name: Sample11


title: SCN, control1, 10hours, rep3


title: SCN, control1, 14hours, rep2


title: Pt1, Stable Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt1_SD_Day15_Blood


title: 19577X41 UD04 Washed Plts


title: CPB2

description: Library name: Sample6


title: Pt1, Stable Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt1_SD_Day8_Tumor

value: Tumor


title: SCN, control1, 10hours, rep1


title: SCN, control1, 6hours, rep4

value: 6 hours


title: CPB1

description: Library name: Sample5


title: Pt1, Stable Disease, Screening, Tumor, TCR-seq

description: Library name: Pt1_SD_Screening_Tumor

value: Screening


title: 19577X39 UD03 Washed Plts


title: 19577X40 UD03 Bead


title: Pt1, Stable Disease, Screening, Blood, TCR-seq

description: Library name: Pt1_SD_Screening_Blood


title: sham4

description: Library name: Sample4

value: sham


title: 19577X42 UD04 Bead

value: Blood


title: SCN, control1, 6hours, rep3


title: sham3

description: Library name: Sample3


title: CPB3

description: Library name: Sample7


title: 19577X37 C05 Bead

value: platelets


title: Pt6, Progressive Disease, 4 Weeks post-infusion, Tumor, TCR-seq

description: Library name: Pt6_PD_Week4_Tumor

value: CT-0508 CAR Macrophages


title: SCN, control1, 6hours, rep2


title: SCN, control1, 10hours, rep2


title: 19577X36 C05 Washed Plts


title: Pt6, Progressive Disease, 15 Days post-infusion, Blood, TCR-seq

description: Library name: Pt6_PD_Day15_Blood


title: sham1

description: Library name: Sample1


title: SCN, control1, 6hours, rep1


title: sham2

description: Library name: Sample2


title: 19577X34 C04 Bead


title: Pt6, Progressive Disease, 8 Days post-infusion, Tumor, TCR-seq

description: Library name: Pt6_PD_Day8_Tumor


title: mesenchymal stromal cells, 1 month old, no treatment

city: tianjin

first: huizhen

last: wang

address: tingjiang westroad

institute: Tasly Pharmaceutical Group Co., Ltd.

description:
Library name: Sample 5
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting made using the Cell Ranger software v8.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Rat  mRatBN7.2
Assembly: Rattus norvegicus GCF_015227675.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: adipose

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
The freshly prepared single-cell suspension was adjusted to 700-1200 cells/μl according to the 10× Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (No. 1000268) Operation manual for computer and library construction.

treatment_protocol: mesenchymal stem cells (AD-MSCs) intravenous injection

value: adipose

value: 1 month old

value: male


title: SCN, control1, 2hours, rep3

value: 2 hours

value: tamoxifen dosed


title: 19577X33 C04 Washed Plts


title: mesenchymal stromal cells, 12 months old, no treatment

description:
Library name: Sample 6
10x Genomics

value: 12 months old


title: Pt6, Progressive Disease, Screening, Blood, TCR-seq

description: Library name: Pt6_PD_Screening_Blood


title: Pt6, Progressive Disease, Screening, Tumor, TCR-seq

description: Library name: Pt6_PD_Screening_Tumor


title: SCN, control1, 2hours, rep4


title: SCN, control1, 2hours, rep2


title: SCN, control1, 2hours, rep1


title: Pt6, Progressive Disease, 4 Weeks post-infusion, Blood, TCR-seq

description: Library name: Pt6_PD_Week4_Blood


title: subj6, Lesional skin2, Day29, PLACEBO

city: San Antonio

first: Mark

last: Lee

state: TX

address: 1973 NW Loop 410 Suite 106

institute: Progressive Clinical Research

description: Library name: subj6_D29_skin_2

data_processing:
Raw read counts/TPM/FPKM generated using omicsoft software v 11.4.0.3
Assembly: hg38.refGene.gtf
Supplementary files format and content: raw read counts (xlsx file)

source_name: skin

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (QIAgen, cat # 74704)
Illumina RNA prep With Enrichment , (L) Tagmentation (Illumina Cat # 20040537) + IDT® for Illumina® DNA/RNA UD Indexes, Tagmentation (Illumina cat# 20027213) + Panel KAPA HyperExome (Roche cat# 09062572001)

treatment_protocol: Skin biopsies stored in 5

value: skin


title: 19577X31 C03 Washed Plts

value: Washed Platelet Isolation


title: the right striatum of  brain, ICH model, 1 month old mesenchymal stromal cells intravenous infusion

description:
Library name: Sample 3
10x Genomics

source_name: brain

value: brain

value: 8-10 weeks old


title: subj6, Lesional skin1, Day29, SAR444727

description: Library name: subj6_D29_skin_1


title: the right striatum of  brain, ICH model, 12 months old mesenchymal stromal cells intravenous infusion

description:
Library name: Sample 4
10x Genomics


title: 19577X35 C04 Filter

value: PALL-Filtration Isolation


title: cDCsFL-Notch IgG cut&tag

city: Guangzhou

first: Ling

last: Wang

address: zhongshan road No.74

institute: Sun Yat-sen University

library_source: genomic

data_processing:
*library strategy: CUT&Tag
The raw FASTQ data were first processed through fastp version 0.23.2 with options: -q 20 -u 50 -n 15 -l 50 and all the downstream analyses were based on high-quality clean data. An index of the reference genome was built and paired-end clean reads were aligned to the reference genome (mm10) using Bowtie2 version 2.2.5 with default parameters. For peak calling, parameters used were macs2 callpeak--shift 0 --extsize 200 --nomodel -B --SPMR -g mm -p 0.05.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: BM

extract_protocol:
cDCsFL-Notch were cultured for 6 days and stimulated with 100 nM TLR stimulation. Live B220- MHCII+ CD11c+ cells were FACS-sorted after 18 hours of TLR stimulation.
For CUT&Tag library preparation, CUT&Tag assay was performed following the manufacturer’s instructions (Vazyme, #TD903).

value: BM

value: cDCsFL-Notch

tag: strain background

value: WT

value: TLR stimulation


title: the right striatum of  brain, ICH model, no treatment

description:
Library name: Sample 2
10x Genomics


title: cDCsFL-Notch CKO cut&tag

value: CKO


title: 19577X29 UU09 Washed Plts

value: Blood

value: platelets


title: the right striatum of  brain, normal tissue, no treatment

description:
Library name: Sample 1
10x Genomics


title: 19577X38 C05 Filter


title: subj6, Lesional skin2, Day15, PLACEBO

description: Library name: subj6_D15_skin_2


title: 19577X28 UU08 Bead

value: Leukocyte-bead depletion Isolation


title: 19577X32 C03 Bead


title: cDCsFL-Notch WT cut&tag


title: subj6, Lesional skin1, Day15, SAR444727

description: Library name: subj6_D15_skin_1


title: 19577X30 UU09 Bead


title: PLF-TLR stimulation

data_processing:
Cellranger (10x Genomics, v6.1.2) was used for demultiplexing and generation of barcodes and count matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneal cavity

extract_protocol:
Mice were immunized intraperitoneally (i.p.)  with or without 10 µgTLR stimulation in 100 µL PBS, peritoneal cavity cells were obtained by peritoneal cavity lavage twice with 5 mL of ice-cold PBS. They were collected 6 hrs after injection for cDCs (live MHCII+ CD11c+) FACS-sorting for scRNA-seq library preparation.
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: peritoneal cavity

value: DCs

value: wt


title: control, low glucose treatment 3

city: Shanghai

first: Yingying

state: Shanghai

address: No.639 Zhizaoju Road

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Firstly, Q30 was used to perform quality control
The adaptor sequences were trimmed and the adaptor-trimmed-reads(>=15nt) were left by cutadapt software(v1.9.3).
trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs
The trimmed reads were aligned to the merged Rat pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs)using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Assembly: miRBase v22
Supplementary files format and content: TagCounts

source_name: nerve

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nerve

value: low glucose


title: subj6, Non-lesional skin, Day1, None

description: Library name: subj6_D1_Normskin_OL

value: skin


title: 19577X27 UU08 Washed Plts

value: Washed Platelet Isolation


title: control, low glucose treatment 1


title: PLF-PBS

value: PBS


title: subj6, Lesional skin2, Day1, PLACEBO

description: Library name: subj6_D1_skin_2


title: 19577X26 UU07 Bead


title: subj6, Lesional skin1, Day1, SAR444727

description: Library name: subj6_D1_skin_1


title: 19577X25 UU07 Washed Plts


title: High glucose treatment 3

value: High glucose


title: High glucose treatment 1


title: subj5, Lesional skin2, Day29, SAR444727

description: Library name: subj5_D29_skin_2


title: High glucose treatment 2


title: SPL-TLR stimulation

source_name: Spleen

extract_protocol:
Mice were immunized intraperitoneally (i.p.) with or without 60 µg TLR stimulation in 100 µL PBS. Splenic cells were collected 18 hrs after  injection for cDCs (live MHCII+ CD11c+) FACS-sorting for scRNA-seq library preparation.
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: Spleen


title: 19577X22 PG02 C Bead


title: subj5, Lesional skin2, Day15, SAR444727

description: Library name: subj5_D15_skin_2


title: pLN-PBS

source_name: lymph nodes

extract_protocol:
Mice were immunized subcutaneously (s.c.) in the rear footpads with or without 10 µg TLR stimulation in 40 µL PBS. Popliteal lymph node cells were collected 48 hrs after TLR stimulation  for cDCs (live MHCII+ CD11c+) FACS-sorting for scRNA-seq library preparation.
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: lymph nodes


title: pLN-TLR stimulation


title: Spl-PBS


title: Fractured-NICD-CD45p

city: Farmington

first: Sanja

last: Novak

state: CT

address: 263 Farmington Ave

institute: UConn Health

data_processing:
3.1.0 Cell Ranger
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Bone

extract_protocol: Chromium Single Cell 3' Reagent Kits v3.1

value: Bone

value: Peroiosteal cells


title: Intact-NICD-CD45p


title: subj5, Lesional skin2, Day1, SAR444727

description: Library name: subj5_D1_skin_2


title: Fractured-Control-CD45p


title: 19577X19 PG01 B Washed Plts

source_name: Blood


title: subj5, Lesional skin1, Day1, PLACEBO

description: Library name: subj5_D1_skin_1


title: Fib_IPAH_rep4

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: IPAH patient

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: hPASMCs s were thawed at passage 1 and cultured with full SMC Medium (lifeScience) with 5% FCS and 0.1% Antibiotic/antimicotic. Cells were harvested at 70-80% confulency.hPFs s were thawed at passage 1 and cultured with full DMEM F12 Medium (GIBCO) with 10% FCS and 0.1% Antibiotic/antimicotic. Cells were harvested at 70-80% confulency.

extract_protocol: QIAgen RNeasy Mini Kit

value: lung

value: adventitial fibroblasts


title: PASMC_donor_rep4

source_name: donor lung

value: pulmonary arterial smooth muscle cells


title: subj5, Non-lesional skin, Day1, None

description: Library name: subj5_D1_Normskin_OL


title: subj4, Lesional skin2, Day29, SAR444727

description: Library name: subj4_D29_skin_2


title: Intact-Control-CD45p


title: 19577X21 PG02 B Washed Plts

value: Blood

value: platelets


title: 19577X18 UD02 Bead

value: Leukocyte-bead depletion Isolation


title: 19577X24 UU06 Bead


title: subj5, Lesional skin1, Day29, PLACEBO

description: Library name: subj5_D29_skin_1


title: 19577X23 UU06 Washed Plts


title: Fractured-NICD-CD45n


title: subj4, Lesional skin1, Day29, PLACEBO

description: Library name: subj4_D29_skin_1


title: Fractured-Control-CD45n


title: Intact-NICD-CD45n


title: 19577X17 UD02 Washed Plts


title: 19577X16 UD01 Bead


title: 19577X20 PG01 C Bead


title: Intact-Control-CD45n


title: control, low glucose treatment 2


title: Fib_donor_rep4


title: subj4, Lesional skin2, Day15, SAR444727

description: Library name: subj4_D15_skin_2


title: 19577X14 C02 Bead


title: subj4, Non-lesional skin, Day1, None

description: Library name: subj4_D1_Normskin_OL


title: subj4, Lesional skin1, Day15, PLACEBO

description: Library name: subj4_D15_skin_1


title: R1/E cells shTrim28, mRNA, rep4

first: Mangmang

state: Baiyun District

address: 1023 Shatai South Road

institute: Southern Medical University

data_processing:
fastp -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} --adapter_fasta {adapter} --trim_poly_g -5 -3 -W 4 -M 20 -q 20 -u 40 -n 10 -l 20 -w {threads} -j {output.json} -h {output.html} --detect_adapter_for_pe -c 1>{log.std} 2>{log.err}
STAR --runMode alignReads --runThreadN {threads} --genomeDir {reference} --readFilesIn {input.r1} {input.r2} --readFilesCommand zcat --sjdbGTFfile {input.gtf} --outFileNamePrefix {params.prefix} --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 1>{log.std} 2>{log.err}
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: R1/E cells

extract_protocol:
Total RNA was isolated from samples using TRIzol ® Reagent (Thermo Fisher, 15596018) followed by isopropanol precipitation protocol.
Libraries were sequenced on NoveSeq 6000 (100bp PE).

value: R1/E cells


title: 19577X12 C01 Bead


title: R1/E cells shTrim28, mRNA, rep2


title: subj4, Lesional skin1, Day1, PLACEBO

description: Library name: subj4_D1_skin_1


title: 19577X13 C02 Washed Plts


title: R1/E cells shTrim28, mRNA, rep3


title: subj3, Lesional skin1, Day29, SAR444727

description: Library name: subj3_D29_skin_1


title: 19577X10 UU05 Bead


title: subj4, Lesional skin2, Day1, SAR444727

description: Library name: subj4_D1_skin_2


title: subj3, Lesional skin2, Day29, PLACEBO

description: Library name: subj3_D29_skin_2


title: R1/E cells shTrim28, mRNA, rep1


title: 19577X11 C01 Washed Plts


title: R1/E cells shControl, mRNA, rep2

value: WT


title: PASMC_IPAH_rep3


title: Fib_IPAH_rep3


title: Fib_donor_rep3


title: PASMC_IPAH_rep4


title: PASMC_IPAH_rep2


title: subj3, Lesional skin2, Day15, PLACEBO

description: Library name: subj3_D15_skin_2


title: R1/E cells shControl, mRNA, rep1


title: PASMC_IPAH_rep1


title: 19577X9 UU05 Washed Plts


title: subj3, Lesional skin1, Day15, SAR444727

description: Library name: subj3_D15_skin_1


title: subj3, Non-lesional skin, Day1, None

description: Library name: subj3_D1_Normskin_OL


title: 19577X8 UU04 Bead


title: 19577X6 UU03 Bead


title: Fib_IPAH_rep2


title: R1/E cells siTop2a, mRNA, rep2


title: R1/E cells siTop2a, mRNA, rep3


title: Human Retinoblastoma Tumor Replicate 2 - Sample_83268

city: St. Louis

first: Brian

middle: Stewart

last: Clark

state: Missouri

address: 660 S Euclid Ave; Campus Box #8096

department: Ophthalmology and Visual Sciences

institute: Washington University

description: Library name: Retinoblastoma Tumor Replicate 2

data_processing:
Quality control of raw sequencing reads was performed using FastQC (v0.11.9), with summaries generated by MultiQC (v1.19). Adapter trimming and removal of low-quality bases were conducted using Trim Galore (v0.6.7). Trimmed reads were aligned to the GRCh38 reference genome, using STAR (v2.7.0f) with default parameters optimized for paired-end data, followed by post-alignment processing, including sorting and indexing of BAM files, using Samtools (v1.9). Gene-level quantification was performed using HTSeq (v0.11.2), and genome-wide read coverage was visualized using deepTools (v3.5). Differential expression analysis was conducted in edgeR (v4.2.2) within R (v4.4.1), employing TMM normalization and statistical modeling, with significance thresholds set at |log2FC| ≥ 1 and FDR < 0.01.
Human-mouse and mouse-human orthologs were identified by mapping Ensembl gene IDs between species using biomaRt (2.60.1)
Assembly: GRCh38
Supplementary files format and content: Human_Normal_Tumor_RNAseq.csv

source_name: Retina Tumor

extract_protocol:
For each specimen, 3–7 10μm formalin-fixed, paraffin-embedded sections were cut from a single representative block per case, using macrodissection with a scalpel as needed, to enrich tumor content. RNA was isolated using the Qiagen Allprep formalin-fixed, paraffin-embedded DNA/RNA kit (Qiagen, Valencia, CA) and quantified as previously described (PMID: 27102345).
Library preparation and sequencing was performed using TruSeq® RNA Access Library Preparation Kit (Illumina) and Illumina HiSeq 4000 Libraries platform at University of Michigan Sequencing Core. Qiagen Allprep formalin-fixed, paraffin-embedded DNA/RNA kit (Qiagen, Valencia, CA)

treatment_protocol: FFPE tissue from RB specimens and normal retina (control)

value: Retina Tumor

value: Tumor

value: FFPE


title: Human Retinoblastoma Tumor Replicate 3 - Sample_83269

description: Library name: Retinoblastoma Tumor Replicate 3


title: subj3, Lesional skin1, Day1, SAR444727

description: Library name: subj3_D1_skin_1

value: skin


title: subj3, Lesional skin2, Day1, PLACEBO

description: Library name: subj3_D1_skin_2


title: R1/E cells siTop2a, mRNA, rep1


title: 19577X15 UD01 Washed Plts

extract_protocol:
RNA from with Washed Platelets or Leukocyte-depletion using CD45 beads, or PALL-filtered platelets, were isolated using the standard TRIzol® protocol (ThermoFisher #15596018) with the addition of 20 µg glycogen (Sigma #10901393001) at the isopropanol precipitation step.  Following a 75% ethanol wash, RNA pellets were allowed to air dry. RNA pellets were next suspended in nuclease-free water. Any potential contaminating DNA was digested 25 minutes at 37°C using Turbo DNA Free Kit (ThermoFisher AM1907) and the final RNA was cleaned and eluted in 26 µl nuclease-free water using Zymo RNA Clean & Concentrate kit (Zymo R1017) following the product instructions.
Intact poly(A) RNA was purified from total RNA samples (150 ng) with oligo(dT) magnetic beads. RNA concentration was evaluated using a Nanodrop (ThermoFisher Scientific; Illkirch, France). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102) with PolyA Selection. The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 5 nM and equal volumes were pooled in preparation for sequencing. RNA was sequenced by an Illumina NovaSeq sequencer using the NovaSeq 6000 using v1.5 reagents and S4 flow cell to produceKit 1 150x150 bp (paired end reads).

value: Washed Platelet Isolation


title: PASMC_donor_rep3


title: 19577X4 UU02 Bead


title: subj2, Lesional skin2, Day29, SAR444727

description: Library name: subj2_D29_skin_2


title: subj2, Lesional skin1, Day29, PLACEBO

description: Library name: subj2_D29_skin_1


title: 19577X3 UU02 Washed Plts


title: R1/E cells siControl, mRNA, rep2


title: R1/E cells siTop2a, mRNA, rep4


title: Fib_IPAH_rep1


title: PASMC_donor_rep2


title: R1/E cells siControl, mRNA, rep1


title: subj2, Lesional skin2, Day15, SAR444727

description: Library name: subj2_D15_skin_2


title: Human Retinoblastoma Tumor Replicate 1 - Sample_83267

description: Library name: Retinoblastoma Tumor Replicate 1


title: Fib_donor_rep1


title: PASMC_donor_rep1


title: subj2, Lesional skin1, Day15, PLACEBO

description: Library name: subj2_D15_skin_1


title: 19577X2 UU01 Bead


title: Human Normal Retina RNA-seq Replicate 1 - Sample_83265

description: Library name: Normal Retina Replicate 1

source_name: Retina

value: Retina

value: Control


title: R1/E cells shTrim28, ATAC, rep3

data_processing:
bwa mem -o {output} -t {threads} {params.reference} {input.r1} {input.r2} 1>{log.std} 2>{log.err}
samtools view -@ {threads} -bS -o {output} {input} 1>{log.std} 2>{log.err}
samtools sort -@ {threads} -o {output} {input} 1>{log.std} 2>{log.err}
samtools index -@ {threads} {input} 1>{log.std} 2>{log.err}
samtools view -F 1804 -f 2 -q 30 -bS -@ {threads} -o {output} {input} 1>{log.std} 2>{log.err}
bedtools intersect -v -a {input.bam} -b {input.blackList} 1>{output} 2>{log.err}
samtools index -@ {threads} {input} 1>{log.std} 2>{log.err}
bamCoverage --bam {input.bam} --outFileName {output} --outFileFormat bigwig --binSize 10 --numberOfProcessors {threads} 1>{log.std} 2>{log.err}
bigWig files were normalized using S3V2_IDEAS packages with binsize=50
Assembly: mm10
Supplementary files format and content: bigWig files normalized using S3V2_IDEAS packages with binsize=50

extract_protocol:
A total of fifty thousand viable cells were lysis on ice and incubated with Transposase for 30min at 37°C.
Libraries were prepared by Nextera DNA Sample Preparation Kit (Illumina, FC-121-1030).


title: Fib_donor_rep2


title: SKOV3, RSF1delUAB overexpression, 3

city: RICHMOND

first: Hengbin

state: VA

address: 401 college st

institute: Virginia Commonwealth University

data_processing:
Raw FASTQ sequences were quality-controlled using FastQC. Samples were aligned to the GRCh38/hg38 human primary assembly genome (version release 108) using STAR aligner (version 2.7.9a.). The SourceForge Subread package was used to generate raw counts, with reads counted over exons using the ENSEMBL gtf file for Homo sapiens, GRCm38 assembly (version release 108)
Assembly: GRCh38/hg38
Supplementary files format and content: Combined raw count

source_name: Cell line

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen™, #15596018) and purified with the Direct-zol™ RNA Microprep kit (Zymo, #R1051).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: OVCAR3 treated with 2000 ng/ml doxycycline for 6days before harvest

value: Cell line

value: ovarian cancer cell

value: RSF1delUAB overexpression


title: Human Normal Retina RNA-seq Replicate 2 - Sample_83266

description: Library name: Normal Retina Replicate 2


title: SKOV3, RSF1delUAB overexpression, 2


title: PBMC-TLR stimulation

data_processing:
Cellranger (10x Genomics, v6.1.2) was used for demultiplexing and generation of barcodes and count matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by using Ficoll (Solarbio, #P8900) gradient centrifugation. PBMC DCs were sorted as Lin- (CD3/CD19/CD14/) CD123- CD11C+ HLA-DR+ from freshly isolated PBMCs (purity>93%).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: PBMC

value: DCs

value: TLR stimulation


title: subj2, Non-lesional skin, Day1, None

description: Library name: subj2_D1_Normskin_OL


title: R1/E cells shTrim28, ATAC, rep1


title: Control3

city: shanghai

first: liu

last: huan

address: shanghaisongjiang

institute: cloudseq

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC hg19) by STAR software.
Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: hg19
Supplementary files format and content: excel of  peak calling

source_name: nucleus pulposus

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A MeRIP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in a NovaSeq platform (Illumina).

value: nucleus pulposus


title: subj2, Lesional skin2, Day1, SAR444727

description: Library name: subj2_D1_skin_2

source_name: skin


title: R1/E cells shTrim28, ATAC, rep2


title: SKOV3, RSF1delUAB overexpression, 1


title: SKOV3, RSF1 overexpression, 3

value: RSF1 overexpression


title: subj2, Lesional skin1, Day1, PLACEBO

description: Library name: subj2_D1_skin_1


title: SKOV3, RSF1 overexpression, 2


title: Control2


title: Control1


title: subj1, Lesional skin2, Day15, PLACEBO

description: Library name: subj1_D15_skin_2


title: R1/E cells shControl, ATAC

value: R1/E cells


title: R1/E cells siTop2a, ATAC, rep2


title: subj1, Lesional skin1, Day15, SAR444727

description: Library name: subj1_D15_skin_1


title: SKOV3, RSF1 overexpression, 1


title: IDD3


title: subj1, Non-lesional skin, Day1, None

description: Library name: subj1_D1_Normskin_OL


title: IDD2


title: SKOV3, control, 3

value: control vector


title: R1/E cells siTop2a, ATAC, rep1


title: subj1, Lesional skin2, Day1, PLACEBO

description: Library name: subj1_D1_skin_2


title: IDD1


title: PHx48hETO_4

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from mouse livers using TRIzol (Vazyme, Nnajing, China) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: liver

tag: strain

value: Wild-type

value: 70% hepatectomy with etomoxir

tag: time (hours_post_resection)


title: R1/E cells siControl, ATAC

value: WT


title: R1/E cells siTop2a, ATAC, rep3


title: SKOV3, control, 1


title: Input Control3


title: subj1, Lesional skin1, Day1, SAR444727

description: Library name: subj1_D1_skin_1

value: skin


title: PHx48hETO_2


title: PHx48hETO_3


title: Unsorted from native capsule 2

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

state: CA

address: 257 Campus Drive

department: Surgery

institute: Stanford University

description: 10x Genomics

data_processing:
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell. Case calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against the GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Hashtag oligos (HTOs) for human samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a “negative” HTO distribution is calculated. For each HTO, the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Sample tubes contained cells from either bowel or mesentery with a similar disease state. Cells for which ambiguous HTO identity could not be clearly established were preserved and assigned to the hashtag for which it was most highly expressed.
Assembly: GCRh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Breast Capsule

extract_protocol:
Capsule tissue specimens from human specimens were minced on ice. The tissue was then digested for 60 min in a 37 °C water bath agitator in 2 mg/mL collagenase type IV (ThermoFisher Scientific™, Waltham, MA) digestion buffer in Medium 199 (HyClone, South Logan, UT) consisting of 5% fetal bovine serum (ThermoFisher Scientific™, Waltham, MA), DNase I (Fisher Scientific, Hampton, NH), Poloxamer 188 (Cat. P5556-100ML, Sigma-Aldrich, St. Louis, MO), HEPES, and CaCl2. The digest was quenched with FACS buffer (ThermoFisher Scientific™, Waltham, MA) containing 2X FBS, 1X Penicillin-Streptomycin, 1X Poloxamer 188), then centrifuged at 1250rpm for 5 min at 4 °C, resuspended in FACS buffer, and filtered through 100, 70, and 40 μm cell strainers (Falcon cell strainer, ThermoFisher Scientific™, Waltham, MA). Histopaque was performed using Histopaque-1119 (Sigma-Aldrich, St. Louis, MO), per the manufacturer’s protocol. For samples that were sorted, cells were counted and resuspended in FACS buffer. Primary antibodies were applied, and cells were stained in the dark with gentle agitation for 30 min. Cells were then washed thoroughly in FACS buffer. A BD II FACS Aria machine was used for FACS sorting analysis. For lineage negative (Lin-) FACS analysis, the following primary antibodies were used: Tie2, CD45, CD31, CD324, CD326, Ter119. For ADM_1, hashed unsorted samples with hashes #8, and 9 correspond to the same biological replicates as sorted samples with hashes #5 and 7, respectively. For Cap_1, hashed unsorted samples with hashes #8 and 9 correspond to the same biological replicates as sorted samples with hashes #5 and 7, respectively.
Performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines.

value: Breast Capsule

value: all cells (hashed)

tag: disease state

value: human breast capsule

tag: library type

value: HTO

tag: hto

value: TotalSeq-B-0252 HumanHashTag2--LNH-94_2M2-TSB; TotalSeq-B-0253 HumanHashTag3--LNH-94_2M2-TSB; TotalSeq-B-0254 HumanHashTag4--LNH-94_2M2-TSB; TotalSeq-B-0255 HumanHashTag5--LNH-94_2M2-TSB; TotalSeq-B-0256 HumanHashTag6--LNH-94_2M2-TSB


title: Input Control2


title: Global-bsa-noBSA

city: Vancouver

first: Marina

last: Bockaj

address: 2222 Health Sciences Mall

country: Canada

institute: University of British Columbia

description: 10X Genomics

data_processing:
cellranger-6.0.1
Assembly: hg38
Supplementary files format and content: counts (raw)

source_name: embryonic stem cells

extract_protocol:
organoids were dissociated with TRYPLE for 3 minutes, washed, pooled and tagged with hashing antibodies (TotalSeq™-B0251, B0252, B0253 anti-human Hashtag Antibodies, BioLegend)
10X Chromium Single Cell 3' v3.1 and cell hashing

value: embryonic stem cells

value: human embryonic stem cells


title: Unsorted from ADM-adjacent capsule 2

description: 10x Genomics


title: Unsorted Cells and Lin- Sorted from native capsule 1

description: 10x Genomics

value: Fibroblasts (Lin-) (hashed) + all cells (hashed)

value: Fibroblasts:TotalSeq-B-0253 HumanHashTag3--LNH-94_2M2-TSB; TotalSeq-B-0254 HumanHashTag4--LNH-94_2M2-TSB; TotalSeq-B-0255 HumanHashTag5--LNH-94_2M2-TSB; TotalSeq-B-0256 HumanHashTag6--LNH-94_2M2-TSB; TotalSeq-B-0257 HumanHashTag7--LNH-94_2M2-TSB; All cells:TotalSeq-B-0258 HumanHashTag8--LNH-94_2M2-TSB; TotalSeq-B-0259 HumanHashTag9--LNH-94_2M2-TSB; TotalSeq-B-0260 HumanHashTag10--LNH-94_2M2-TSB


title: SKOV3, control, 2

value: Cell line

value: ovarian cancer cell


title: Input IDD3

value: nucleus pulposus


title: Input IDD2


title: PHx48h_7

value: liver

value: 70% hepatectomy


title: Unsorted Cells and Lin- Sorted from ADM-adjacent capsule 1

description: 10x Genomics


title: hRAB39B_5d_2

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

country: Switzerland

institute: ETH Zurich

data_processing:
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger RNA (version 3.0.2) count pipeline.
Assembly: custom Dm6 genome built (based on Dm6 (v6.03) with an artifical chromosome added containing the transgene)

organism: Drosophila melanogaster

source_name: Adult Brain

extract_protocol: 10x Genomics CHROMIUM Single Cell RNA Library 7 Gel Bead kit v2

value: Brain

tag: developmental stage

value: Adult


title: hRAB39B_5d_3


title: hRAB39B_5d_1


title: Input IDD1


title: HEK293T, R26C, Rep2

city: Pittsburgh

first: Benjamin

middle: Alexander

last: Nacev

address: 5117 Centre Avenue, Suite 2.6b

department: Medicine

institute: University of Pittsburgh

data_processing:
Read Alignment with Rsubread ( version 1.30.6)
Counts were summarized and bigwigs were exported with rtracklayer (version  1.40.6)
Assembly: BSgenome.Hsapiens.UCSC.hg19 (version 1.4.0 and TxDb.Mmusculus.UCSC.hg19.knownGene (version 3.4.0)
Supplementary files format and content: Bigwig; RPM

source_name: Human embryonic kidney

extract_protocol:
Cells were washed with ice cold PBS and then flash frozen with liquid nitrogen.  Total RNA was extracted from fresh frozen cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions

value: Human embryonic kidney

value: cell line


title: PHx48h_5

value: Wild-type


title: HEK293T, R26C, Rep3


title: hPINK_5d_2

value: hPINK


title: RNA-SeqofAML primary sample of patient 136

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

data_processing:
usegalaxy.eu
Initial Assessment with FastQC tool to control the quality of raw sequencing data.
Cutadapt tool was used for trimming adapter sequences, removing low-quality bases, and filtering out sequences of inadequate length.
Aligning sequencing reads to a reference genome is accomplished using STAR (Spliced Transcripts Alignment to a Reference) tool.
Quantifying gene expression levels is performed using the featureCounts tool, while the identification of differentially expressed features is carried out using the DESeq2 tool.
Assembly: manipulation of de Bruijn graphs, via the removal of errors and the simplification of repeated regions
Supplementary files format and content: A tabular file containing normalized abundance measurements generated by the DESeq2 tool

source_name: Peripheralblood

value: Peripheralblood

tag: diagnosis

value: AML

value: M

tag: age (year)


title: PHx48h_4

tag: tissue

tag: treatment


title: PHx48hETO_1

value: 70% hepatectomy with etomoxir


title: PHx48h_3


title: hPINK_5d_4


title: HEK293T, R17C, Rep3

tag: cell type


title: 19577X1 UU01 Washed Plts

city: Salt Lake City

first: Matthew

last: Rondina

institute: University of Utah

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 104 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
The output files were summarized using MultiQC to check for sample outliers and plot alignment statistics
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCh38
Supplementary files format and content: featureCount ouput files combined into a single tab-delimited raw count matrix

value: Blood

value: platelets

tag: isolation technique

value: Washed Platelet Isolation


title: hPINK_5d_3

tag: age

tag: genotype


title: PHx48h_6


title: RNA-SeqofAML primary sample of patient 137

tag: Sex

value: F


title: RNA-SeqofAML primary sample of patient 134


title: HEK293T, R26C, Rep1

tag: cell line


title: RNA-SeqofAML primary sample of patient 131


title: PHx48h_2


title: RNA-SeqofAML primary sample of patient 129


title: HEK293T, R17C, Rep1


title: hPINK_5d_1


title: PHx24hETO_4


title: RNA-SeqofAML primary sample of patient 128


title: HEK293T, R8C, Rep3


title: hLRRK_OPN_GCAMP_25d_1

extract_protocol: 10x Genomics CHROMIUM Single Cell RNA Library 7 Gel Bead kit v3


title: PHx24hETO_3


title: HEK293T, R17C, Rep2


title: PHx48h_1


title: HEK293T, R8C, Rep2


title: hLRRK_OPN_GAL4_25d_1


title: PHx24hETO_2


title: HEK293T, R8C, Rep1


title: RNA-SeqofAML primary sample of patient 125


title: PHx24hETO_1


title: RNA-SeqofAML primary sample of patient 123


title: RNA-SeqofAML primary sample of patient 127


title: hLRRK_OPN_EndoA_25d_4


title: PHx24h_7


title: HEK293T, R2C, Rep2


title: HEK293T, R2C, Rep3


title: PHx24h_6


title: RNA-SeqofAML primary sample of patient 119


title: RNA-SeqofAML primary sample of patient 116


title: hLRRK_OPN_GAL4_25d_2


title: HEK293T, R2C, Rep1


title: hLRRK_OPN_GCAMP_25d_2


title: HEK293T, WT, Rep3

value: H3.1 WT


title: PHx24h_5

value: liver


title: hLRRK_OPN_EndoA_25d_3


title: 19577X7 UU04 Washed Plts


title: RNA-SeqofAML primary sample of patient 115


title: hLRRK_OPN_EndoA_25d_2


title: PHx24h_4

value: 70% hepatectomy


title: hLRRK_OPN_EndoA_25d_1

value: Brain


title: LRRK_3__25d

value: Adult

value: LRRK


title: HEK293T, WT, Rep1

value: Human embryonic kidney

value: cell line


title: RNA-SeqofAML primary sample of patient 113


title: hRAB39B_5d_4


title: RNA-SeqofAML primary sample of patient 112


title: LRRK_1__5d


title: HEK293T, WT, Rep2


title: PHx24h_3

value: Wild-type


title: LRRK_2__25d


title: RNA-SeqofAML primary sample of patient 111

value: Peripheralblood


title: PHx24h_1


title: Unsorted Lin- Sorted from native mouse FBR capsule

description: 10x Genomics

data_processing:
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell. Case calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against the mm10 mouse reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Hashtag oligos (HTOs) for mouse samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a “negative” HTO distribution is calculated. For each HTO, the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Sample tubes contained cells from either bowel or mesentery with a similar disease state. Cells for which ambiguous HTO identity could not be clearly established were preserved and assigned to the hashtag for which it was most highly expressed.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: FBR Capsule

extract_protocol:
C57BL/6J mice underwent dorsal implantation with sterilized 0.2 mL PDMS implants.Mouse capsules were harvested at POD 28. Capsules were mechanically digested with sharp dissecting scissors (n = 6 per condition). Tissue was then added to an enzymatic digestion consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were added to an orbital shaker at 150 rpm for 90 minutes at 37ºC. FACS buffer was added to quench the digest and samples were filtered through 70 µm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C. For samples that were sorted, cells were counted and resuspended in FACS buffer. Primary antibodies were applied, and cells were stained in the dark with gentle agitation for 30 min. Cells were then washed thoroughly in FACS buffer. A BD II FACS Aria machine was used for FACS sorting analysis. For lineage negative (Lin-) FACS analysis, the following primary antibodies were used: Tie2, CD45, CD31, CD324, CD326, Ter119.
Performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines.

value: FBR Capsule

value: Fibroblasts (Lin-) (hashed); all cells (hashed)

tag: diseases state

value: mouse FBR capsule

value: HTO

value: Fibroblasts:TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11; TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; TotalSeq-B-0304 MouseHashTag4--M1-42_30-F11; All Cells:TotalSeq-B-0305 MouseHashTag5--M1-42_30-F11; TotalSeq-B-0306 MouseHashTag6--M1-42_30-F11; TotalSeq-B-0307 MouseHashTag7--M1-42_30-F11


title: RNA-SeqofAML primary sample of patient 110

value: AML


title: PHx24h_2

tag: strain


title: LRRK_3__5d


title: Unsorted and Lin- Sorted from ADM-adjacent mouse FBR capsule

description: 10x Genomics

value: Fibroblasts:TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11; TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; TotalSeq-B-0304 MouseHashTag4--M1-42_30-F11; All Cells:TotalSeq-B-0305 MouseHashTag5--M1-42_30-F11; TotalSeq-B-0306 MouseHashTag6--M1-42_30-F11


title: NWSN174

city: Marseille

first: Thibaud

last: Parpaite

address: 51 Bd Pierre Dramard

department: Neural basis of the Somatosensory System

country: France

institute: Aix-Marseille University

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_129

data_processing:
cDNAds libraries were sequenced on an Illumina HiSeq 4000 using single-end reads (50 pb) with an average depth of 4,7 million reads per cell. Image analysis and base calling were performed using RTA version 2.7.7. Demultiplexing was performed using bcl2fastq version 2.20.0.422 and quality control was performed using FastQC v0.11.5n.
Sequences were uniquely mapped to the mm10 genome using Subread (C version 1.4.6-p2) using default values.
Reads mapping to gene exons (GRCm38.90 gene assembly) were counted using featureCounts57 (C version 1.4.6-p2).
Read counts were analyzed in the R/Bioconductor environment (version 4.2.2; www.bioconductor.org). Genes with less than one read per cell on average were removed (n = 26,546 genes remaining) and the count data were normalized between samples by TMM (trimmed mean of the M-values) using the scran package in R Bioconductor (Lun et al., 2016). Quality control plots were performed using scran as described in Lun et al. (2016).
Relative abundance were obtained by sample normalization using TPM (transcripts per kilobase million).
Assembly: mm10
Supplementary files format and content: Text file containing tab-delimited matrices of Transcripts Per Million (TPM) transformed values.
Supplementary files format and content: Text file containing tab-delimited matrices of count data normalized by Trimmed Mean of the M-value (TMM).

source_name: sensory neuron

growth_protocol: All dorsal root ganglion (DRG) sensory neurons were carefully extracted and digested with 2mg/mL of collagenase type II, 5mg/mL of dispase and 5mM of CaCl2 in HBSS media (magnesium- and calcium- free) containing 5mM HEPES, 10mM D-Glucose and 1% penicillin/streptomycin, at pH 7.5 for 1h at 37°C. After removing the supernatant, DRGs were resuspended with Leibovitz-15 complete medium (L-15 supplemented with 5% FCS and 1% penicillin/streptomycin), and then mechanically dissociated with two glass Pasteur pipettes of decreasing diameter (1 and 0.5 mm). The resulting suspensions were subjected to a density gradient centrifugation through Percoll (onto 12.5 and 28% Percoll gradient in Leibovitz-15 complete medium) at a speed of 1300g (acc=6, break=3) for 20 minutes, to eliminate cell debris. Cells were washed with Leibovitz-15 complete medium and centrifuged at 900g (acc=7, break=8) for 5 minutes. Cells were then resuspended in Neurobasal complete medium (Neurobasal A medium supplemented with 2mM L-glutamine, 1% penicillin/streptomycin and B27 1X) containing the following factors: Nerve growth factor (NGF) at 50ng/mL, Glial cell-derived neurotrophic factor (GDNF) at 50ng/mL, Neurotrophin-3 (NT3) at 50ng/mL, Neurotrophin-4 (NT4) at 10ng/mL and Brain Derived Neurotrophic Factor (BDNF) at 5ng/mL. Cells were plated in a Poly-D-lysine- (50 µg/ml) Laminin- (10 µg/ml) coated ibidi Polymer Coverslip Bottom (ibidi μ−Dish 35 mm, high-81156) and incubated at 37°C for 24 hours.

extract_protocol:
After calcium imaging recording, the cytoplasmic content of the neuron was harvested using a glass pipette, transferred into a lysis solution (RNaseOUT 8 U.µl-1, 2% Triton X-100) and flash frozen. Reverse transcription was performed using a SMART-seq v4 Low Input Kit (Clontech) directly on the cell lysate according to the manufacturer’s protocol.
After cDNAds amplification, 50 μl of the sample were subjected to cDNA purification on AMPure XP beads. 0.5 ng of each purified cDNAds were used to construct the sequencing library using Nextera XT kit (Illumina) with fragments over 300-bp length from each neuron.

treatment_protocol: Primary neuronal cultures were stimulated with a focused ultrasound (FUS) transducer (Olympus V317-SM, central frequency of 20 MHz, active diameter of 6.32 mm, focal distance of 12.7 mm). The FUS transducer was tilted at an angle of approximately 20° relative to the axis perpendicular to the culture dish in order to reduce standing wave formation within the cavity formed by the transducer and the culture dish. In addition, an acoustic absorber (Aptflex F28, Precision Acoustics, UK) was attached to the transducer to avoid reflected waves at the water/air interface. The FUS stimulus consisted of a 20-MHz sinusoidal signal with peak positive pressure of 4 to 5 MPa and stimulus duration of 0.1 to 1 ms. Calcium responses were recorded before, during and after FUS stimulation. All experiments were performed at room temperature.

value: sensory neuron

value: female


title: LRRK_1__25d


title: Control_sham_4

value: liver

value: sham

tag: time (hours_post_resection)


title: RNA-SeqofAML primary sample of patient 102

value: M


title: LRRK_2__5d

value: Brain

value: Adult

value: LRRK


title: NWSN171

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_126


title: NWSN169

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_124


title: LRRK_4__5d


title: RNA-SeqofAML primary sample of patient 97

value: F


title: 19577X5 UU03 Washed Plts

source_name: Blood

value: Blood

value: platelets

value: Washed Platelet Isolation


title: NWSN166

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_121


title: LRRK_4__25d


title: RNA-SeqofAML primary sample of patient 50

value: Peripheralblood


title: dSynj_5d_3

value: dSynj


title: NWSN163

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_118


title: dSynj_5d_2


title: Control_sham_2

value: Wild-type


title: NWSN165

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_120


title: NWSN168

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_123


title: NWSN161

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_116


title: RNA-SeqofAML primary sample of patient 94

value: AML


title: RNA-seq_PHx12h_2

value: 70% hepatectomy


title: RNA-seq_PHx12h_3


title: Control_sham_5


title: RNA-SeqofAML primary sample of patient 104

value: MDS


title: RNA-SeqofAML primary sample of patient 47


title: RNA-SeqofAML primary sample of patient 49


title: RNA-SeqofAML primary sample of patient 48


title: RNA-seq_PHx12h_1


title: Control_sham_1


title: Input Control1

value: nucleus pulposus


title: dSynj_5d_4


title: RNA-seq_PHx6h_3

value: liver


title: Control_sham_3

value: sham


title: dSynj_5d_1


title: NWSN158

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_113

value: sensory neuron

value: female


title: RNA-SeqofAML primary sample of patient 46

value: M


title: dAux_5d_2

value: Brain

value: Adult

value: dAux


title: RNA-seq_PHx6h_2


title: RNA-SeqofAML primary sample of patient 44

value: F


title: NWSN157

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_112


title: RNA-seq_PHx6h_1


title: RNA-SeqofAML primary sample of patient 45


title: NWSN155

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_109


title: dAux_5d_3


title: RNA-SeqofAML primary sample of patient 42


title: RNA-SeqofAML primary sample of patient 41


title: NWSN150

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_100

value: male


title: W1118CS_5d_2


title: RNA-seq_Control_3


title: W1118CS_5d_1


title: RNA-seq_PHx3h_2


title: dAux_5d_1


title: RNA-SeqofAML primary sample of patient 43

value: Peripheralblood


title: RNA-SeqofAML primary sample of patient 40


title: NWSN145

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_095


title: RNA-seq_PHx3h_1


title: W1118CS_5d_4


title: RNA-seq_PHx3h_3


title: dAux_5d_4


title: W1118CS_5d_3


title: RNA-SeqofAML primary sample of patient 39


title: NWSN149

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_099


title: NWSN141

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_091


title: NWSN144

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_094


title: RNA-seq_Control_2


title: NWSN143

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_093


title: RNA-SeqofAML primary sample of patient 38


title: RNA-seq_Control_1


title: W1118CS_25d_1


title: NWSN138

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_088


title: PHx12h_2

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads. Then the clean reads were aligned to the GRCm39/mm39 using Bowtie2 and subsequently analyzed by the SEACR software based the ‘stringent’parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV. Peaks were then annotated using chipseeker software to obtain the genes and gene annotations about peaks.
Significant Motif of peaks were analyzed by MEME and DREME software and aligned to the motif database.
Different peaks between case (12h post-PHx) and control groups were analyzed using Diffbind software. Firstly, the overlapping and merging of peaks were processed and the reads counts of peaks was calculated. Then, the statistically significant differential binding sites were identified based on binding affinity with the threshold of p-value<0.05 and |log2(Fold)|>1.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include gene annotations for peak calls of each group
Library strategy: CUT&Tag

extract_protocol:
Harvesting mouse liver,excising desired size, and flash freezing on liquid nitrogen. Extracting nuclei from the tissue according to manufacturer's instruction.
CUT&Tag assay was performed using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (cat.no.TD901-TD902, Vazyme Biotech, China) according to manufacturer's instruction. Prepared concanavalin A-coated magnetic beads (ConA beads) were added to resuspended cells and incubated at room temperature to bound cells. Non-ionic detergent Digitonin was used to permeate cell membrane. Primary anti-H3K27ac antibody (ab177178, Abcam), secondary antibody and the Hyperactive pA-Tn5 Transposase were incubated with the cells that were bounded by ConA beads in order. Therefore, the Hyperactive pA-Tn5 Transposase can exactly cut off the DNA fragments that were bound with target protein. In addition, the cut DNA fragments can be ligated with P5 and P7 adaptors by Tn5 transposase and the libraries were amplified by PCR with the P5 and P7 primers. The purified PCR products were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Finally, these libraries were sequenced on the Illumina NovaSeq6000 platform and 150bp paired-end reads were generated for the following analysis.


title: W1118CS_25d_2


title: PHx12h_1


title: RNA-SeqofAML primary sample of patient 37


title: Control_1


title: RNA-SeqofAML primary sample of patient 36


title: Control_2


title: zebrafish sperm, biological repeat  5

city: WuHan

first: Yi-Xuan

last: Tu

state: HuBei

address: 1 Shizishan Rd

department: College of Life Science and Technology

institute: Huazhong agricultural university

data_processing:
Illumina Casava software used for basecalling.
FastQC was used to check the quality of the raw sequence fastq files. High-quality pruning was performed using fastp.
Paired end reads were mapped to the reference genome of NCBI (HZGC01) using HISAT2. And SAMtools is used to sort and index aligned BAM files.
Reads were counted using the featureCounts program in the Subread.
Assembly: HZGC01
Supplementary files format and content: counts

organism: Danio rerio

source_name: sperm

extract_protocol:
Sperm samples were collected from five zebrafish, three GSCT zebrafish and five wild-type grass carps. 0.5 μL sperm from each fish was diluted into 20 μL Hank’s buffer. For one sample, 1μL of diluted sperm was used to extract RNA and synthetize cDNA in one reaction using the single cell full length mRNA-amplification kit (N712, Vazyme) following manufacturer's protocols.
cDNA was used to prepare DNA library for sequencing using the DNA Library Prep Kit for Illumina (TD504, Vazyme) following manufacturer's protocols.

value: sperm

value: wildtype


title: TOX_iKO_P14_ArmRechallenge_RNA_S3

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
scRNA-seq and scATAC-seq sample demultiplexing, barcode processing, alignment, filtering, unique molecular identifier (UMI) counting and aggregating sequencing runs were performed using 10x Cell Ranger pipeline (6.0.0) and mm10 genome.
Downstream scRNA-seq amd scATAC-seq analysis was performed in R using Signac and Archr packages
Union peak list was generated using peaks called in ArchR and using macs2 with sample bam files.
Assembly: GRCm38/mm10
Supplementary files format and content: Filtered feature-barcode matrices containing only cellular barcodes corresponding to gene expression and chromatin accessibility

source_name: Sorted TOX iKO T exhausted cells from 11days post KO were transferred  to mice rechallenged with LCMV Armstrong infection  and  d8 post infection WT cells were recovered

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
scRNAseq and scATACseq coAssay:
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.

value: Spleen

value: Knockout

value: Tamoxifen


title: NWSN137

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_085


title: NWSN131

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_078


title: RNA-SeqofAML primary sample of patient 35

value: AML


title: RNA-SeqofAML primary sample of patient 32


title: zebrafish sperm, biological repeat  1


title: zebrafish sperm, biological repeat  4


title: RNA-SeqofAML primary sample of patient 33


title: NWSN127

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_072


title: zebrafish sperm, biological repeat  2


title: Naive_P14_ArmRechallenge_RNA_S4

source_name: Adoptively transferred Naive CD8 T cells


title: RNA-SeqofAML primary sample of patient 34


title: HEK293T, NS2A, rep3

city: Jiangsu suzhou

first: Jingfei

last: Zhu

state: CN

address: Chongwen Road 215123

institute: ISM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit following standard Illumina protocol

value: Human embryonic kidney

value: NS2A overexpression


title: TOX_WT_P14_ArmRechallenge_RNA_S2

source_name: Sorted TOX WT T exhausted  cells from 11days post KO were transferred  to mice rechallenged with LCMV Armstrong infection  and  d8 post infection WT cells were recovered

value: WildType


title: NWSN133

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_081

value: sensory neuron


title: zebrafish sperm, biological repeat  3


title: NWSN129

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_075


title: NWSN123

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_068


title: RNA-SeqofAML primary sample of patient 31

value: M


title: RNA-SeqofAML primary sample of patient 29


title: NWSN122

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_067


title: RNA-SeqofAML primary sample of patient 27


title: NWSN124

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_069


title: RNA-SeqofAML primary sample of patient 28


title: HEK293T, EV, rep2

value: EV overexpression


title: NWSN118

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_063


title: Naive_P14_run2_RNA_S1

source_name: Naive CD8 T cells used as control


title: HEK293T, NS2A, rep1


title: Naive_P14_ArmRechallenge_ATAC_S4

library_source: genomic single cell


title: HEK293T, EV, rep1


title: TOX_WT_P14_ArmRechallenge_ATAC_S2


title: TOX_iKO_P14_ArmRechallenge_ATAC_S3


title: NWSN115

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_059


title: NWSN116

description:
polyA RNA isolated from individual dorsal root ganglia (DRG) sensory neurons after focused ultrasound stimulation
S_060


title: H3K36me2 H2A.Z-DKO FGO rep2

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

description: Library name: Sample4

data_processing:
*library strategy: CATCH-seq, CUT&RUN
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10, dm6
Supplementary files format and content: bigwig

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). The antibodies used were mouse anti-H2A (1/100, MBL D210-3), rabbit anti-H2A.X (1/100, Abcam 11175), and rabbit anti-TH2A antibody (1/100) (Shinagawa et al. 2014). Protein A-MNase was provided by the Steven Henikoff Lab (Skene and Henikoff 2017). For CATCH-seq, 3 uL of rabbit anti-H2A.Z (Active motif 39113, 200 oocytes/library), 500 ng of mouse anti-H2A (MBL D210-3, 200 oocytes/library), 1 uL of rabbit anti-H2A.X (Abcam ab11175, 200 oocytes/library), 500 ng of rabbit anti-TH2A antibody (a gift from Shunsuke Ishii, 200 oocytes/library) (Shinagawa et al. 2014), 0.25 uL of rabbit anti-H3K4me3 (Active Motif 39159, 40 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 80 oocytes/library), or 1.0 µl of rabbit anti-H2AK119ub1 antibody (Cell Signaling Technology 8240, 500 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H2A.Z (Murphy et al. 2018), H2A (Inoue and Zhang 2014), H2A.X (Inoue and Zhang 2014), TH2A (Shinagawa et al. 2014), H3K4me3 (Kaya-Okur et al. 2020), H3K27me3 (Inoue et al. 2018), H2AK119ub1 (Mei et al. 2021)]. After immunoprecipitation at 4C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37C for 2 hrs followed by heat inactivation at 65C for 20 min and purified by 0.9x SPRIselect beads.

treatment_protocol: Growing oocytes (GO) were collected from ovaries of 10-11 day-old BDF1 females. They were incubated in α-MEM/5% FBS containing 100 µM 5, 6-Dichloro-1-β-D-Ribofuranosyl-1H-Benzimidazole (DRB, Cayman Chemical 53-85-0), 0.2% DMSO (the solvent of DRB), or 100 µg/mL α-amanitin (Fiji-film 010-22961). For each CATCH-seq library construction, 250-300 GOs were collected at 24 hrs culture under the inhibitors.

value: ovary

value: Full-grown oocyte

value: H2A.Z.1 and H2A.Z.2 double knockout


title: Naive_P14_run2_ATAC_S1


title: RNA-SeqofAML primary sample of patient 24

value: F


title: TOX_iKO_P14_RNA_S5

source_name: CD8 T cells from Inducibe cre for TOX KO mice 5 days post infection of LCMV chronic infection

extract_protocol:
Cells were loaded onto the Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells.
scRNAseq and scATACseq coAssay
The scRNAseq and scATACseq libraries were generated using 10x Genomics multiome coAssay according to the manufacturer’s protocol.


title: RNA-SeqofAML primary sample of patient 25

value: Peripheralblood


title: RNA-SeqofAML primary sample of patient 23


title: H3K36me2 H2A.Z-DKO FGO rep1

description: Library name: Sample3


title: HEK293T, EV, rep3


title: RNA-SeqofAML primary sample of patient 26