title: HK2, Dsh, RNA-seq, repeat3

data_processing:
For the data analysis, 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 groups was performed using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: featurecounts output files

extract_protocol:
Total RNA was extracted from corresponding cells using TRIzol (Invitrogen, 15596018).
sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA).
The sample integrity was assessed using Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies).

value: KDM5C and YY1 double knockdown


title: ACHN_Parental, YY1, ChIP

status: Public on Jun 28 2024

type: SRA

city: Wuhan

first: Jie

last: Xiong

address: 185, Donghu road

country: China

institute: Wuhan University

library_source: genomic

data_processing:
Basecalls were performed using fastq Novaseq output.
ChIP-seq reads were trimmed with fastp.
ChIP-seq reads were aligned to the hg38 and mm10 genome using Bowtie2 (v2.4.2).
Peaks were called uing MACS v2.2.7.1 (q-value takes default setting).
BigWig files were obtained by deepTools (v3.5.1).
Assembly: Heatmap and metaplot files were made by plotHeatmap and plotProfile of deepTools (v3.5.1).
Supplementary files format and content: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: ACHN

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed in 1% formaldehyde for 10min and then quenched with 0.125M glycine for 10min at room temperature with rotation. Cell pellet was lysed with cell lysis buffer (10mM Tris, pH8.0; 10mM NaCl; 0.2% NP-40; protease inhibitor) on ice for 10min and chromatin DNA was sonicated to 200-500bp average in size. Chromatin fragments lysates were immune-precipitated with primary antibodies at 4°C overnight and then conjugated with protein A/G Beads 4FF (Smart-lifesciences, SA032500). Bound fractions were washed and eluted from agarose beads. ChIP and input samples were de-crosslinked at 55°C overnight.
ChIP-seq libraries were prepared using the NEBNext ultra II DNA library prep kit for Illumina.

tag: cell line

value: ACHN

tag: cell type

value: ccRCC

tag: chip antibody


title: pre-metastatic liver, pancreatic cancer, patient #41 [41JA_IGO_06756_G_20]

city: New York

first: Linda

last: Bojmar

state: NY

address: 413 E 69th St, Belfer Research Bldg

department: Department of Pediatrics

country: USA

institute: Weill Cornell Medicine

description:
Y
41JA_Liver_IGO_06756_G_20

library_source: transcriptomic

data_processing:
The output data (FASTQ files) are mapped to the target genome using the STAR aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used).
After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: Normalized count matrix

molecule: total RNA

source_name: liver

extract_protocol:
total RNA from 5 mg of fresh-frozen liver tissue was extracted using the RNeasy Mini Kit (QIAGEN catalog # 74104)
Samples underwent ribosomal RNA depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202)

treatment_protocol: fresh liver tissue was snap frozen in liquid nitrogen and stored in -80C until RNA extraction

tag: tissue

value: liver

tag: tissue type

value: pre-metastatic liver

value: whole liver tissue

tag: genotype

tag: treatment


title: Liver from patient with benign pancreatic lesion, #39 [39WD_IGO_06756_G_18]

description:
W
39WD_Liver_IGO_06756_G_18


title: Corpse_Rxr_1

city: New York City

first: Katherine

last: Stewart

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

description:
Corpse_Rxr_1
corpse_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm39) using Burrows-Wheeler Aligner (BWA, v.0.7.18)
The output .sam files were name-sorted and duplicate reads were marked and removed using SAMtools (v.1.17)
Reads were filtered to less than 121 bp using SAMtools (v.1.3.1).
BAM files for each replicate were combined using Samtools.
Bigwig files were generated using Deeptools (v.3.1.2) with reads per kilobase of transcript per million mapped reads (RPKM) normalization
CNR peaks were called using SEACR (v.1.3) 91 from bedGraph files generated from RPKM-normalized Bigwig files (bigWigToBedGraph, UCSC Tools) using stringent setting and a numeric threshold of 0.01
Assembly: mm39 (UCSC release)
Supplementary files format and content: bedgraph files of peaks called from SEACR
Supplementary files format and content: bigwig files of processed data
Library strategy: CUT&RUN

organism: Mus musculus

source_name: cultured wild type hair follicle stem cells

extract_protocol:
Cells were isolated by 0.25% trypsin/EDTA, pelleted and washed with PBS. Cells were pelleted and were cross-linked. Cut-&-Run libraries were prepared on these cross-linked nuclei, according to Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6 (2017).
CNR sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1X ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen). All CNR libraries were sequenced on Illumina NextSeq using 40 bp paired-end reads.

value: Corpses


title: pre-metastatic liver, pancreatic cancer, patient #2 [2NS_re_IGO_06756_G_2]

description:
S
2NS_re_Liver_IGO_06756_G_2


title: HK2, Dsh, RNA-seq, repeat2

value: Human Kidney


title: pre-metastatic liver, pancreatic cancer, patient #1 [1RB_IGO_06756_G_1]

description:
R
1RB_Liver_IGO_06756_G_1


title: BEL_Rxr_1

description:
BEL_Rxr_1
BEL_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph

value: cultured wild type hair follicle stem cells

value: Corpses+BEL


title: Liver from patient with benign pancreatic lesion, #31 [31VK_IGO_06756_G_14]

description:
T
31VK_Liver_IGO_06756_G_14


title: pre-metastatic liver, pancreatic cancer, patient #44 [44LJ_IGO_06756_G_23]

description:
AB
44LJ_Liver_IGO_06756_G_23


title: HK2, shYY1, RNA-seq, repeat3

value: YY1 knockdown


title: HK2, Dsh, RNA-seq, repeat1


title: pre-metastatic liver, pancreatic cancer, patient #18 [18EB_IGO_06756_G_13]

description:
Q
18EB_Liver_IGO_06756_G_13


title: NK_Fibrin_4day_rep2

city: San Francisco

first: Zhaoqi

last: Yan

state: CA

address: 1650 Owen St

institute: Gladstone Institutes

data_processing:
Demultiplexed fastq files were aligned to the GRCm38 reference genome to obtain the count matrix using the nf-core RNA-seq pipeline (revision 3.6). The sequencing depth and gene length normalized gene expression counts from the Salmon aligner generated by nf-core RNA-sequencing pipeline were used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: Raw data was analyzed with EdgeR and the processed data is normalized count per million reads for each file

molecule: polyA RNA

source_name: NK Cell

extract_protocol:
NK Cells were sorted in 500ul of RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Gibco) and followed by QIAshredder centrifugation (Qiagen). Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions
Complementary DNA was generated using Illumina Stranded mRNA Ligation-Library Preparation. The quality of each library was determined using Agilent High Sensitivity DNA Kit on Agilent Bioanalyzer, followed by quantification with qPCR using a Roche KAPA Library Quantification Complete Kit (ABI Prism).

value: NK Cell

value: Wildtype

value: IL-15 + Fibrin


title: NK_Fibrin_4day_rep3


title: pre-metastatic liver, pancreatic cancer, patient #15 [15MS_IGO_06756_G_10]

description:
O
15MS_Liver_IGO_06756_G_10


title: Liver from patient with benign pancreatic lesion, #17 [17LD_IGO_06756_G_12]

description:
P
17LD_Liver_IGO_06756_G_12


title: pre-metastatic liver, pancreatic cancer, patient #11 [11DB_IGO_06756_G_7]

description:
L
11DB_Liver_IGO_06756_G_7


title: pre-metastatic liver, pancreatic cancer, patient #34 [34RB_IGO_06756_G_16]

description:
U
34RB_Liver_IGO_06756_G_16


title: NK_Fibrin_4day_rep1


title: HK2, shYY1, RNA-seq, repeat2


title: pre-metastatic liver, pancreatic cancer, patient #78 [78_IGO_06756_I_9]

description:
J
78_Liver_IGO_06756_I_9


title: pre-metastatic liver, pancreatic cancer, patient #14 [14JR_IGO_06756_G_9]

description:
N
14JR_Liver_IGO_06756_G_9


title: NK_Unstimulated_4day_rep3

value: IL-15 Only


title: pre-metastatic liver, pancreatic cancer, patient #10 [10FC_IGO_06756_G_6]

description:
K
10FC_Liver_IGO_06756_G_6


title: BEL_Rxr_2

description:
BEL_Rxr_2
BEL_RXR_pool_dedup_RPGCnorm10bin_sub120.bedgraph


title: HK2, shKDM5C, RNA-seq, repeat2

value: KDM5C knockdown


title: pre-metastatic liver, pancreatic cancer, patient #64 [64_IGO_06756_I_7]

description:
H
64_Liver_IGO_06756_I_7


title: HK2, shKDM5C, RNA-seq, repeat3


title: NK_Unstimulated_4day_rep2


title: pre-metastatic liver, pancreatic cancer, patient #58 [58_IGO_06756_I_6]

description:
G
58_Liver_IGO_06756_I_6


title: NK_Unstimulated_4day_rep1


title: HK2, shKDM5C, RNA-seq, repeat1


title: pre-metastatic liver, pancreatic cancer, patient #57 [57_IGO_06756_I_5]

description:
F
57_Liver_IGO_06756_I_5


title: pre-metastatic liver, pancreatic cancer, patient #53 [53_IGO_06756_I_3]

description:
D
53_Liver_IGO_06756_I_3


title: Liver from patient with benign pancreatic lesion, #55 [55_IGO_06756_I_4]

description:
E
55_Liver_IGO_06756_I_4


title: HK2, shNC, RNA-seq, repeat3

value: shNC


title: HK2, shNC, RNA-seq, repeat2


title: Liver from patient with benign pancreatic lesion, #86 [86_IGO_06756_I_10]

description:
C
86_Liver_IGO_06756_I_10


title: V3_S39_L001_R1_001

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

data_processing:
Sequence reads were assessed for quality, adaptor content, and duplication rates using FastQC version 0.11.9 (PMID: 24381581).
Raw reads were trimmed to remove adapters, then trimmed and filtered based on quality scores using trimmomatic version 0.40 (PMID: 24695404).
Sequences with lengths ≥16 nt were aligned against miRNA from miRBase (PMID: 30423142) and human GRCh38 reference genome with Bowtie (version 1.1.1) (PMID: 19261174). The alignment parameters used were: -m 3 -n 1 -f -a --best --strata. Differential gene expression was performed using DESeq2 version 1.36.0 (PMID: 25516281).
Read count extraction was performed using featureCounts from the subread package version 2.0.3 (PMID: 24227677).
Differential gene expression was performed using DESeq2 version 1.36.0 (PMID: 25516281).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: exacellular vesicle

growth_protocol: Exosomal RNA was prepared from the supernatant of mock- and VZV-infected HD10 neurons collected at 4 days post infection.

extract_protocol:
ExoQuick Exosome Isolation and RNA Purification Kit from System Biosciences
System Biosciences Exosomal RNA-Seq according to manufacturer's guidelines

value: HD10 neurons

value: VZV infected


title: Lung_Wildtype_UN_Rep4

source_name: Lung

extract_protocol:
Lung tissues were lysed in 350 ul of RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Gibco) by mechanical dissociation followed by QIAshredder centrifugation (Qiagen). Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions
Complementary DNA was generated using Illumina Stranded mRNA Ligation-Library Preparation. The quality of each library was determined using Agilent High Sensitivity DNA Kit on Agilent Bioanalyzer, followed by quantification with qPCR using a Roche KAPA Library Quantification Complete Kit (ABI Prism).

value: Lung

value: Uninfected


title: Lung_Wildtype_UN_Rep3


title: HK2, shYY1, RNA-seq, repeat1


title: HK2, shNC, RNA-seq, repeat1


title: V1_S37_L001_R1_001


title: ACHN, Dsh, RNA-seq, repeat3

value: ACHN

value: ccRCC

value: KDM5C and YY1 double knockdown


title: pre-metastatic liver, pancreatic cancer, patient #13 [13RB_IGO_06756_G_8]

description:
M
13RB_Liver_IGO_06756_G_8

value: liver

value: pre-metastatic liver

value: whole liver tissue


title: Lung_Wildtype_UN_Rep1


title: M3_S42_L001_R1_001

value: mock infected


title: Lung_Wildtype_UN_Rep2


title: pre-metastatic liver, pancreatic cancer, patient #67 [67_IGO_06756_I_8]

description:
I
67_Liver_IGO_06756_I_8


title: V2_S38_L001_R1_001


title: M2_S41_L001_R1_001


title: M1_S40_L001_R1_001


title: ACHN, Dsh, RNA-seq, repeat2


title: PB_96h_rp4

city: Guangzhou

first: Tian

last: Zhang

state: Guangdong

address: 190 Kaiyuan Avenue,Science Park

institute: GIBH

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: count

source_name: Hematopoietic Stem Cells from Peripheral blood after mobilization

extract_protocol:
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: Hematopoietic Stem Cells

value: Lin-CD34+CD38- cells sorted from Peripheral blood mononuclear cells and cultured in vitro for 96h


title: ACHN, Dsh, RNA-seq, repeat1


title: Lung_Wildtype_Cov2_Rep3

value: Wildtype

value: Cov2 Infected


title: PB_0h_rp4

value: Lin-CD34+CD38- cells sorted from Peripheral blood mononuclear cells


title: ACHN, shYY1, RNA-seq, repeat3

value: YY1 knockdown


title: TSC22D3/GFP+ Hematopoietic Stem Cell_rp3

description:
PB0527-96h-TSC22D3
kallisto.tpm.rebatch.xls

value: TSC22D3/GFP+ cells of Lin-CD34+CD38- HSPCs cultured in vitro for 96h


title: TSC22D3/GFP+ Hematopoietic Stem Cell_rp2

description:
PB-96h-TSC22D3
kallisto.tpm.rebatch.xls


title: ACHN, shYY1, RNA-seq, repeat2


title: Lung_Wildtype_Cov2_Rep2


title: pre-metastatic liver, pancreatic cancer, patient #49 [49_IGO_06756_I_1]

description:
B
49_Liver_IGO_06756_I_1


title: GFP+ Hematopoietic Stem Cell rp3

description:
PB0527-96h-GFP
kallisto.tpm.rebatch.xls

value: GFP+ cells of Lin-CD34+CD38- HSPCs cultured in vitro for 96h


title: ACHN, shYY1, RNA-seq, repeat1


title: GFP+ Hematopoietic Stem Cell rp2

description:
PB-96h-GFP
kallisto.tpm.rebatch.xls


title: GFP+ Hematopoietic Stem Cell rp1

description:
PB-96h-GFP1102
kallisto.tpm.rebatch.xls


title: ACHN, shKDM5C, RNA-seq, repeat3

value: KDM5C knockdown


title: Lung_Wildtype_Cov2_Rep4

value: Lung


title: Lung_FgaKO_UN_Rep2

value: Fga -/-

value: Uninfected


title: CFPAC-1_ADRA2A overexpression_3 [Yuuki_47]

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description: CFPAC-1 with ADRA2A transgene

data_processing:
mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 32 to 60 million pass filter reads with more than 93% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Pancreatic ductal adenocarcinoma cell line (CFPAC-1)

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

value: ADRA2A transgene

value: No treatment. The cells were cultured in IMDM medium, supplemented with 10% FBS and 1% penicillin–streptomycin for 72 hours.


title: Lung_FgaKO_UN_Rep3


title: ACHN, shKDM5C, RNA-seq, repeat2

value: ACHN

value: ccRCC


title: HPC_D10_rp2

description:
H1-P55-D10
20181208_ZHANGT.edaseq.count.tsv

source_name: Hematopoitic progenitor cells generated from human embryonic stem cell----H1

value: Hematopoitic progenitor cells

value: CD43+CD45+ cells sorted from hematopoietic differentiation day 10 of hESC-H1


title: CFPAC-1_ADRA2A overexpression_2 [Yuuki_46]

description: CFPAC-1 with ADRA2A transgene

growth_protocol: The cells were cultured in IMDM medium, supplemented with 10% FBS and 1% penicillin–streptomycin for 72 hours.

value: Pancreatic ductal adenocarcinoma cell line (CFPAC-1)


title: Lung_FgaKO_Cov2_Rep5


title: HPC_D10_rp3

description:
H1-P50-D10
20181208_ZHANGT.edaseq.count.tsv


title: HPC_D10_rp1

description:
H1-P57-D10
20181208_ZHANGT.edaseq.count.tsv


title: Lung_FgaKO_Cov2_Rep4


title: Lung_FgaKO_UN_Rep1


title: ACHN, shKDM5C, RNA-seq, repeat1


title: CFPAC-1_ADRA2A overexpression_1 [Yuuki_45]

description: CFPAC-1 with ADRA2A transgene


title: CFPAC-1_Ctrl_4 [Yuuki_44]

description: CFPAC-1 with empty vector control

value: empty vector


title: HPC_D6_rp3

description:
H1-P50-D6
20181208_ZHANGT.edaseq.count.tsv

value: CD31+CD43+ cells sorted from hematopoietic differentiation day 6 of hESC-H1


title: TSC22D3/GFP+ Hematopoietic Stem Cell_rp1

description:
PB-96h-TSC1102
kallisto.tpm.rebatch.xls

value: Hematopoietic Stem Cells


title: ACHN, shNC, RNA-seq, repeat3

value: shNC


title: Lung_FgaKO_Cov2_Rep3

value: Cov2 Infected


title: Lung_Wildtype_Cov2_Rep1

value: Wildtype


title: ACHN, shNC, RNA-seq, repeat1


title: HPC_D6_rp2

description:
H1-P55-D6
20181208_ZHANGT.edaseq.count.tsv


title: CFPAC-1_Ctrl_2 [Yuuki_42]

description: CFPAC-1 with empty vector control


title: CFPAC-1_ADRA2A overexpression_4 [Yuuki_48]

description: CFPAC-1 with ADRA2A transgene


title: HPC_D6_rp1

description:
H1-P57-D6
20181208_ZHANGT.edaseq.count.tsv


title: Lung_FgaKO_Cov2_Rep2


title: K562-U2AF1_S34F treated with SF1-8 at 30 uM, 48h, 2

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

data_processing:
Cutadapt was used to remove reads with adaptor contamination, low quality bases and undetermined bases. The sequence quality was verified using FastQC. Mapping reads to the human genome (v101) were performed using Bowtie2 and HISAT2. The mapped reads were then assembled using StringTie and normalized into Fragments per kilobase per million (FPKM).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files includes FPKM values for four Samples

source_name: Bone Marrow

growth_protocol: Cells were maintained in IMDM (Gibco, Hampton, NH, USA) with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was purified using RNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA concentration was quantified using nanodrop. RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). RNA Integrity of the samples was checked with Agilent Technologies 2100 Bioanalyzer (Agilent, Santa Clara, CA). Ribosomal RNA was removed and the rRNA depleted samples were prepared with fragmentation with divalent cation buffers in elevated temperature.
The sequencing library was prepared by following Illumina’s TruSeq-standard-total-RNA-sample preparation protocol.

treatment_protocol: Cells were treated with DMSO or SF1-8 at 30 uM for 48h.

value: Bone Marrow

value: erythroleukemia

value: U2AF1_S34F overexpression


title: CFPAC-1_Ctrl_1 [Yuuki_41]

description: CFPAC-1 with empty vector control


title: CB_96h_rp4

description:
CB-4-96H
20181208_ZHANGT.edaseq.count.tsv

source_name: Hematopoietic Stem Cells from umbilical cord blood

value: Lin-CD34+CD38- cells sorted from umbilical cord blood mononuclear cells and cultured in vitro for 96h


title: K562-U2AF1_S34F treated with SF1-8 at 30 uM, 48h, 1


title: MDF from WT-WT mice treated with Nutlin - Replicate  4

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 2000 to produce paired-end reads.
Reads were aligned to the mouse genome mm39 with R/Bioconductor Rsubread package and its align function.
Bam files from biological replicates were merged with samtools prior to creating BigWig files for each drug-genotype combination.
Assembly: mm39
Supplementary files format and content: BigWig files were created with the deepTools BamCoverage program with reads per genomic content (RPGC) normalization in 10 bp windows. Duplicated reads, reads from sex and mitochondrial chromosomes, and reads overlapping ENCODE blacklisted regions from the mm39 genome were discarded for normalization purposes
Supplementary files format and content: narrowPeak files (in BED format) are peak regions called by MACS2 for each genotype-drug combination. Biological replicates were combined by the MACS2 program during the peak calling step.

source_name: Mouse tail skin

extract_protocol:
500,000 MDFs were plated and left to settle for 24 h in an incubator with 10% CO2 at 37°C. Medium was replaced with medium containing nutlin-3a (10 μM, Cayman Chemicals #18585) or DMSO (vehicle control) and cells incubated for 6 h. Adherent cells were dissociated with trypsin (0.25 mg/mL, Sigma #T4174), keeping both the supernatant and the trypsinised fractions for analysis. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN kit v2 (Epicypher, 14-1408) as per the manufacture’s protocol. Nuceli were isolated prior to the start of the assay. Nuclei were bound to activated conA beads. Samples were incubated with 0.5 μg of anti-FLAG antibody (Sigma, F1804) overnight. DNA was cut using pAG-MNase, and unbound fragments washed away. Bound chromatin was release from the beads, and DNA was purified.
Total recovered DNA was taken into library preparation using the NEBNext Ultra II DNA library Prep Kit for Illumina (#E7645L).
CUT&RUN

value: Mouse tail skin

value: MDF

tag: antibody

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

tag: strain

tag: developmental stage

value: adult (8-12 weeks of age)

tag: mouse pool

value: C

tag: Sex

value: male

tag: sequencing run

value: 11-Oct-2022; Read Length:61 bp; Cycle Kit:P2 100


title: CB_96h_rp3

description:
CB-3-96H
20181208_ZHANGT.edaseq.count.tsv


title: LDS, rep2

city: Baltimore

first: Tyler

middle: J

last: Creamer

state: Maryland

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

description: LDS

library_source: transcriptomic single cell

data_processing:
Cellranger software (V6 from 10x Genomics) was used to process, align (mm10), and aggregate (--normalize=none) the raw data
Assembly: mm10
Supplementary files format and content: There are 3 matricies containing all of the cells from all the samples prior to filtering (barcodes.tsv.gz, matrix.mtx.gz, and features.tsv.gz) and the SampleOrderforAllSamplesMatrix.rtf is a rich text file with the order of the samples within the matricies.

source_name: Single cell suspension of aortic root and ascending aorta

extract_protocol:
The aorta was perfused with 5mls of PBS injected through the left ventricle of the heart. The thoracic aorta from the aortic root to the arch (sinus of Valsalva to the branchpoint of the left subclavian artery) was collected and cut into small pieces and placed into a room temperature in 500 ul of solution A (HBSS (Thermo Fisher Scientific, 14175095), 50% D-Trehalose (Quality Biosciences, A611-K480-95), RNase inhibitor [20u/ul] (Applied Biosystems, N8080119)). 1ul/ml of room temperature DyeCycle Violet (DCV) (ThermoFisher, V35003) was added to stain double stranded DNA. After all aortic samples were collected, the tissue enzymatically digested by adding 500ul of solution B (Collagenase II [315U/mg] (Worthington-Biochem, LS004176), Elastase (MilliporeSigma, E1250), Dnase I [2620U/mg] (Zymo Research, E1009) in a thermomixer set to 800 rpm for 30 minutes or 1 hour at 37oC. After incubation, each sample was gently pushed through a 3ml syringe with a 21G needle 8 times to further disrupt the tissue. 100ul of 100% FBS (Corning, 35-010-CV) was added to each sample tube to inhibit the enzymes. The tubes were spun down at 800xg for 3.5 minutes at room temperature. The supernatant was discarded, and cells were resuspended in 500ul of solution A and 1ul/ml of DCV. The cell suspension was carefully pipetted through a 40um filter cap tube. Propidium iodide (PI) (ThermoFisher Scientific, P1304MP) was added to each sample and cells were sorted by flow cytometry to produce a single cell suspension of DCV+, PI- cells. 20ul of 1% BSA in HBSS was used as catch buffer.
10x Genomics 3' single index chemistry for single cell RNA sequencing as per manufacturer's protocol.
10x Genomics Chromium 3’ v3 chemistry, sequenced on an Illumina NovaSeq


title: Lung_FgaKO_Cov2_Rep1

value: Lung

value: Fga -/-


title: K562-U2AF1_S34F control2

value: DMSO


title: MDF from WT-WT mice treated with Nutlin - Replicate  2

value: D


title: K562-U2AF1_S34F control1


title: CB_96h_rp2

description:
CB-2-96H
20181208_ZHANGT.edaseq.count.tsv

value: Hematopoietic Stem Cells


title: CTL, rep1

description: Control, CNC-traced

value: Single cell suspension of aortic root and ascending aorta

value: Tgfbr1+/+; Wnt2CRE; EGFP-L10a


title: CTL, rep4

description: Control


title: MDF from WT-WT mice treated with Nutlin - Replicate  3


title: CB_96h_rp1

description:
CB-1-96H
20181208_ZHANGT.edaseq.count.tsv


title: ACHN, shNC, RNA-seq, repeat2

value: ACHN

value: ccRCC

value: shNC


title: CFPAC-1_Ctrl_3 [Yuuki_43]

description: CFPAC-1 with empty vector control

value: Pancreatic ductal adenocarcinoma cell line (CFPAC-1)

value: empty vector

value: No treatment. The cells were cultured in IMDM medium, supplemented with 10% FBS and 1% penicillin–streptomycin for 72 hours.


title: MDF from WT-WT mice treated with Nutlin - Replicate  1

value: Mouse tail skin

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: adult (8-12 weeks of age)

value: B

value: female

value: 26-Aug-2022; Read Length:161 bp; Cycle Kit:P1 300


title: CTL, rep3

description: Control


title: CB_0h_rp4

description:
CB-4
20181208_ZHANGT.edaseq.count.tsv

value: Lin-CD34+CD38- cells sorted from umbilical cord blood mononuclear cells


title: MDF from WT-WT mice treated with DMSO - Replicate  4

value: C

value: male

value: 11-Oct-2022; Read Length:61 bp; Cycle Kit:P2 100


title: LDS, rep1

description: LDS

value: Single cell suspension of aortic root and ascending aorta


title: CB_0h_rp3

description:
CB-3
20181208_ZHANGT.edaseq.count.tsv

value: Hematopoietic Stem Cells


title: invitroNK_sorteddims_Donor331_IL121518_GEX

city: Saint Louis

first: Todd

last: Fehniger

state: Missouri

address: 660 South Euclid Avenue, Campus Box 8007

department: Medicine

institute: Washington University School of Medicine

data_processing:
CellRanger 6.1.2 was used to align the fastq files to the genome.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix from CellRanger

source_name: human natural killer cells

growth_protocol: NK cells were isolated from LRS chambers from normal human donors, rested overnight in 1 ng/mL IL-15, sorted for CD56bright or CD56dim, and then activated with IL-12/15/18 overnight and then cultured in low-dose IL-15 for 1 week.

extract_protocol:
Single-cell suspensions of samples were processed according to manufacturer's instructions for 10x Genomics 5' droplet-based scRNA-seq.
cDNA was prepared after 10x Genomics GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified before being cleaned up using SPRIselect beads. Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation. GEX (Gene Expression) libraries were prepared as recommended by 10x Genomics (5’v2 Chemistry) user guides with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the IlluminaNovaSeq6000 or Nova SeqX Plusinstrument.

tag: donor

value: human natural killer cells

tag: sorted cells


title: invitroNK_sortedbrights_Donor331_IL121518_GEX

description: Sequenced on both an Illumina NovaSeq6000 & NovaSeqx

value: activated with IL-12/15/18 overnight and then cultured in low-dose IL-15 for 1 week


title: MDF from WT-WT mice treated with DMSO - Replicate  3


title: CTL, rep2

description: Control, CNC-traced

value: Tgfbr1+/+; Wnt2CRE; EGFP-L10a


title: CB_0h_rp2

description:
CB-2
20181208_ZHANGT.edaseq.count.tsv


title: 172784_eML

description: Illumina NovaSeq 6000

data_processing:
Fastq files were trimmed of their adapters using CutAdapt. Trimmed sequences were then aligned using Bowtie2 with the hg38 genome. Samtools was then used to convert alignment file to bam and filtered. Picard was used ro remove PCR duplicate reads. Peaks were then called using Genrich.
Assembly: GRCh38
Supplementary files format and content: Peaks were then called using Genrich and to generate processed narrowpeak files

growth_protocol: NK cells were isolated from LRS chambers from normal human donors, rested overnight in 1 ng/mL IL-15 then cultured in vitro in 1 ng/mL IL-15 or activated with IL-12/15/18 overnight and then cultured in low-dose IL-15 for 1 week. For the samples labeled cNK, eML, or effcNK without D7 included, these were sorted for ML subsets after 7 days of culture in 1ng/mL IL-15.

extract_protocol:
Cells were washed with PBS twice and spun down at 500g for 5 minutes. Nuclei were prepared by lysis cells using lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) and incubating on ice for 10 minutes. Followed with 500g spin for 10mins at 4C. Supernatant was removed for subsequent library preparation.
After obtaining nuclei, cells were incubated with transpoase from Illumina DNA Prep, (M) Tagmentation kit for 30mins at 37C. Immediately following transposition, purify DNA and remove excess enzyme using Qiagen MinElute PCR purification kit. To amplify tranposed DNA fragments the NEBNext® High-Fidelity 2X PCR Master Mix was used and IDT for Illumina DNA/RNA UD Indexes Set A, Tagmentation to barcode samples. To reduce GC and size bias in PCR, the appropriate number of PCR cycles is determined using qPCR between 5-8 cycles followed with a PCR cleanup using the Qiagen MinElute PCR purification kit.
Bulk ATAC-seq

tag: time

value: Sorted D7 CD117-, CD57-, NKG2A+, CD39+


title: CB_0h_rp1

description:
CB-1
20181208_ZHANGT.edaseq.count.tsv


title: MDF from WT-WT mice treated with DMSO - Replicate  2

value: Mouse tail skin

value: D


title: 172784_cNK

description: Illumina NovaSeq 6000

value: Sorted D7 CD117±, CD57±, NK2GA±, CD39-


title: 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 4 [Bt88_24_GD4]

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

institute: University of Washington

data_processing:
Whole lung RNA-seq data underwent QC and filtering of low quality reads. Mapping to reference mouse genome was performed using HISAT2 (v2.0.5) and transcript counts were quantified with featureCounts (v1.5.0-p3).
Assembly: mm10
Supplementary files format and content: Tab delimited text file for each sample

source_name: lung

extract_protocol:
The right ventricle was perfused with 3 ml of RNAlater (Thermo Fisher Scientific, Waltham, MA), whole lungs excised and immersed in RNA later and then cryopreserved. Whole lung RNA was extracted (NucleoSpin RNA Midi, Takara Bio, Shiga, Japan) and RNA concentration and integrity was assessed by sample absorbance at 260 and 280 nm.
RNA-seq was performed by Novogene using Illumina sequencers. Briefly,  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.

value: lung

tag: strain background

value: Tcrd-/-

value: B. thailandensis infection


title: MDF from KI-WT mice treated with Nutlin - Replicate  3

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: adult (8-12 weeks of age)

value: 15-Nov-2022; Read Length:75 bp; Cycle Kit:P1 300


title: 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 1 [Bt88_24_GD1]

value: female


title: 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 2 [Bt88_24_GD2]


title: 146724_eML

description: Illumina NovaSeq 6000


title: MDF from KI-WT mice treated with Nutlin - Replicate  2

value: B

value: male

value: 11-Oct-2022; Read Length:61 bp; Cycle Kit:P2 100


title: PB_96h_rp3

description:
PB-3-96H
20181208_ZHANGT.edaseq.count.tsv

value: Hematopoietic Stem Cells

value: Lin-CD34+CD38- cells sorted from Peripheral blood mononuclear cells and cultured in vitro for 96h


title: 172784_effcNK

description: Illumina NovaSeq 6000

value: human natural killer cells


title: PB_96h_rp2

description:
PB-2-96H
20181208_ZHANGT.edaseq.count.tsv


title: 24 hours after B. thailandensis-infection, Tcrd-/-, Mouse 3 [Bt88_24_GD3]


title: PB_0h_rp3

description:
PB-3
20181208_ZHANGT.edaseq.count.tsv

value: Lin-CD34+CD38- cells sorted from Peripheral blood mononuclear cells


title: Uninfected Tcrd-/-, Mouse 4 [NI_GD4]


title: MDF from KI-WT mice treated with DMSO - Replicate  3

value: Mouse tail skin


title: 146724_cNK

description: Illumina NovaSeq 6000

value: Sorted D7 CD117±, CD57±, NK2GA±, CD39-


title: Uninfected Tcrd-/-, Mouse 3 [NI_GD3]

value: lung


title: 146724_effcNK

description: Illumina NovaSeq 6000


title: MDF from KI-WT mice treated with Nutlin - Replicate  1

value: C


title: PB_0h_rp2

description:
PB-2
20181208_ZHANGT.edaseq.count.tsv


title: 153147_eML

description: Illumina NovaSeq 6000

value: Sorted D7 CD117-, CD57-, NKG2A+, CD39+


title: Uninfected Tcrd-/-, Mouse 2 [NI_GD2]

value: Tcrd-/-


title: PB_0h_rp1

description:
PB-1
20181208_ZHANGT.edaseq.count.tsv


title: PB_96h_rp1

description:
PB-1-96H
20181208_ZHANGT.edaseq.count.tsv


title: MDF from WT-WT mice treated with DMSO - Replicate  1

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: 26-Aug-2022; Read Length:161 bp; Cycle Kit:P1 300


title: 153147_cNK

description: Illumina NovaSeq 6000


title: Uninfected Tcrd-/-, Mouse 1 [NI_GD1]

value: female


title: 147429_effcNK

description: Illumina NovaSeq 6000


title: MDF from KI-KI mice treated with Nutlin - Replicate  4

value: adult (8-12 weeks of age)

value: 15-Nov-2022; Read Length:75 bp; Cycle Kit:P1 300


title: 24 hours after B. thailandensis-infection, wild type control, Mouse 4 [Bt88_24_WT4]

value: WT

value: B. thailandensis infection


title: 153147_effcNK

description: Illumina NovaSeq 6000


title: optic_nerve_inj

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

data_processing:
Illumina base-call files (*.bcl) were converted to FASTQs using CellRanger v1.3, which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger v1.3 software pipeline with default parameters which demultiplexes the samples and generates a gene versus cell expression matrix based on the barcodes and assigned unique molecular identifiers (UMIs) that enable determining the individual cells from which each RNA molecule originated.
Cell ranger output was loaded into Rstudio using the single cell RNAseq R package Seurat (v. 4.0.3). A seurat object was created for optic nerve cells.  Batches were merged, normalized and scaled in Seurat.
RunUMAP with "dims=1:4" and all other parameters as default was run. A cell counts matrix for the merged dataset was then generating by extracting counts matrix from the merged Seurat object and condition (uninjured or injured) metadata was appended to the first two rows of the matrix which was saved as csv file.
Assembly: mm10
Supplementary files format and content: One CSV files: Containing all retinal and optic nerve macrophage/microglia

source_name: Mus musculus (P56); 129S1/SvlmJ strain

extract_protocol:
Dissected optic nerve digested and triturated into a single cell suspension
The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on HiSeq 4000 with 150 cycle sequencing.

value: Optic Nerve

value: optic nerve microglia/macrophage

value: Wildtype

value: 2 weeks after crush


title: Winnie10

city: Boston

first: Rhian

last: Stavely

state: MA

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
Raw FASTQ files were analysed using the RNAsik pipeline version 1.5.4 and the Mus musculus reference genome GRCm38 (GenBank accession GCA_000001635.2)
Raw read counts were quantified using the featureCounts program
Analysed with Degust
limma voom normalisation to produce counts per million library size normalisation and trimmed means of M values and normalisation for RNA composition normalisation
Assembly: GRCm38
Supplementary files format and content: tab-limited text file includes counts per million for each sample - Counts_per_million.txt

source_name: brain

extract_protocol:
Mice were euthanised by lethal injection, brain were extracted, frozen in -80 degrees until required. Qiagen and Trozol were used to prepare the Brain RNA from each mouse.
The MGIEasy V2 chemistry set was used to generate the library, with at least 400 m raw reads per lane and paired-end 100b reads for accuracy and processing to compressed FASTQ files.

value: brain

value: Winnie

value: Male


title: MDF from KI-KI mice treated with Nutlin - Replicate  2

value: Mouse tail skin

value: C

value: male

value: 11-Oct-2022; Read Length:61 bp; Cycle Kit:P2 100


title: Winnie9


title: 24 hours after B. thailandensis-infection, wild type control, Mouse 2 [Bt88_24_WT2]

value: lung


title: MDF from KI-WT mice treated with DMSO - Replicate  2

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: D


title: MDF from KI-KI mice treated with Nutlin - Replicate  1

value: adult (8-12 weeks of age)

value: A

value: 26-Aug-2022; Read Length:161 bp; Cycle Kit:P1 300


title: optic_nerve_uninj

value: Optic Nerve

value: optic nerve microglia/macrophage


title: MDF from KI-KI mice treated with DMSO - Replicate  5

value: 15-Nov-2022; Read Length:75 bp; Cycle Kit:P1 300


title: 24 hours after B. thailandensis-infection, wild type control, Mouse 1 [Bt88_24_WT1]

value: female

value: WT

value: B. thailandensis infection


title: 147429_cNK

description: Illumina NovaSeq 6000

value: Sorted D7 CD117±, CD57±, NK2GA±, CD39-

value: human natural killer cells


title: 56546_D7_ML_D

description: Illumina NovaSeq 6000


title: Uninfected wild type control, Mouse 4 [NI_WT4]


title: Winnie8

value: brain

value: Winnie

value: Male


title: 56546_D7_cNK_D

description: Illumina NovaSeq 6000


title: 56546_OvernightIL121518_D

description: Illumina NovaSeq 6000

value: Overnight


title: MDF from KI-WT mice treated with DMSO - Replicate  1

value: Mouse tail skin

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: male

value: 11-Oct-2022; Read Length:61 bp; Cycle Kit:P2 100


title: Uninfected wild type control, Mouse 3 [NI_WT3]

value: lung


title: Winnie6


title: 56546_OvernightIL15_D

description: Illumina NovaSeq 6000


title: MDF from KI-KI mice treated with DMSO - Replicate  3

value: adult (8-12 weeks of age)

value: C


title: Uninfected wild type control, Mouse 2 [NI_WT2]

value: female


title: 147429_eML

description: Illumina NovaSeq 6000

value: Sorted D7 CD117-, CD57-, NKG2A+, CD39+


title: MDF from KI-KI mice treated with Nutlin - Replicate  3

value: 15-Nov-2022; Read Length:75 bp; Cycle Kit:P1 300


title: Winnie5

value: Female


title: 24 hours after B. thailandensis-infection, wild type control, Mouse 3 [Bt88_24_WT3]

value: WT

value: B. thailandensis infection


title: MDF from KI-KI mice treated with DMSO - Replicate  2

value: A


title: 5249_D7_ML_C

description: Illumina NovaSeq 6000

value: human natural killer cells


title: Winnie7

value: brain

value: Winnie

value: Male


title: Winnie4


title: Uninfected wild type control, Mouse 1 [NI_WT1]


title: 5249_D7_cNK_C

description: Illumina NovaSeq 6000


title: MDF from KI-KI mice treated with DMSO - Replicate  1

value: Mouse tail skin

value: MDF

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: B

value: 26-Aug-2022; Read Length:161 bp; Cycle Kit:P1 300


title: M5Day7BeadsUC

city: Rehovot

first: Benjamin

last: Geiger

address: POB 26

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Data was processed using UTAP  transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing was done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered.
Normalization of the counts and differential expression analysis was performed using DESeq2 package. Differential expression analysis was performed with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: tab delimited file include raw counts, normalized abundance measurements and DESeq2 analysis

source_name: Spleen

growth_protocol: Freshly isolated CD8+ T-cells were activated either with anti-CD3 and anti-CD28-coated microbeads at a 1:1 bead:cell ratio and IL-2, 100U/ml or by using ovalbumin peptide presented by preloaded DCs (used at 3:1 T-to-DC ratio) . T-cells were suspended in RPMI 1640 medium w/o phenol red, supplemented with 10% FBS, 100 U/ml of penicillin, 100 mg/ml of streptomycin, 2 mM glutamine, 1 mM sodium pyruvate, and 50 mM β-mercaptoethanol.

extract_protocol:
Naïve CD8+ T-cells were purified from a cell suspension, harvested from crushed spleens of OT-I mice, using the CD8a+ T Cell Isolation Kit and magnetic-associated cell sorting (MACS), according to the manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany). Similarly, DCs were purified (>90%) from spleens of C57BL/6 mice, using MACS CD11c microbeads (Miltenyi Biotec).
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et. Al. 2014)
Bulk Mars-Seq (3' end-RNA-seq)

treatment_protocol: Cells were cultured at 37ºC in a 96-well plate (250 µl/well), either uncoated or pre-coated with the CCL21-ICAM1 SIN.

value: Spleen

value: CD8+ T-cells

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)

tag: treatment type

tag: treatment day


title: Winnie3


title: MDF from KI-KI mice treated with DMSO - Replicate  4

tag: cell type

value: adult (8-12 weeks of age)

value: male

value: 15-Nov-2022; Read Length:75 bp; Cycle Kit:P1 300


title: M3Day7BeadsUC

tag: tissue


title: M4Day7BeadsUC


title: Winnie2

value: Female


title: 4995_D7_cNK_C

description: Illumina NovaSeq 6000


title: 4995_D7_ML_C

description: Illumina NovaSeq 6000


title: Cau_only_C

city: Houston

first: Michael

last: Lorenz

state: TX

address: 6431 Fannin

institute: UTHealth Houston

description: C-negative

data_processing:
Base-calling was performed by Psomagen using Illumina Real Time Analysis RTA software followed by fastq file generation with the Illumina package bcl2fastq.
To deplete reads derived from mouse macrophages, reads were first mapped to the GRCm38.p6 Mus musculus reference genome (Ensembl release 98) using Hisat2 v2.1.0, removing all reads that did align.
Reads mapping to the C. auris transcriptome were quantified using Salmon v1.10 with --gcBias and –seqBias flags enabled.
Assembly: C. auris B8441 reference transcriptome (FungiDB release 39 at fungidb.org)
Supplementary files format and content: Salmon output files (.quant.sf). These contain gene name, length, and effective length (modeled based on factors affecting the probablility of sampling fragments from this transcript), TPM (transcripts per million, a normalized measure of abundance) and estimated number of mapped reads. For more information, see https://salmon.readthedocs.io/en/latest/file_formats.html.

organism: Candidozyma auris

source_name: Whole cell

growth_protocol: C.auris cultures were grown overnight in YPD medium at 30 °C then diluted back into YPD medium at 30 °C to allow return to exponential phase. Cultures were then washed twice in phosphate buffered saline followed by dilution into Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
C. auris-only cultures were scraped in ice cold water followed by centrifugation. For C auris-macrophage co-cultures, medium was aspirated and ice cold water was added to lyse macrophages. Wells were then scraped and samples were pelleted by centrifugation, resuspended again in ice-cold water followed by further centrifugation. Fungal cell walls were digested with zymolyase at 37 °C, followed by RNA extraction using the SV Total RNA Isolation System (Promega).
Libraries were constructed using the TruSeq Stranded RNA library preparation protocol. Sequencing was carried out using the NovaSeq platform (Illumina) to obtain 35-45 million 2 x 151 paired-end reads. All library preparation and sequencing was performed by Psomagen.

treatment_protocol: C. auris cultures were incubated for 1 hr at 37 °C, 5% CO2 in the presence or absence of primary murine bone marrow derived macrophages (5:1 C. auris:macrophage ratio).

value: Whole cell

value: only


title: Cau_mac_B

description: B-positive

value: macrophage


title: Control10

value: brain


title: Winnie1

value: Winnie


title: 4965_D7_ML_C

description: Illumina NovaSeq 6000

value: human natural killer cells


title: 4965_D7_cNK_C

description: Illumina NovaSeq 6000


title: Cau_only_B

description: B-negative


title: M1Day7BeadsUC


title: Control9

value: Male


title: M3Day7BeadsC


title: M2Day7BeadsUC


title: 48846_D7_ML_C

description: Illumina NovaSeq 6000


title: Cau_mac_A

description: A-positive


title: Cau_only_A

description: A-negative


title: Control8


title: 48846_D7_cNK_C

description: Illumina NovaSeq 6000


title: Cau_mac_C

description: C-positive


title: 9792_D7_ML_B

description: Illumina NovaSeq 6000


title: 9792_D7_cNK_B

description: Illumina NovaSeq 6000


title: Control7


title: 9792_OvernightIL121518_B

description: Illumina NovaSeq 6000

value: Overnight


title: M1Day7BeadsC


title: Control5


title: M2Day7BeadsC


title: WT_BEL_3

description:
WT_BEL_3
WT_BEL_POOL_RPGCnorm10bin_scaled.bw

data_processing:
Sequence reads were obtained, and mapped to the mouse genome (UCSC release mm39) using Burrows-Wheeler Aligner (BWA, v.0.7.18)
The output .sam files were name-sorted and duplicate reads were marked and removed using SAMtools (v.1.17)
Peaks were called on each replicate using MACS3 (v.3.0.0)
Bamfiles from biological replicates are combined with Samtools (1.9)
Bigwig files were created from deduplicated, pooled replicate bam files using deepTools (v.2.0.0), and normalized as reads per genome coverage
Assembly: mm39 (UCSC release)
Supplementary files format and content: bedfiles of narrowpeaks called from MACS3
Supplementary files format and content: bigwigs of pooled replicate samples, RPGC normalized

source_name: skin

extract_protocol:
Cells were isolated by FACS into FACS sorting buffer. Cells were pelleted and lysed using 0.01% IGEPAL CA-630. ATAC libraries were prepared on these solubilized nuclei, according to Buenrostro et al. 2015.
Illumina Nextera, Buenrostro et al., 2015

value: skin

tag: cell line

value: cultured

value: hair follicle stem cell

tag: hair cycle_stage

value: in vitro

value: BEL-treated corpses

value: Rxra WT


title: M9Day4DCs120UC

value: Spleen

value: CD8+ T-cells

tag: genotype

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)


title: Control6


title: 9792_OvernightIL15_B

description: Illumina NovaSeq 6000

tag: treatment


title: M5Day7BeadsC


title: RNA bound with xPAC

city: Chengdu

first: pengliang

last: chi

state: Sichuan province

address: No.17 People's South Road

institute: Sichuan University

library_source: other

data_processing:
The quality of sequence data was checked by FastQC software (v0.11.8) .
(1) For data from xPAC sample, 5’adaptor and 3’-adaptor trimmed reads were aligned to the reference genome of Spodoptera frugiperda (fall armyworm) using STAR (v2.7.1a) with default parameters and the NCBI annotation version 1.0 was used (https://www.ncbi.nlm.nih.gov/assembly/GCF_011064685.1/). The 1.24 million reads including unique and multiple mapped reads were retained. The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”. Genes with raw counts of less than 10 reads were filtered out. Gene biotypes and tRNA types were from the gene transfer format (GTF) file.
(2) For data from the hPAC sample, 5’-adaptor and 3’-adaptor trimmed reads were aligned to the reference genome of hg38 using BWA (0.7.17-r1198-dirt) with default parameters, and the NCBI annotation version 14 was used (https://www.ncbi.nlm.nih.gov/genome/?term=GRCh38.p14). A total of 1.7 million reads including unique and multiple mapped reads were retained. The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”. Gene biotypes and tRNA types were from the GTF file.
The gene expression was quantified using the HTSeq (v0.11.2) with parameters of “-s yes” and “--nonunique all”.
Genes with raw counts of less than 10 reads were filtered out.
Assembly: (1) Spodoptera frugiperda version 1.0; (2) Homo sapiens reference genome GRCh38.p14.
Supplementary files format and content: The tab-delimited text files include gene biotypes, gene raw counts and RPKM values for each sample
Library strategy: Hydro-tRNAseq

molecule: other

organism: Spodoptera frugiperda

growth_protocol: (1) Sf9 cells were maintain in SIM SF Expression Medium (Sino Biological Inc.) with 120 rpm at 27°C in a shaker. (2) HEK293F cells were maintained in SMM 293T-II medium (Sino Biological Inc.) at 37 °C, 5% CO2, and 130 rpm shaking.

extract_protocol:
(1) The xPAC was expressed in Sf9 and the cells were centrifuged at 800 × g for 15 min and suspended in lysis buffer (25 mM Tris, 150 mM NaCl, pH 8.0) with protease inhibitors (1 mM phenylmethylsulfonyl fluoride, 0.8 µM aprotinin, 2 µM pepstatin A and 5 µg/mL leupeptin). The collected cells were flash-frozen in liquid nitrogen and stored at −80 °C before purification. The thawed cells were solubilized by adding 2% (w/v) n-Dodecyl β-D-maltoside (DDM, Anatrace) and stirring at 4 °C for 2 h. The resulting cell lysate was centrifuged at 27,000 × g at 4 °C for 30 min. The supernatant was incubated with Strep-tactin resin (GE Healthcare) at 4 °C for 1 h. The resin was washed with lysis buffer supplemented with either 0.06% (w/v) digitonin (Biosynth). Proteins were eluted with elution buffer (25 mM Tris, 150 mM NaCl, 5 mM desthiobiotin, pH 8.0) containing with 0.06 % digitonin. The protein samples were further purified by size-exclusion chromatography (SEC, Superose 6 increase 10/300 GL, GE Healthcare) in lysis buffer containing 0.06% digitonin. The purified xPAC proteins were used to extract RNA by using a phenol-chloroform extraction followed by ethanol precipitation. (2) The hPAC was expressed in HEK293F cells. The purification procedure was similar to that described for xPAC, with the following modification. The wash buffer contained 25 mM Tris pH 8.0, 150 mM NaCl, and 0.05% DDM. The protein was eluted with elution buffer containing 25 mM Tris, pH 8.0, 150 mM NaCl, 0.05% DDM, and 5 mM desthiobiotin. The RNAs enriched in the hPAC samples were extracted using the phenol-chloroform method followed by ethanol precipitation.
The purified RNA was demethylated by rtStarTM tRF&tiRNA Pretreatment Kit (Arraystar, AS-FS-005) and partially hydrolyzed according to Hydro-tRNAseq mothod. The library was prepared by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (New England Biolabs, E7300L/E7850L)

treatment_protocol: (1) For expression xPAC, recombinnant baculovirus were generated following the standard protocol of Bac-to-Bac Expression Systems (Invitrogen), Sf9 cell (cell density: 1.5-2.0 ×10^6 cells/ml) were infected with P2 virus,  and incubated at 27 °C for 60 hours. (2) For expression hPAC, expression plasmids were transfected into HEK293F cells (cell density: 1.5-2.0 ×10^6 cells/ml)  using PEI (25 kDa, Polysciences Inc.). The transfected cells were incubated at 37 °C for 60 hours.

value: cell derived from pupa ovarian tissue

value: WT

value: infected with recombinant baculovirus for expression of wild type Xenopus tropical acid-sensitive outwardly rectifying channel ASOR

value: Day 3


title: WT_BEL_2

description:
WT_BEL_2
WT_BEL_POOL_RPGCnorm10bin_scaled.bw


title: WT_BEL_4

description:
WT_BEL_4
WT_BEL_POOL_RPGCnorm10bin_scaled.bw


title: M8Day4DCs120UC


title: Control4

value: brain

value: Female


title: 870_D7_ML_B

description: Illumina NovaSeq 6000

value: human natural killer cells


title: Control3


title: Control2


title: 870_D7_cNK_B

description: Illumina NovaSeq 6000


title: M6Day4DCs120UC


title: cKO_corpses_3

description:
cKO_corpses_3
cKO_corpses_POOL_RPGCnorm10bin_scaled.bw

value: Corpses

value: Rxra cKO


title: Control1


title: WT_BEL_1

description:
WT_BEL_1
WT_BEL_POOL_RPGCnorm10bin_scaled.bw

value: skin

value: cultured


title: M7Day4DCs120UC


title: 870_OvernightIL121518_B

description: Illumina NovaSeq 6000

value: Overnight


title: M10Day4DCs120UC


title: cKO_corpses_2

description:
cKO_corpses_2
cKO_corpses_POOL_RPGCnorm10bin_scaled.bw

value: hair follicle stem cell

value: in vitro


title: TKO4

city: The Bronx

first: Alexander

last: Ferrena

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description:
10X Genomics 3' v3
Sample-10_TL784M10B

data_processing:
Sequencing reads were mapped to the mouse reference genome mm10 using CellRanger (6.0.1)
Assembly: Mouse reference genome mm10-2020-a prepared by 10x
Supplementary files format and content: filtered_feature_bc_matrix.h5 files containing cell by gene UMI count matrices from Cellranger

source_name: Osteosarcoma tumor

extract_protocol:
We followed instructions provided by 10x Chromium.  Briefly, tumors were isolated, single-cell suspension was prepared (see methods), then submitted for cell capture using the 10X chromium device targetting 10000 cells each.
10x Genomics Single Cell 3’ kit v3

value: Osteosarcoma tumor

value: Tumor and microenvironment

value: Osx-Cre;Rb1lox/lox;p53lox/lox; Skp2-/-


title: TKO3

description:
10X Genomics 3' v3
Sample-09_TL60F0W


title: 837_D7_cNK_A

description: Illumina NovaSeq 6000


title: cKO_corpses_1

description:
cKO_corpses_1
cKO_corpses_POOL_RPGCnorm10bin_scaled.bw


title: M6Day4DCs120C

value: Spleen

value: CD8+ T-cells

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)


title: WT_corpses_4

description:
WT_corpses_4
WT_corpses_POOL_RPGCnorm10bin_scaled.bw

value: Rxra WT


title: M7Day4DCs120C


title: 870_OvernightIL15_B

description: Illumina NovaSeq 6000


title: DKO3

description:
10X Genomics 3' v3
Sample-07_DL215M2B


title: WT_corpses_3

description:
WT_corpses_3
WT_corpses_POOL_RPGCnorm10bin_scaled.bw


title: M9Day4DCs120C


title: TKO1

description:
10X Genomics 3' v3
Sample-06_TL494


title: 837_OvernightIL15_A

description: Illumina NovaSeq 6000


title: TKO2

description:
10X Genomics 3' v3
Sample-08_TL190M10B


title: M8Day4DCs120C


title: 837_D7_ML_A

description: Illumina NovaSeq 6000


title: WT_corpses_2

description:
WT_corpses_2
WT_corpses_POOL_RPGCnorm10bin_scaled.bw


title: WT_corpses_1

description:
WT_corpses_1
WT_corpses_POOL_RPGCnorm10bin_scaled.bw


title: M10Day4DCs120C


title: DKO2

description:
10X Genomics 3' v3
Sample-05_DL608F11


title: cKO_recomb_2

description:
cKO_recomb_2
cKO_recomb_POOL_RPGCnorm10bin_scaled.bw

value: Recombinant AA+LPC+RA


title: 527_D7_cNK_A

description: Illumina NovaSeq 6000


title: DKO1

description:
10X Genomics 3' v3
Sample-04_DJ582M11


title: M5Day3DCs30UC


title: 527_OvernightIL121518_A

description: Illumina NovaSeq 6000


title: cKO_recomb_1

description:
cKO_recomb_1
cKO_recomb_POOL_RPGCnorm10bin_scaled.bw


title: M5Day3DCs120UC


title: 527_OvernightIL15_A

description: Illumina NovaSeq 6000


title: DKOAA3

description:
10X Genomics 3' v3
Sample-03_AL483M11


title: WT_recomb_3

description:
WT_recomb_3
WT_recomb_POOL_RPGCnorm10bin_scaled.bw


title: M4Day3DCs120UC


title: 527_D7_ML_A

description: Illumina NovaSeq 6000


title: WT_recomb_1

description:
WT_recomb_1
WT_recomb_POOL_RPGCnorm10bin_scaled.bw


title: FIL-ADSCs 3+WX390

city: Shanghai

first: Hongrui

last: Chen

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

department: Plastic and reconstruction surgery

institute: Shanghai ninth people's hospital

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome  using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Assembly: hg19
Supplementary files format and content: file includes raw counts for each Sample

source_name: Adipose tissue

growth_protocol: FIL-ADSCs were maintained in basal medium (Cyagen, USA, HUXMD-90011) with antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany) , after which the RNA concentration and quality were determined by the Qubit®3.0 Fluorometer (Life Technologies, USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA).
Paired-end libraries were synthesized by using the Stranded mRNA-seq Lib Prep Kit for lllumina (ABclonal, China) following Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: FIL-ADSCs was cultured in basal medium with 50nM WX390 for 24h

value: Adipose tissue

value: mesenchymal stem cell

value: PIK3CA H1047Y

value: 50nM WX390 treated for 24h


title: DKOAA2

description:
10X Genomics 3' v3
Sample-02_A253F1W


title: FIL-ADSCs 2+WX390

value: PIK3CA E418K


title: cKO_un_2

city: New York City

first: Katherine

last: Stewart

address: 1230 York Avenue

institute: The Rockefeller University

description:
cKO_un_2
cKO_un_POOL_RPGCnorm10bin_scaled.bw

value: skin

value: cultured

value: Media

value: Rxra cKO


title: M4Day3DCs30UC


title: FIL-ADSCs 1+WX390

value: PIK3CA H1047R


title: FIL-ADSCs 3


title: M1Day3DCs30UC


title: DKOAA1

description:
10X Genomics 3' v3
Sample-01_A204F30B

value: Osteosarcoma tumor

value: Tumor and microenvironment


title: ILC2_Mef2d_KO_2

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

data_processing:
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Supplementary files format and content: GRCm38
Supplementary files format and content: DEseq2 output file

source_name: Lung

extract_protocol:
ILC2s Purified from the lung of IL-33 intranasally treated mice. Cells were flow sorted into PBS 50% FCS and RNA was extracted using RNeasy Plus micro kit (Qiagen). After assessment using a Bioanalyser (Agilent), RNA was processed for RNA-sequencing using an Ovation RNA-seq System V2 (Nugen), fragmented using the Covaris M220,
and bar-coded using Ovation Ultralow Library Systems (Nugen)

value: Lung


title: ILC2_Mef2d_KO_3


title: WT_un_4

description:
WT_un_4
WT_un_POOL_RPGCnorm10bin_scaled.bw

value: hair follicle stem cell

value: in vitro


title: M1Day3DCs120UC

value: Spleen

value: CD8+ T-cells

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)


title: ILC2_Mef2d_KO_1


title: FIL-ADSCs 2

value: Adipose tissue

value: mesenchymal stem cell


title: WT_un_3

description:
WT_un_3
WT_un_POOL_RPGCnorm10bin_scaled.bw

value: Rxra WT


title: M5Day3DCs30C


title: ILC2_Cont_4


title: FIL-ADSCs 1


title: ILC2_Cont_3


title: cKO_m2_HFSC

description:
cKO_m2_HFSC
RXRa_cKO_dedup_POOL_RPGCnorm10bin_scaled.bw

value: in vivo sample

value: CatVII


title: M4Day3DCs30C


title: M3Day3DCs120UC


title: CTRL1_D

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: FFPE gene expression human transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline (v2.0.1) to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression level of genes in FFPE probe sets were quantified using Space Ranger's default settings
The h5ad files are AnnData objects that contain the final processed and analyzed 10x Visium data (from the samples that are already on GEO) using the Scanpy and anndata Python libraries.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:  low-res image of tissue
Supplementary files format and content: tissue_positions.csv:  list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: .h5ad: final processed object

source_name: Kidney

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) kidney tissue sections from kidney were prepared as per recommendations from the 10x.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction
Spatial Transcriptomics

value: Kidney

tag: condition

value: Control


title: cKO_un_1

description:
cKO_un_1
cKO_un_POOL_RPGCnorm10bin_scaled.bw

value: skin

value: cultured

value: Media

value: Rxra cKO


title: M4Day3DCs120C


title: ILC2_Cont_2

value: Lung


title: ILC2_Cont_1


title: cKO_m1_HFSC

description:
cKO_m1_HFSC
RXRa_cKO_dedup_POOL_RPGCnorm10bin_scaled.bw

value: hair follicle stem cell


title: WT_m4_HFSC

description:
WT_m4_HFSC
RXRa_WT_dedup_POOL_RPGCnorm10bin_scaled.bw


title: M3Day3DCs30C


title: purified CD8+ T cells sch58261 treat2 (ATAC-seq)

city: Chicago

first: Bin

last: Zhang

state: Illinois

address: 300E superior street, Tarry 4-726

institute: Northwestern University

description:
con sch atac diffPeaksHomer
SCA-7_S7

data_processing:
Illumina Casava1.8 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 v0.12.7 and normalized by CPM
Genome_build: mm10
Supplementary_files_format_and_content: peak score from every gene and every sample
Supplementary_files_format_and_content: Matrix tables with normalized gene counts for every gene and every sample, normalized gene peak score

growth_protocol: Purified CD8+ T cells were cultured with the peptide/anti-CD28 for 7 days

extract_protocol:
Purified CD8+ T cells were stored in single cell suspension in Trizol and RNA was harvested using Direct-zol RNA kit; Purified CD8+ T cells were resuspended in ATAC Lysis Buffer and DNA was harvested using Active motif ATAC-seq kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep Kit for Illumina; Active motif ATAC-seq kit for ATAC sequence

treatment_protocol: For in vivo, E0771 TBA were treated with anti-CD73 every 3 day; For in vitro, purified CD8+ T cells were treated with Lip-1, SCH58261 or Lip-1/SCH combination

tag: strain

value: CD8+ T cells


title: purified CD8+ T cells sch58261 treat1 (ATAC-seq)

description:
con sch atac diffPeaksHomer
SCA-3_S3

value: Spleen


title: CTRL1_C


title: M2Day3DCs120C

value: CD8+ T-cells


title: WT_m3_HFSC

description:
WT_m3_HFSC
RXRa_WT_dedup_POOL_RPGCnorm10bin_scaled.bw


title: WT_m2_HFSC

description:
WT_m2_HFSC
RXRa_WT_dedup_POOL_RPGCnorm10bin_scaled.bw


title: purified CD8+ T cells con2 (ATAC-seq)

description:
con sch atac diffPeaksHomer
SCA-5_S5

value: con


title: V4_C

value: ANCA-GN


title: cKO_m3_HFSC

description:
cKO_m3_HFSC
RXRa_cKO_dedup_POOL_RPGCnorm10bin_scaled.bw


title: M1Day3DCs30C

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)


title: purified CD8+ T cells con1 (ATAC-seq)

description:
con sch atac diffPeaksHomer
SCA-1_S1


title: M2Day3DCs30C


title: M5Day3DCs120C


title: V3_D


title: WT_m1_HFSC

description:
WT_m1_HFSC
RXRa_WT_dedup_POOL_RPGCnorm10bin_scaled.bw

value: Rxra WT


title: V3_C


title: Cat_HFSC_6

description:
Cat_HFSC_6
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw

value: in vivo sample

value: wild type


title: M1Day3DCs120C


title: CTRL1_B

value: Kidney


title: purified CD8+ T cells lip-1/sch58261 combination-treat3 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-PX-38S-F04_S4


title: Cat_HFSC_5

description:
Cat_HFSC_5
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw

value: CatVII


title: V2_B


title: purified CD8+ T cells lip-1/sch58261 combination-treat2 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-F6_S6


title: Cat_HFSC_4

description:
Cat_HFSC_4
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw

value: skin


title: M1Day3BeadsUC


title: purified CD8+ T cells lip-1/sch58261 combination-treat1 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-C3_S3


title: V6_D


title: V1_A


title: M4Day3BeadsUC


title: Cat_HFSC_3

description:
Cat_HFSC_3
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw


title: purified CD8+ T cells sch58261 single-treat3 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-PX-38S-F03_S3


title: M4Day3BeadsC


title: Cat_HFSC_2

description:
Cat_HFSC_2
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw


title: purified CD8+ T cells sch58261 single-treat1 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-B2_S2


title: Cat_HFSC_1

description:
Cat_HFSC_1
Cat_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw


title: Ana_HFSC_2

description:
Ana_HFSC_2
Ana_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw

value: AnaVI


title: V1_D

description: FFPE gene expression human transcriptome sequencing


title: V2_C


title: V5_B


title: V5_C


title: V4_A


title: purified CD8+ T cells lip-1 single-treat3 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-PX-38S-F02_S2


title: M2Day3BeadsUC


title: purified CD8+ T cells lip-1 single-treat2 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-D4_S4


title: M2Day3BeadsC


title: V2_D


title: purified CD8+ T cells sch58261 treat3 (RNA-Seq)

description:
con sch Differential_Expression
SC-9


title: PyMT 15 weeks 2

first: Christopher

middle: Russell

last: Chin

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

description: all.tumor.sobj.rds

data_processing:
CellRanger 3.0.2
Seurat 3.0.2
Assembly: mm10
Supplementary files format and content: Cellranger filtered_feature_bc_matrix.h5
Supplementary files format and content: Seurat object RDS file

source_name: Tumor

extract_protocol:
Tumors were dissected and collected in cold PBS. Tumors were minced and placed in dissociation media consisting of RPMI supplemented with 2 mg/ml collagenase I, 5% FBS and 15 U/ml DNAse. Samples were dissociated using the gentleMACS dissociator (Miltenyi Biotec), and filtered through a 70 μm cell strainer. After red blood cell lysis, cell suspensions were washed with PBS with 0.04% BSA and 6000 cells were loaded into a Single Cell A Chip.
Library preparation was done following manufacturer's instructions for the ChromiumTM Single Cell Reagent Kit v2

value: Tumor

tag: age

value: 15 weeks


title: M10Day0


title: purified CD8+ T cells lip-1 single-treat1 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-A1_S1


title: PyMT 12 weeks 2

description: all.tumor.sobj.rds

value: 12 weeks


title: V3_A


title: purified CD8+ T cells sch58261 single-treat2 (RNA-Seq)

description:
lip sch cm norm counts annotated
BZh-24S-pl3-E5_S5


title: PyMT 15 weeks 1

description: all.tumor.sobj.rds


title: M5Day3BeadsC


title: M1Day3BeadsC


title: purified CD8+ T cells sch58261 treat2 (RNA-Seq)

description:
con sch Differential_Expression
SC-8


title: M2Day0


title: purified CD8+ T cells sch58261 treat1 (RNA-Seq)

description:
con sch Differential_Expression
SC-7


title: M3Day3BeadsC


title: V5_D


title: purified CD8+ T cells con3 (RNA-Seq)

description:
con sch Differential_Expression
SC-3


title: 30-Day idSCs r2

first: Kristina

middle: M

last: Holton

address: 7 Divinity Ave

department: HSCRB

institute: Harvard University

data_processing:
Basecalls were performed with bcl2fastq for NextSeq output.
Raw reads were trimmed of adapters using Ngmerge and aligned to mm10 using Bowtie2.
Mitochondrial reads were removed using removeChrom and PCR duplicates removed using Picard.
Peak calling was performed using Genrich. BAM files were sorted by name using SAMtools, and peaks were called using default ATAC parameters (-j -p 0.01 -a 200) and excluding the ENCODE blacklist for mm10.  Consensus peaksets from replicates were called using IDR.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak except for input files

source_name: Skeletal muscle in vitro derived satellite cell

growth_protocol: Satellite cells refer to cells freshly isolated by FACS and immediately used, whereas primary myoblasts refer to cells derived from satellite cells, cultured in vitro for longer than two weeks, and used for experiments between passage 5-15. Satellite cells and primary myoblast lines were derived using hindlimb skeletal muscle from C57BL/6J, Tg:Pax7nGFP. Hindlimb skeletal muscles were aseptically dissected from either male or female 2-6 month old mice. For the derivation of primary myoblast lines, cells were cultured in GROWTH media: Ham’s F10 (Wisent), 20% heat inactivated FBS (Sigma Aldrich), 5ng/mL human bFGF, Aldevron), Non-Essential Amino Acids and GlutaMAX (Gibco) on collagen coated plates (Rat tail collagen, (Corning) at 37˚C with 5% CO2. Following culture ex vivo for 1 week, myoblasts were purified based on nGFP (Tg:Pax7nGFP) or α7 integrin (UBC Ablab). Purified myoblasts were passaged 5 times prior to being frozen as cell stocks. Differentiated myotubes or reserve cells were generated from proliferative myoblasts, grown to confluence, and subsequently cultured for 5 days in DIFFERENTIATION medium composed of DMEM (Gibco), 5% heat inactivated Horse Serum (Life Technologies), Non-Essential Amino Acids (Gibco) and Glutamax (Gibco) on laminin coated plates (Thermo Fisher).    Mouse skeletal muscle organoids (SkMOs) were generated from myoblasts (passage 5-15) cultured in GROWTH medium on collagen coated plates. Cells were seeded in SPIN medium (DMEM:F12 (Gibco), 20% heat inactivated FBS (Sigma Aldrich), 10ng/mL human bFGF (Aldevron), Non-Essential Amino Acids and Glutamax (Gibco)). SkMOs were fed every 48hrs by allowing the organoids to settle, aspirating media, and adding 50mls of fresh SPIN medium. After 20 days, the medium was changed to DIFFERENTIATION medium for 10 days. SkMOs were cultured for 10 (D10), 20 (D20), or 30 (D30) days before isolating the in vitro derived satellite cells (idSCs).  idSCs are defined as the SkMO-derived GFP+ cells.

extract_protocol:
ATAC-seq experiments were conducted according to the Omni-ATAC protocol (Corces, M.R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959-962 (2017).)
Library preparation was completed with 55ng input using a Nextera DNA kit (Illumina) following the manufacturer’s instructions


title: V6_A


title: M8Day0


title: PyMT 12 weeks 1

description: all.tumor.sobj.rds


title: Ana_HFSC_1

description:
Ana_HFSC_1
Ana_HFSC_dedup_POOL_RPGCnorm10bin_scaled.bw

value: hair follicle stem cell


title: 30-Day idSCs r1

value: Skeletal muscle in vitro derived satellite cell


title: M5Day0

value: Spleen


title: V5_A


title: purified CD8+ T cells con2 (RNA-Seq)

description:
con sch Differential_Expression
SC-2

value: CD8+ T cells


title: V6_C


title: 20-Day idSCs r2


title: V4_D


title: M1Day0

value: CD8+ T-cells


title: M6Day0


title: purified CD8+ T cells con1 (RNA-Seq)

description:
con sch Differential_Expression
SC-1

value: con


title: 20-Day idSCs r1


title: M4Day0

value: T cell receptor (TCR)-transgenic OT-I mice (harboring ovalbumin (OVA)-specific CD8+ T cells)


title: V6_B

value: ANCA-GN


title: 10-Day idSCs r2


title: enriched CD8+ T cells from tumor tissue anti-CD73-2 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
73-3

source_name: tumor microenvironment

value: tumor microenvironment


title: M7Day0


title: 10-Day idSCs r1


title: V2 day 7 [CR4]

city: Duarte

first: Adolfo

middle: Garcia

last: Ocana

state: California

address: 1500 E Duarte Rd

department: Molecular and Cellular Endocrinology

institute: City of Hope Beckman Research Center

description: Sequenced with pair-end 150 bpss on an Illumina NovaSeq 6000 instrument.

data_processing:
Sequenced reads were trimmed for low-quality bases and adapter sequences using TrimGalore v0.6.0, a wrapper for cutadapt and fastQC. STAR v2.7.0e was used to align raw sequencing reads to the human GRCh37 reference genome. SARTools and DESeq2 v1.26.0 were used to generate normalized counts and statistical analysis of differential gene expression.
Expression data were normalized per gene across samples by subtracting their mean and then dividing by their SD. This normalization was performed separately for the two donors to remove human variations.

source_name: Human islet graft

growth_protocol: Human islets were transplanted in Rag1-/- mice and treated with the drugs described below for 7 days.

extract_protocol:
total RNA was isolated using the RNAeasy mini kit (Qiagen) according to the manufacturer’s protocol,
TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra II [Directional] RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Transplanted mice were treated with vehicle (water) or harmine (3mg/kg/d) plus exendin-4 (0.1mg/kg/d) with alzet minipumps.

value: Human islet graft

value: Human islet cells

value: V


title: M3Day0


title: enriched CD8+ T cells from tumor tissue anti-CD73-1 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
73-2


title: Myoblasts r2

source_name: Skeletal muscle myoblast

value: Skeletal muscle myoblast


title: ST2 cells,rhWnt3aOSMI3,72h

city: Chendu

first: Fangyuan

last: Shen

state: --- Select a state ---

address: No.29 Jiuyanqiao Wangjiang Road, Chengdu, 610064

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through fastp software.
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.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPkM values for each Sample

source_name: bone

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: bone

value: ST2 cell line

value: mesenchymal stem cell

value: WT

value: OSMI (20 μM)


title: enriched CD8+ T cells from tumor tissue con3 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
Con4


title: enriched CD8+ T cells from tumor tissue con2 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
Con2


title: Myoblasts r1


title: H+E1 day 7 [CR1]

value: H+E


title: Satellite Cells r2

source_name: Skeletal muscle satellite cell

value: Skeletal muscle satellite cell


title: ST2 cells,rhWnt3aOSMI1,72h


title: enriched CD8+ T cells from tumor tissue con1 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
Con1

value: CD8+ T cells


title: Satellite Cells r1


title: shGLS1-2

city: Atlanta

first: Liwei

last: Lang

state: GA

address: 1701 Uppergate Drive

institute: Emory University

description: Cells treated with shGLS1

data_processing:
NovaSeq 6000 software RTA3 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, reads containing N > 10% (N represents base that could not be determined) and  low-quality reads, then mapped to hg38 whole genome using STAR (v2.5).
The counts coincide with those produced by htseq-count with default parameters. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor for each sequenced library. Differential expression analysis of two conditions was performed using the edgeR R package (v3.16.5).
Differential expression analysis between shGLS1 and shGFP was performed using the DESeq2 R package (v2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene of each sample
Supplementary files format and content: Tab-delimited text files including FPKM values for each Sample

growth_protocol: Human HN6 cells were grown in DMEM/F12 medium containing 10% FCS, 100 units/mL penicillin and 100 µg/mL streptomycin.

extract_protocol:
Total RNA of cells was extracted with TRIzol™ reagent. NEBNext Ultra™ II RNA Library Prep Kit (Cat#NEB-E7765) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HN6 cells were transduced with shGFP or shGLS1 lentivirus, and stable cell lines were established through selection with 1µg/ml puromycin.

value: HNSCC

tag: transduction


title: enriched CD8+ T cells from tumor tissue anti-CD73-3 (RNA-Seq)

description:
in vivo E0771 con CD73i deseq norm counts annotated
73-4


title: ST2 cells,rhWnt3a3,72h

value: rhWnt3a (50ng/ml) for 72 hours


title: shGLS1-1

description: Cells treated with shGLS1


title: Growth plate chondrocytes, Idh1 mutant 124-3

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

description: single cell RNA

data_processing:
Raw base call demultiplex into Fastq Files
Matrix generation 10X cell ranger software 3.0.1
PCA analysis, clustering, and gene expression analysis Seurat version 3
Monocle trajectory analysis Monocle3
Assembly: mm10
Supplementary files format and content: h5 files provided the output of cellRanger count; RDS file provided after PCA and clustering, from which gene expression was taken and monocle3 was performed

source_name: E18.5 Growth plate chondrocytes

growth_protocol: Animals were bred in accordance to Duke University IACUC protocols and aged to 2 months.

extract_protocol:
Animals were euthanized according to IACUC protocol and hind limbs were isolated. Surrounding tissues were dissected off growth plates (GP) from distal femur and proximal tibia were washed with PBS. GP chondrocytes were digested using 2mg/ml Pronase I at 37C for 1 hour with agitation followed by two times, 3mg/ml Collagenase IV digestion at 37C. Cells were washed in PBS. Live cells were FACS sorted followed by GEM generation and RT using for 10X Genomics single cell isolation and barcoding.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Col2a1-Cre; Idh1 LSL/+

value: distal femur and proximal tibia

value: chondrocytes


title: shGFP-2

description: Cells treated with shGFP

value: shGFP


title: V4_B

value: Kidney

value: ANCA-GN


title: ST2 cells,rhWnt3a2,72h


title: Growth plate chondrocytes, Idh1 mutant 119-2

description: single cell RNA


title: shGFP-1

description: Cells treated with shGFP


title: ST2 cells,rhWnt3a1,72h


title: Growth plate chondrocytes, Idh1 mutant 119-1

description: single cell RNA


title: H+E2 day 7 [CR2]

value: Human islet graft

value: Human islet cells


title: ST2 cells,Veh3,72h

value: bone

value: ST2 cell line

value: vehicle


title: P25801_127

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Library preparation, sequencing and data processing was done at SciLifeLab, Stockholm (Sweden) and was carried out under ISO/IEC 17025 accreditation. All samples had  a >=Q30 (aggregated percentage of bases that have quality score more the Q30) above 90%.
Mayo Analysis Pipeline for RNA sequencing (MAP-RSeq, version 3.1.1) was used to process raw RNA-Seq fastq data for read alignment, quality control, and gene expression quantification. Specifically, the RNA-Seq  reads were aligned to the human genome build GRCh38 (hg38) by the STAR aligner (version 2.5.2b). Gene expression quantification was performed using the Subread package (version1.5.1) for raw and RPKM counts
Assembly: Human (Homo sapiens, GRCh38)
Supplementary files format and content: Tab-separated values (TSV) containing merged gene count for all samples

source_name: breast

growth_protocol: The human breast cancer cell lines MDA-MB 231 were obtained from ATCC (Manassas, VA, USA). SUM149-PT breast cancer cells were obtained from Dr. Couch’s laboratory (Mayo Clinic). All cell lines were maintained in DMEM medium containing 5 mM glutamine, 1% penicillin/streptomycin and 10% FBS at 37 C in 5% CO2 atmosphere. PDX-derived TNBC cells (M14, M25 and M40) were established from metastatic PDX models in Dr. Sarkaria’s laboratory (Mayo Clinic Cancer Center).

extract_protocol:
Frozen cell pellets stored in RNAlater (Applied Biosystems) were allowed to thaw on ice, diluted 1:2 with cold PBS (Gibco) and centrifugated for 10 min at 200 xg for MDA-MB-231 and 300xg for SUM149-PT cells. The supernatatant was discarded and the cell pellet was resuspended in cold PBS and centrifugated at 200xg. RNA was extracted using the RNeasy mini kit (Qiagen) following the manufacturer’s instruction (including DNAse digestion). The RNA amount was determined with Qbit and RIN score of selected samples were assessed using Agilent BioAnalyzer (Agilent Technologies).
RNA samples were then processed for further quality control and library preparation at SciLifeLab (Stockholm, Sweden). All samples passed SciLifeLab’s reception quality control and were processed by the Illumina TruSeq Stranded mRNA (polyA) protocol. Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-19nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used was Sanger / phred33 / Illumina 1.8+.
RNA-seq , bulk (llumina TruSeq Stranded mRNA (polyA))

treatment_protocol: Scrambled (control) and GFP-tagged NOTCH3 and PD-L1 shRNA, lenti-vectors were purchased by OriGene Technologies (Rockville, MD, USA) and used according to the manufacturer’s instructions. Antibody treatment was carroued out as described in the mansucript

value: breast

value: epithelial

tag: mreads

tag: average fragment_size


title: ST2 cells,rhWnt3aOSMI2,72h

value: mesenchymal stem cell

value: WT

value: OSMI (20 μM)


title: Growth plate chondrocytes, control con119-3

description: single cell RNA

value: Idh1 LSL/+


title: P25801_126


title: Growth plate chondrocytes, control con116, 3

description: single cell RNA


title: ST2 cells,Veh1,72h


title: Growth plate chondrocytes, control con116, 4

description: single cell RNA


title: P25801_124


title: SVEC4-10 cells, 24h, nattokinase, rep3

city: Taipei

first: Hui-Wen

last: Chiu

address: No.301, Yuantong Rd., Zhonghe Dist., New Taipei City

country: Taiwan

institute: Taipei medical university

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: murine endothelial cells

growth_protocol: SVEC4-10 cells were maintained in Dulbecco's modified Eagle's medium with 1.5 g/L sodium bicarbonate, 4.5 g/L glucose and 10% fetal bovine serum at 37℃ and 5% CO2 in a humidified chamber.

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SVEC4-10 cells were seeded 24 hours before treatment on 6-cm dish with 4 ml of medium per dish. Cells were treated at ~80% confluency with the required doses for the required timepoints.

value: immortalized murine endothelial cells

value: treated with nattokinase for 24 hours


title: P25801_125


title: invitroNK_Donor56546_LDandML2hrand4hr1215_GEX

city: Saint Louis

first: Todd

last: Fehniger

address: 660 South Euclid Avenue, Campus Box 8007

institute: Washington University School of Medicine

description:
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXbarcodes.tsv.gz
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXfeatures.tsv.gz
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXmatrix.mtx.gz

data_processing:
CellRanger 6.1.2 was used to align the fastq files to the genome, including determing antibody derived tag and hashtag counts. CellRanger was run separately for ADT and HTO reads.
Assembly: GRCh38; mm10 for human/mouse experiments
Supplementary files format and content: filtered_feature_bc_matrix from cellranger outs. CellRanger was run separately for ADT and HTO libraries
Supplementary files format and content: The feature reference csv files for hashtag demultiplexing and ADT assignments.
Library strategy: CITE-seq

organism:
Homo sapiens
Mus musculus

source_name: human natural killer cells

growth_protocol: NK cells were isolated from LRS chambers from normal human donors, and cultured in vitro in 1 ng/mL IL-15 or activated with IL-12/15/18 overnight and then cultured in low-dose IL-15.

extract_protocol:
Single-cell suspensions of samples were processed according to manufacturer's instructions for 10x Genomics 5' droplet-based scRNA-seq, including staining of CITE-seq and hashtagging antibodies for pooling and demultiplexing for 30 minutes.
cDNA was prepared after 10x Genomics GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified before being cleaned up using SPRIselect beads. The supernatant was then collected for the Cell Surface Protein Library. Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation. GEX (Gene Expression) and TotalSeqC Feature libraries were prepared as recommended by 10x Genomics for Feature Barcode technology for Cell Surface Protein(v1/v2 Chemistry) user guides with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the IlluminaNovaSeq6000instrument.

tag: donor

value: human natural killer cells

tag: library type

value: GEX


title: Jelly-like structure, biological rep3

type: RNA

city: Kyoto

first: Megumi

last: Ikeda

address: 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, JAPAN

department: Department of Clinical Application

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

hyb_protocol: Hybridization was performed using Applied Biosystems, GeneChip® Hybridization Oven 640.

scan_protocol: GeneChips were scanned using Applied Biosystems, GeneChip® Scanner 3000 7G System.

data_processing: The data were analyzed with Applied Byosystems GeneChip® Expression Console Software ver 1.3.0. (RMA)

label: biotin

source_name: An organoid with Jelly-like structure generated from human iPS cells in cortical differentiation culture (day35).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® 3' IVT Pico Reagent Kit, P/N 703308 Rev. 1).

growth_protocol: Human iPS cells are cultured following cortical organoid differentiation protocol described in Kitahara et al., 2020 for 35 days.

extract_protocol: Extraction of total RNA was performed using RNeasy micro kit (QIAGEN) following manufacturer's protocol.

treatment_protocol: Each morphological structures in organoids were dissected under the stereo microscope.

value: organoid generated from human iPS cells

tag: morphology

value: Jelly-like structure


title: SVEC4-10 cells, 24h, nattokinase, rep2


title: SVEC4-10 cells, 24h, nattokinase, rep1


title: Jelly-like structure, biological rep2


title: P25801_123


title: ST2 cells,Veh2,72h


title: invitroNK_Donor56546_K562_LD2hr_ML2hr4hr_GEX

description:
56546_K562_LD2hr_ML2hr4hr_HTO_GEXbarcodes.tsv.gz
56546_K562_LD2hr_ML2hr4hr_HTO_GEXfeatures.tsv.gz
56546_K562_LD2hr_ML2hr4hr_HTO_GEXmatrix.mtx.gz


title: invitroNK_Donor56546_LDandML2hrand4hr1215_ADT_HTO

description:
Conditions are ctrl with K562 for 4 hours (Hashtag-1), or IL-12/15 for 2 hours (Hashtag-2), or 4 hours (Hashtag-3); or bulk ML with IL-12/15 for 2 hours (Hashtag-4) or 4 hours (Hashtag-5). Use Hashtag_five.csv.
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXbarcodes.tsv.gz
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXfeatures.tsv.gz
56546_LD4hrK562_LDandML2hrand4hr1215_HTO_GEXmatrix.mtx.gz

molecule: protein


title: Transparent area, biological rep3

source_name: An organoid with transparent area generated from human iPS cells in cortical differentiation culture (day35).

value: Transparent area


title: Jelly-like structure, biological rep1


title: P25801_121

value: control


title: P25801_122


title: SVEC4-10 cells, 24h, control sample, rep3

value: untreated


title: SVEC4-10 cells, 24h, control sample, rep2


title: invitroNK_Donor56546_K562_LD2hr_ML2hr4hr_ADT_HTO

description:
Conditions are ctrl with K562 for 2 hours (Hashtag-1), bulk ML with K562 for 2 hours (Hashtag-2) and bulk ML with K562 for 4 hours (Hashtag-3). Use Hashtag_five.csv.
56546_K562_LD2hr_ML2hr4hr_HTO_GEXbarcodes.tsv.gz
56546_K562_LD2hr_ML2hr4hr_HTO_GEXfeatures.tsv.gz
56546_K562_LD2hr_ML2hr4hr_HTO_GEXmatrix.mtx.gz


title: Transparent area, biological rep1


title: Pigmented area, biological rep3

source_name: An organoid with pigmented area generated from human iPS cells in cortical differentiation culture (day35).

value: Pigmented area


title: invitroNK_Donor56546_LDuns_MLuns_OvernightIL15_Act_GEX

description:
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXbarcodes.tsv.gz
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXfeatures.tsv.gz
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXmatrix.mtx.gz


title: SVEC4-10 cells, 24h, control sample, rep1


title: P25801_119


title: Pigmented area, biological rep2


title: Pigmented area, biological rep1


title: Transparent area, biological rep2


title: invitroNK_Donor56546_LDuns_MLuns_OvernightIL15_Act_ADT_HTO

description:
Conditions are ctrl unstimulated (Hashtag-1), bulk ML unstimulated (Hashtag-2), overnight 1 ng/mL IL-15 (Hashtag-4), and overnight IL-12/15/18 (Hashtag-5). Use Hashtag_five.csv.
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXbarcodes.tsv.gz
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXfeatures.tsv.gz
56546_LDuns_MLuns_OvernightIL15_Act_HTO_GEXmatrix.mtx.gz


title: Cotton-like structure, biological rep3

source_name: An organoid with cotton-like structure generated from human iPS cells in cortical differentiation culture (day35).

value: Cotton-like structure


title: P25801_112

value: breast