title: Mitotic-K562-input

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
ChIP-seq analysis was performed on the raw FASTQ files. FASTQ reads were aligned to the human genome (hg38) using the BWA v0.7.12. Only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome
Mapped output files were processed through MACS v2.1.0 and Genrich v0.6.1 software to determine peaks.
Bigwig files were created from bam files with deeptools v2.5.4.
Assembly: hg38
Supplementary files format and content: bigwig, bed

extract_protocol:
Genomic DNA (input) was prepared for asynchronous and mitotic K562 cells by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). 40 µg of chromatin was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 5 µg of antibody against GATA2 (Santa Cruz, sc-9008). Complexes were washed, eluted from the beads with SDS buffer, and treated with RNase and proteinase K. Crosslinks were reversed by incubation overnight at 65 ºC, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (qPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (BioRad). The resulting signals were normalized for primer efficiency by carrying out qPCR for each primer pair using Input DNA.
Illumina sequencing libraries were prepared from ChIP and Input DNAs by standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end)

treatment_protocol: Asynchronous cells: 1x10E7 asynchronous K562 cells were crosslinked in 1 mL 2 mM PBS-disuccinimidyl glutarate (DSG) (Sigma) for 50 min at RT with occasional shaking. Then, cells were spun down, resuspended in 10 mL PBS and crosslinked again with 1 mL formaldehyde solution (11% FA, 0.1 M NaCl, 1 mM EDTA, 50 mM, HEPES in H2O, FA final concentration 1%), with agitation for 15 min at RT – double fixation (DSG+FA). FA was quenched with 0.125M glycine for 5 min. Cells were centrifuged at 800g at 4 ºC for 10 min and washed twice with PBS 0.5% Igepal, supplemented with 100 mM PMSF. Cell pellet was snap-frozen and stored at -80 ºC. Mitotic cells: 1x10E8 K562 nocodazole arrested cells were crosslinked in 2 mL 2 mM PBS-DSG for 50 min at RT, spun down and fixed with 1% FA, as described for asynchronous cells. Cells were stained for FACS with MPM-2 primary antibody and anti-mouse AF647 secondary antibody, as described by Campbell et al., with the exception that FA was quenched with 0.5 M glycine. Approximately 5x10E6 mitotic (MPM-2+) K562 were sorted in several rounds, after doublet exclusion resulting in <10% contamination with asynchronous cells. After each sorting, cell pellets were snap-frozen, stored at -80 ºC and pulled together for ChIP-seq.

value: chronic myeloid leukaemia

tag: chip antibody

tag: condition

value: Mitotic


title: SAUSA300_1650 [S20]

status: Public on Jun 27 2023

type: SRA

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

country: USA

institute: Rutgers New Jersey Medical School

library_source: transcriptomic

data_processing:
Analysis was performed using Partek Flow
Reads were trimmed with Phred scores <20, 20bp minimum length and a maximum N of 10%, along with adaptor sequences removed
Trimmed reads were aligned using Bowtie 2
Combined alignments were quantified to the annotation model
Filtered counts were normalized by using TMM and adding 1 then excluding feature less than 1
Differential analysis was conducted using ANOVA and Limma-voom
Genome_build: GCA_000013465.1_ASM1346v1_cds_from_genomic
Supplementary_files_format_and_content: xlsx

molecule: total RNA

organism: Staphylococcus aureus

growth_protocol: Grown in LB broth up to 1.0 (OD600)

extract_protocol:
6 hypothetical mutants (SAUSA300_1720, SAUSA300_1902, SAUSA300_1650, SAUSA300_2068, SAUSA300_0903 and SAUSA300_0917 ) were grown in LB broth up to 1.0 (OD600nm). Bacterial RNA was extracted by using the RNA kit (E.Z.N.A. Total RNA kit I) after a brief lysostaphin step.
RNA libraries were prepared on 8ug of total RNA. rRNA was removed using the Ribo-zero kit. mRNA was fragmented and cDNA synthesized using random hexamers, after which  custom second-strand synthesis buffer (Illumina), dNTPS, Rnase H and DNA polymerase I were added to intiate the second-strand synthesis. A series of terminal repair, ligation and sequencing adaptor ligation, the double-stranded cDNA library is size selection and PCR enriched.

tag: strain background

tag: genotype/variation

value: Mutant in SAUSA300_1650


title: Asynchronous-K562-input

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: Asynchronous


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-41

city: Seattle

first: John

middle: Kenneth

last: Mich

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

library_source: transcriptomic single cell

data_processing:
Base-calling using standard Illumina software.
Alignment with STAR (https://github.com/alexdobin/STAR)
Transformed by counts per million.
Assembly: mm10
Supplementary files format and content: Processed data in counts per million (CPM) format.

molecule: polyA RNA

organism: Mus musculus

source_name: VISp

extract_protocol:
Single SYFP2-expressing cells from mouse brain were flow sorted into individual tubes in SMARTerv4 collection buffer.
SMARTerv4

tag: tissue

value: VISp

tag: genotype

tag: treatment


title: SAUSA300_0903 [S18]

value: Mutant in SAUSA300_0903


title: SAUSA300_1720 [S19]

value: Mutant in SAUSA300_1720


title: Mitotic-K562-GATA2

value: GATA2 (Santa Cruz, sc-9008)


title: SAUSA300_0917 [S17]

value: Mutant in SAUSA300_0917


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-31


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-30


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-33


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-32


title: Mammary gland tumors, Nr1d1-/-;PyMT, rep2

city: Goyang

first: Mi Kyung

last: Park

address: 323, Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

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(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Mammary gland tumors

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

value: Mammary gland tumors

tag: strain

value: FVB

tag: Sex

value: Female

tag: time

value: 14 weeks old


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-27


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-28


title: Mammary gland tumors, Nr1d1-/-;PyMT, rep1


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-38


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-25


title: SAUSA300_1902 [S21]

value: Mutant in SAUSA300_1902


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-24


title: Mammary gland tumors, Nr1d1+/+;PyMT, rep2


title: SAUSA300_2068 [S16]

value: Mutant in SAUSA300_2068


title: WT, USA300 (JE2) [S15]

source_name: WT, USA300 (JE2)

value: WT


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-22


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-23


title: SAUSA300_1650 [S13]


title: SAUSA300_1902 [S14]


title: Asynchronous-K562-GATA2


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-34


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-29


title: SAUSA300_1720 [S12]


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-20


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-19


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-21


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-26


title: SAUSA300_0903 [S11]


title: SAUSA300_0917 [S10]


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-17


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-18


title: SAUSA300_2068 [S9]


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-16


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-48


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-47


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-46


title: Sertoli_PRC1RdKO_rep1 [1110]

city: Noda

first: Ryo

last: Sugiyama

state: Chiba

department: Applied Biological Science

country: Japan

institute: Tokyo University of Science

description: BioWardrobe Ides: 1110

data_processing:
RNA-seq data analysis was performed in the Wardrobe experiment management system (PMID: 26248465 ).   Briefly, reads were mapped to the mm10 genome using TopHat version 2.0.9 (PMID: 22383036) and assigned to the RefSeq genes (or isoforms) using the Wardrobe algorithm.   Differential gene expression analysis was performed using DESeq2 (PMID: 25516281) in the Wardrobe environment.  For GO analysis, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to identify the GO terms (PMID: 19131956).
Assembly: mm10
Supplementary files format and content: csv file includes analyzed transcripts of isoforms.

growth_protocol: Generation of mutant Ring1 and Rnf2 floxed alleles were previously reported (PMID: 18039844).  Amh-Cre mice were purchased from Jackson lab (PMID: 14701682).   Conditional mutants were mated with Amh-Cre mice (Ring1A−/−; Ring1Bfl/fl; AmhCreTg/+ ).

extract_protocol:
Total RNA was purified from Sertoli cells using an RNeasy microkit (Qiagen) according to the manual provided.
For RNA-seq, RNA quality and quantity were checked using Bioanalyzer (Agilent) and Qubit (Life Technologies), respectively.   The initial amplification step was performed with the NuGEN Ovation RNA-seq system version 2.   The assay was used to amplify RNA samples and create double-stranded cDNA.   Libraries were then created with the Nextera XT DNA sample preparation kit (Illumina).

treatment_protocol: Sertoli cells were isolated as previously described with minor modifications (PMID: 22054547) and collected from C57BL/6N mice aged 6–8 days.

value: testis

tag: age


title: Sertoli_PRC1RdKO_rep2 [1111]

description: BioWardrobe Ides: 1111


title: Sertoli_PRC1Rctrl_rep2 [1109]

description: BioWardrobe Ides: 1109


title: WT, USA300 (JE2) [S8]


title: Mammary gland tumors, Nr1d1+/+;PyMT, rep1


title: Input_rep2

description:
BioWardrobe Ides: 4264
run1787_lane1_read1_index16-1=AD2X16

data_processing:
Data analysis for ChIP-seq was performed in the BioWardrobe Experiment Management System  (PMID: 26248465 ). Briefly, reads were aligned to mouse genome mm10 with Bowtie (version 1.2.0, PMID: 19261174), assigned to NCBI RefSeq genes or isoforms, and coverage was displayed on a local mirror of the UCSC genome browser. ChIP-seq peaks for H2AK119ub, H3K27me3, and RNF2 were identified using MACS2 (version 2.1.1.20160309, PMID: 18798982) with default parameter setting for narrow peak detection in BioWardrobe.   Pearson correlations for the genome-wide enrichment of the peaks among ChIP-seq library replicates were analyzed using SeqMonk (Babraham Institute).
RNA-seq data analysis was performed in the Wardrobe experiment management system (PMID: 26248465 ). Briefly, reads were mapped to the mm10 genome using TopHat version 2.0.9 (PMID: 22383036) and assigned to the RefSeq genes (or isoforms) using the Wardrobe algorithm. Differential gene expression analysis was performed using DESeq2 (PMID: 25516281) in the Wardrobe environment.For GO analysis, the Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to identify the GO terms (PMID: 19131956).
Genome_build: mm10

source_name: Sertoli

growth_protocol: Generation of mutant Ring1 and Rnf2 floxed alleles were previously reported (PMID: 18039844). Rosa-Cre ERT mice were purchased from Jackson lab (PMID: 17251932). Conditional mutants were mated with Rosa-Cre ERT mice mice (Ring1A−/−; Ring1Bfl/fl; Rosa26::CreERT2tg/+ ).

extract_protocol:
Total RNA was purified from Sertoli cells using an RNeasy microkit (Qiagen) according to the manual provided.
For ChIP-seq, libraries were created by ChIPmentation method (PMID: 26280331).For RNA-seq, RNA quality and quantity were checked using Bioanalyzer (Agilent) and Qubit (Life Technologies), respectively. The initial amplification step was performed with the NuGEN Ovation RNA-seq system version 2. The assay was used to amplify RNA samples and create double-stranded cDNA. Libraries were then created with the Nextera XT DNA sample preparation kit (Illumina).

treatment_protocol: Sertoli cells were isolated as previously described with minor modifications (PMID: 22054547) and collected from C57BL/6N mice aged 6–8 days. Isolated cells were grown on Datura Stramonium agglutinin-coated dishs in DMEM/F12 medium containing  1 mM L-glutamine, 5 mM sodium L-lactate, 1 mM sodium pyruvate, 0.1 mM MEM nonessential amino acids, and 10% FBS.4-hydroxy tamoxifen (OHT) at a final concentration of 800 nM for 4 days was added to culture medium to induce Cre recombinase activity and delete Ring1B.

value: wild type

value: Sertoli cells


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-45


title: SAUSA300_1902 [S7_1902]


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-42


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-43


title: Input_rep1

description:
BioWardrobe Ides: 4263
run1787_lane1_read1_index15-1=AD2X15


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-44


title: RNF2_rep2

description:
BioWardrobe Ides: 5934
RNF2_i14_S65_L005_R1_001

value: RNF2 (Ms, monoclonal, MBL 139-3)


title: SAUSA300_1650 [S6_1650]

value: Mutant in SAUSA300_1650


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-40

value: VISp


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-41


title: SAUSA300_1720 [S5_1720]


title: SAUSA300_0903 [S4_0903]

value: Mutant in SAUSA300_0903


title: RNF2_rep1

description:
BioWardrobe Ides: 5933
RNF2_i13_S64_L005_R1_001


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-36


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-38


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-39


title: Sertoli_PRC1Rctrl_rep1 [1163]

description: BioWardrobe Ides: 1163


title: SAUSA300_0917 [S3_0917]


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-35


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-37


title: SAUSA300_2068 [S2_2068]


title: H3K27me3_rep2

description:
BioWardrobe Ides: 4265
run1787_lane1_read1_index19-1=AD2X19

value: H3K27me3 (Rb, polyclonal, Diagenode C15410195)


title: H3K27me3_rep1

description:
BioWardrobe Ides: 2390
run1281_lane12_read1_index3=3


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-34


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-33


title: H2AK119ub_rep2

description:
BioWardrobe Ides: 2483
run1296_lane12_read1_index17=1_4

value: H2AK119ub (Rb, monoclonal, Cell Signaling 8240)


title: WT, USA300 (JE2) [S1_WT]


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-32


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-31


title: Sertoli_PRC1RdKO_rep2

description:
BioWardrobe Ides: 1115
h2A703BF-4186-D7CD-3300-14CBE719F6A6


title: H2AK119ub_rep1

description:
BioWardrobe Ides: 2480
run1296_lane12_read1_index1=1_1


title: U87-HSV3

city: 上海

first: 玮玮

last: 代

state: 上海

address: 徐汇区东安路131号

country: China

institute: 复旦大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: U87 cells were treated with 0.1MOIHSV for 12h

value: glioma cell lines

tag: agent

value: U87 cells were infected with HSV for 12 hr


title: U87-HSV2


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-30


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-28


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-27


title: U87-HSV1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-26


title: Sertoli_PRC1Rctrl_rep2

description:
BioWardrobe Ides: 1113
ZD70352B-079B-07CB-8BF1-BA18DD54C2F8


title: Sertoli_PRC1RdKO_rep1

description:
BioWardrobe Ides: 1114
X23122D5-22AC-9802-2414-4482CEEA0DB1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-25


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-23


title: Sertoli_PRC1Rctrl_rep1

description:
BioWardrobe Ides: 1112
E5DEA39-125E-7A46-7888-C13FC6E9815C


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-22


title: U87-CTRL2

value: DMEM


title: U87-CTRL3


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-19


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-21


title: U87-CTRL1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-18


title: ev_DC_3

city: GUANGZHOU

first: xiaoqing

last: Liu

state: Guangdong

address: 58 Zhongshan Road II, , Guangzhou

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Pre-processing of sequencing reads / Quality Control.1) Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes. 2) Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Quantification of gene expression level. Paired-end reads were aligned to the mouse reference genome mm10/hg19/rn6 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
The statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(foldchange)|> 1 using theDEseq/DESeq2/edgeR/DEGseq software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: DC

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol, The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 T apeStation (Agilent T echnologies, USA) separately.
the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 T apeStation and Qubit(Thermo Fisher Scientific, USA)

value: DC

value: MSC-sEV


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-24


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-17


title: WT+ADAM10-KO (multiplexed) scRNA-seq

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

description: GEO users can load the raw fastq-files into the BD Rhapsody WTA pipeline (access provided by BD upon request) in order to receive Mols_per_cell.csv for every sample

data_processing:
Processing of raw reads was done using the BD Rhapsody WTA Analysis Pipeline v1.0 which  takes the FASTQ files, a reference genome file (GRCm38) and a transcriptome annotation (genecodevM19) file for alignment. Molecular counts per cell generated by the pipeline were used for data analysis in Partek Flow.
Raw paired sequencing data consist of R1 and R2 file. Sample demultiplexing is done based on information from R1 that contain cell label and R2 reads that contain mRNA sequences and tag sequences. Each of R1 reads sequenced contain the cell label although not every corresponding R2 read contain tag sequence. To demultiplex samples, firstly the cell labels are annotated in order to determine putative cells. After determination of putative cells, each of cells have assigned cluster of reads R1 and associated R2 reads. Based on tag sequence in group of R2 reads assigned to cell, each cell is assigned to sample tag.
Detailed description on annotation of cell labels (step 2) and determination of putative cells (step 6) followed by determination of sample of origin (step 7) can be found in BD Single Cell Genomics Bioinformatics Handbook (GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf) Available tag sequences used for sample multiplexing can be found in Attachement_B2_SampleTagSequences_MusMusculus_ver1.fasta for Mouse.
Sample tags used in this experiment are:
>SampleTag01_mm|stAbO [WT1]
GTTGTCAAGATGCTACCGTTCAGAGAAGAGTCGACTGCCATGTCCCCTCCGCGGGTCCGTGCCCCCCAAG
>SampleTag02_mm|stAbO [WT2]
GTTGTCAAGATGCTACCGTTCAGAGACCGATTAGGTGCGAGGCGCTATAGTCGTACGTCGTTGCCGTGCC
>SampleTag03_mm|stAbO [WT3]
GTTGTCAAGATGCTACCGTTCAGAGAGGAGGCCCCGCGTGAGAGTGATCAATCCAGGATACATTCCCGTC
>SampleTag04_mm|stAbO [A10KO1]
GTTGTCAAGATGCTACCGTTCAGAGTTAACCGAGGCGTGAGTTTGGAGCGTACCGGCTTTGCGCAGGGCT
>SampleTag05_mm|stAbO [A10KO2]
GTTGTCAAGATGCTACCGTTCAGAGGGCAAGGTGTCACATTGGGCTACCGCGGGAGGTCGACCAGATCCT
>SampleTag06_mm|stAbO [A10KO3]
GTTGTCAAGATGCTACCGTTCAGAGGCGGGCACAGCGGCTAGGGTGTTCCGGGTGGACCATGGTTCAGGC
Analysis processed data were done using the analysis software Partek Flow (Partek)
Genome_build: reference genome GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: dendritic cell (CD11c+ cells)

extract_protocol:
Spleens were cut in grain size pieces and digested with 200U/ml Collagenase Type IV + 0,5 U/ml Dnase for 30 min at 37 oC. CD11c+ cells were enriched by MACS.
Libraries were generated following the BD Rhapsody System mRNA WTA and Sample Tag Library Preparation protocol (BD Biosciences).

value: spleen

value: 3 WT Samples + 3 ADAM10 KO samples (multiplexed)


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-29


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-15


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-20


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-14


title: mDC_3

value: WT

value: control


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-13


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-12


title: mDC_2


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-10


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-11


title: WGBS_BJ Fibroblast, HRAS, rep 3

city: Washington

first: Katherine

last: Chiappinelli

state: MA

address: 800 22nd Street, NW

department: Molecular Immunology and Tropical Medicine

institute: George Washington University

description:
Bisulfite converted total DNA
BJ Fibroblast cells transduced with hTERT,  SV40, and HRAS

data_processing:
Reads were aligned using Bismark v. 0.23.0 (49). The hg38 reference annotation provided above was bisulfite converted using the bismark_genome_preparation tool and reads were aligned to this reference using default parameters.
Reads were deduplicated using the deduplicate_bismark tool
bismark_methylation_extractor tool was used to generate meethylation coverage files
Assembly: hg38 (bisulfite converted)
Supplementary files format and content: <sample>_deduplicated.bismark.cov.gz - tab delimited files which give chromosome, start, end coordinates, % methylated,  methylated count,  unmethylated count

source_name: Neonatal Foreskin

growth_protocol: BJ Fibroblast cells were maintained in 66.3% KO DMEM, 16.5% Medium 199, 14.5% FBS, 3.5 mM Glutamine, 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
DNA was bisulfite converted using the Zymo EZ DNA Methylation-Lightning Kit (Catalog # D5030)
libraries were created using the Swift Accel-NGS® Methyl-Seq DNA Library Kit (Catalog # 30024).

value: Neonatal Foreskin

value: BJ Fibroblast

value: Fibroblast

value: hTERT, SV40, HRAS overexpression


title: WGBS_BJ Fibroblast, HRAS, rep 1


title: ev_DC_1


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-8

value: VISp


title: L-HCV

type: RNA

city: Kaohsiung

first: Shu-Chi

last: Wang

address: No.100 Shiquan Road

department: Medical Laborstory Science and Biotechnology

country: Taiwan

institute: Kaohsiung Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human miRNA Microarray ( G4872A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent  Microarray Scanner (G2565CA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: L-HCV

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s recommendations. The quality of the total RNA was evaluated using an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA, USA) using an RNA 6000 Nano LabChip kit (Agilent, Palo Alto, CA, USA).

treatment_protocol: The human hepatoma Huh7.5.1 cell line was cultured and incubated in a humidified 5% CO2/95% air atmosphere at 37 °C to reach 5 × 10^6 cells in a 10 cm Petri dish with Dulbecco’s modified Eagle medium (DMEM) (Cat. # 21969035 Thermo Fisher Scientific, Waltham, MA, USA) mixed with 10% fetal bovine serum (FBS) (Lonza, Walkersville, MD, USA), 2% L-glutamate containing 200 mM solution in 0.85% NaCl solution (Lonza, Walkersville, MD, USA) and 2% antibiotics containing 10,000 U Pen./mL, 10,000 ug Strep./mL, 25 ug Amphotericin B/mL (Lonza, Walkersville, MD, USA) and 1% Non-Essential Amino Acids (NEAA) (Lonza, Walkersville, MD, USA). In the range of 1–10 passage numbers, 5 × 10^5 of the Huh7.5.1 cells in the 10 cm Petri dish were infected via incubation with HCV JFH1-EYFP virus with a 1:200 ratio (viral medium: fresh medium) (HCV cc, developed by Dr. Machi Yamamoto) for 6 h, after which the medium was replaced with fresh medium and cells were incubated for 5 days and 30 days.

value: human hepatoma cell

tag: infection

value: HCV


title: WGBS_BJ Fibroblast, SV40, rep 1

description:
Bisulfite converted total DNA
BJ Fibroblast cells transduced with hTERT and SV40

value: hTERT, SV40 overexpression


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-7


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-6


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-5


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-3


title: mDC_1


title: B Cell, CpG 1018 + CXCL4, Donor 3

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
Read quality was assessed and adaptors trimmed using FASTP
Reads were then mapped to the human genome hg38 with STAR aligner
reads in exons were counted against Gencode with featureCounts
Differential gene expression analysis was performed in R using edgeR.
Assembly: hg38
Supplementary files format and content: raw count matrix

source_name: Blood

growth_protocol: Human B cells were isolated with CD19 magnetic beads from PBMCs of healthy donors.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit. SMART-Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation were used to prepare Illumina-compatible sequencing libraries. Quality of all RNA were evaluated with BioAnalyser 2100 (Agilent). Single-end reads were obtained on an Illumina HiSeq 2500 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample. Sequencing quality was measured with fastp (Chen et al., 2018). Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21(Dobin et al., 2013; Frankish et al., 2019). Differential gene expression analysis was performed in R(Team, 2020) using the edgeR package (Robinson et al., 2010).
SMART-Seq v3 Ultra Low Input RNA Kit (Clontech) followed by Nextera library preparation were used to prepare Illumina-compatible sequencing libraries. Quality of all RNA were evaluated with BioAnalyser 2100 (Agilent). Single-end reads were obtained on an Illumina HiSeq 2500 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample. Sequencing quality was measured with fastp (Chen et al., 2018). Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21(Dobin et al., 2013; Frankish et al., 2019). Differential gene expression analysis was performed in R(Team, 2020) using the edgeR package (Robinson et al., 2010).

treatment_protocol: Two hundred thousand purified human B cells were cultured  with medium, CXCL4 (10?g/ml), CpG1018 (0.15?M) alone or with CXCL4 (10?g/ml) for 6h.

value: Blood

value: B Cell

value: Male


title: WGBS_BJ Fibroblast, EP rep 2

description:
Bisulfite converted total DNA
Early passage BJ Fibroblast cells


title: WGBS_BJ Fibroblast, EP rep 1


title: S-HCV

source_name: S-HCV


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-2


title: ev_DC_2

value: DC


title: B Cell, Medium, Donor 3


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-16


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-15


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-9


title: Bone marrow cells, OE_K27me3-2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Raw sequencing reads were first trimmed using Trim Galore to remove low-quality and adapter bases.
bowtie2.3.5 for reads alignment and counts summary
The non-primary alignment, PCR duplicates, and blacklist regions were removed by Samtools (v1.9), Picard “MarkDuplicates” function (ver 2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g mm --keep-dup 1)
The distribution of peaks was calculated by “annotatePeak” function of HOMER (Hypergeometric Optimization of Motif Enrichment)
Deeptools (v3.3.0) was used to make bigwig files (--normalize Using RPKM)
Assembly: mm10
Supplementary files format and content: bigwig files include annotated peaks
Library strategy: CUT&RUN

source_name: Bone marrow cells

extract_protocol:
CUT&RUN assay was performed with a commercially available kit according to manufacturer’s instruction (EpiCypher Cat# 15-1116).
NEB Ultra II DNA Library Prep Kit

value: bone marrow cells

value: 2 months

value: Female

value: Evi1 overexpressing

tag: ip antibody


title: Huh7.5.1

value: control


title: Bone marrow cells, OE_K27me3-1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-13


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-12


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-11


title: B Cell, CpG 1018 + CXCL4, Donor 5


title: Bone marrow cells, WT_K27me3-2

value: WT


title: B Cell, CpG 1018 + CXCL4, Donor 2


title: B Cell, CXCL4, Donor 3


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-10


title: BrainCell_Enhancer-eHGT_078h_MouseID-454782_Cell-4


title: B Cell, CpG 1018, Donor 3


title: B Cell, CpG 1018, Donor 5


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-8


title: Bone marrow cells, WT_K27me3-1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-14


title: Bone marrow cells, OE_FLAG-2

value: FLAG


title: B Cell, CpG 1018, Donor 2


title: WGBS_BJ Fibroblast, hTERT, rep 1

description:
Bisulfite converted total DNA
BJ Fibroblast cells transduced with hTERT

value: Neonatal Foreskin

value: BJ Fibroblast

value: Fibroblast

value: hTERT overexpression


title: Bone marrow cells, OE_FLAG-1


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-6

value: VISp


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-5


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-4


title: Bone marrow cells, OE_IgG

value: IgG


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-3


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-2


title: B Cell, Medium, Donor 2

value: Blood


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-1


title: B Cell, CXCL4, Donor 5

value: B Cell


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-9


title: BrainCell_Enhancer-eHGT_078h_MouseID-453328_Cell-7


title: B Cell, CXCL4, Donor 2


title: Primary cortical microglia, SNI sEVs, biol rep 3

city: Philadelphia

first: Seena

last: Ajit

state: PA

department: Pharmacology & Physiology

institute: Drexel University

data_processing:
Binary base call (BCL) files generated by the sequencing platform were converted to standard FASTQ file formats for downstream analysis by bcl2fastq conversion software with adapter trimming/
Reads were mapped against the mm10 mouse reference genome using Burrows-Wheeler Aligner (BWA).
Gene counts were derived from the number of uniquely mapped reads by Subread:featureCount (version 2.0.2).
Gene counts were normalized to transcripts per kilobase million (TPM).
Low expressed genes (TPM <1) across all samples were filtered out.
Assembly: mm10
Supplementary files format and content: An xlsx file include TPM values of each replicate and differentially expressed genes between pairs of experimental groups.

source_name: Primary cortical microglia

growth_protocol: Primary cortical microglia isolated from cortices of CD-1 mouse pups (postnatal day 2-4) were maintained in DMEM supplemented with 10% fetal bovine serum and 1X penicillinstreptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using the mirVana kit (Life Technologies) according to manufacturer's instructions with on-column DNAse.
cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA High Throughput Library Prep Kit following the manufacturer's protocol.

treatment_protocol: Primary cortical microglia were treated with 1 µg of sham or SNI sEVs, or PBS control in DMEM supplemented with 10% exosome-depleted FBS and 1X penicillin-streptomycin for 24 h.

value: Primary cortical microglia

value: SNI sEVs


title: Primary cortical microglia, SNI sEVs, biol rep 1


title: lung, sorted Schwann cells, LPS treated, replicate1, scRNAseq

city: South San Francisco

first: Josh

last: Kaminker

state: CA

address: 1 DNA Way

department: OMNI Bx, gRED

institute: Genentech Inc

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: h5 files

source_name: lung

extract_protocol:
Upon CO2 euthanasia, serum was collected, and lungs were perfused with 1X PBS-EDTA, via the right ventricle. All lung samples per cohort were processed at the same time by transferring the lungs in c-tubes (Miltenyi) and adding 5mL of digestion media consisting of 0.05% Liberase, 0.1% DNAse I (Roche), 1% BSA (Sigma), 0.1% Dispase II (Sigma) in RPMI. Samples were digested using MACS Miltenyi Dissociator using lung dissociation settings, and incubating samples at 37 degrees celsius for 30 minutes in a shaker at 120 rpm. After digestion incubation, samples were further homogenized using the lung dissociation settings, the supernatants were obtained and centrifuged for 1600rpm for 5mins. The pelleted supernatants were ACK treated followed by resuspension in 1X PBS and passed through a 40um cell strainer. Samples were pelleted, and resuspended in 1X PBS, stained with LIVE/DEAD fixable dye (Invitrogen) at a 1:1000 dilution, incubated on ice for 15 minutes, washed in 1X PBS, resuspended in FACS buffer (PBS + 2.5mM EDTA + 5% BSA) with FcR block (Miltenyi), and stained with the appropriate conjugated fluro-antibodies. Antibodies used: anti-CD45-BV650 (BD cat. 563410), anti-CD31-BV421 (BD cat. 563356), anti-EPCAM-BUV396 (BD cat. 740281).
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

treatment_protocol: For acute lung inflammation study, Oropharyngeal Aspiration (OA) of 50uL PBS for 2hrs, or 50uL of LPS at 0.2mg/kg for 2hrs were used.

value: lung

value: 12-16 weeks

value: female

value: LPS


title: lung, sorted Schwann cells, LPS treated, replicate2, scRNAseq

description: 10X genomics


title: Primary cortical microglia, SNI sEVs, biol rep 2


title: Primary cortical microglia, sham sEVs, biol rep 3

value: sham sEVs


title: lung, sorted Schwann cells, PBS treated, replicate1, scRNAseq

description: 10X genomics

value: PBS


title: Sample 8_NHU12

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

data_processing:
Sequencer: Illumina HiSeq 2500
Read length: 100x100bp
Tool and Alignment method : STAR-2.5.3a
Method: Global alignment - No mismatch in seed alignment (of size 22), 3 mismatches in read length
Data were integrated using Deseq2 default parameters and VST normalisation.
Genome_build: human hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include Deseq2 values for all samples (sample as column)

extract_protocol:
Cell lines RNA were extracted using Qiagen RNeasy kit coupled with DNAse treatment.
RNA sequencing libraries were prepared from 1µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit (Illumina) which allows to perform a strand specific RNA sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification was finally achieved to create the final cDNA library (12 cycles). The resulting barcoded libraries were then equimolarly pooled and quantified using a qPCR method (KAPA library quantification kit, Roche). The sequencing was carried out using paired-end mode (PE100) on a Illumina HiSeq2000 instrument. The sequencing configuration was set to reach an average of 100 million paired-reads per sample.

value: Normal Human Urothelium Culture


title: lung, sorted Schwann cells, PBS treated, replicate2, scRNAseq

description: 10X genomics


title: B Cell, Medium, Donor 5

value: Female


title: Sample 7_NHU11


title: Primary cortical microglia, sham sEVs, biol rep 1


title: Sample 5_Bladder Cell line SD48

value: bladder human cell line


title: Sample 6_Bladder Cell line 5637


title: Primary cortical microglia, sham sEVs, biol rep 2


title: PBMCs, YTg BMCs, replicate 4

city: Chongqing

first: Yun-feng

last: Tu

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing

department: Daping Hospital

institute: Third Military Medical University

description:
Tg_3m_4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 with default parameters. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
PBMCs were isolated by density gradient centrifugation using Ficoll-Hypaque (TBD Science, Tianjin, China), and mononuclear sections were collected and washed three times by PBS. Then the PBMCs were processed for scRNA-seq.
Library  was performed according to the manufacter’s instructions (single cell 3’ Reagent Kits v3.1 (Dual Index)  protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and  loaded together with partitioning oil and gel beads into the chip to generate  the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained  in every single GEM was retrotranscripted to cDNA, which contains an Ilumina  R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.  The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified  by PCR and the apropiated sized fragments were selected with SPRIselect  reagent for subsequent library construction. During the library construction  Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences  and a sample index were added.

value: PBMCs

value: 12 mounth

value: bone marrow transplantation


title: PBMCs, control OTg, replicate 3

description:
Tg_12m_3
10x Genomics

value: control


title: PBMCs, control OTg, replicate 2

description:
Tg_12m_2
10x Genomics


title: PBMCs, control OTg, replicate 4

description:
Tg_12m_4
10x Genomics


title: PBMCs, control OTg, replicate 1

description:
Tg_12m_1
10x Genomics


title: Primary cortical microglia, PBS, biol rep 4


title: Sample 4_Bladder Cell line L1207 rep 2


title: PBMCs, YTg BMCs, replicate 3

description:
Tg_3m_3
10x Genomics


title: Primary cortical microglia, PBS, biol rep 3


title: lung, sorted Schwann cells, LPS treated, replicate3, scRNAseq

description: 10X genomics


title: lung, sorted Schwann cells, PBS treated, replicate3, scRNAseq

description: 10X genomics


title: PBMCs, YTg BMCs, replicate 1

description:
Tg_3m_1
10x Genomics


title: Primary cortical microglia, PBS, biol rep 2


title: Sample 2_Bladder Cell line RT112 rep 2


title: PBMCs, control YTg, replicate 3

description:
Tg_2m_3
10x Genomics

value: 2 mounth


title: Sample 3_Bladder Cell line L1207 rep 1


title: Primary cortical microglia, PBS, biol rep 1


title: PBMCs, control YTg, replicate 2

description:
Tg_2m_2
10x Genomics


title: Bone marrow cells, Evi1-3

data_processing:
Quality check of raw reads and alignment by picard and hisat2
featureCounts v2.0.3 for count extraction
Reads count data were processed using R "edgeR" package for filtering and normalization
Assembly: mm10
Supplementary files format and content: tab-delimited file includes normalized count for each sample: cpm Evi1-LK.txt

extract_protocol:
The cells were lysated by Trizol and total RNA was extracted by phenol-chloroform.
Illumina RNA-Seq libraries (Poly A)

value: bone marrow cells

value: 2 months

value: Evi1 overexpressing


title: Bone marrow cells, Evi1-2


title: Sample 1_Bladder Cell line RT112 rep 1


title: Bone marrow cells, WT-3

value: WT


title: Bone marrow cells, WT-2


title: Mutu bulk RNA-seq

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave

institute: Tulane University

description:
Sample 7
bulk RNA-seq

data_processing:
For scRNA-seq, demultiplexing, alignment, and quantification were performed using the Chromium Cell Ranger pipeline (v1.1.0). Counts per gene were calculated with respect to the Ensembl reference transcriptome (v85).
For CAGE, alignment was performed using STAR (v2.5.2a).
Genome_build: GRCh38 + EBV Akata (Genbank KC207813.1)
Supplementary_files_format_and_content: scRNA-seq counts (UMIs per gene per cell)

source_name: Mutu cells

extract_protocol: Whole-cell RNA was extracted using TRIzol reagent and cDNA libraries were generated using standard Illumina protocols. Libraries were sequenced on Illumina HiSeq 2500 sequencers.

value: Burkitt lymphoma

value: EBV


title: PBMCs, YTg BMCs, replicate 2

description:
Tg_3m_2
10x Genomics


title: YCCEL1 CAGE 2

description:
Sample 6b
CAGE

source_name: YCCEL1 cells

extract_protocol: Whole-cell RNA was extracted using TRIzol reagent (Life Technologies, catalog no. 15596-018), according to the vendor's protocol, and no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) were prepared. Libraries were sequenced on Illumina HiSeq 2500 sequencers.

value: gastric carcinoma


title: CD8+ T cell, co-cultured with 4T1 cells with acetate, Day3, rep3

city: Guangzhou

first: Wanyu

last: Hu

address: 1838 Guangzhou Avenue North

institute: Southern medical university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
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.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0).
Assembly: HISAT2 v2.0.5
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was isolated from purified CD8+ T cells with trizol reagent (Ambion) according to manufacturer instructions  and quantified using Qubit 2.0 (Thermo Fisher Scientific) following the manufacturer’s instructions.
Libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit  for Illumina® (NEB, USA) and sequenced in a novaseq 6000 (Illumina) by the deep-sequencing facility at the Novogene.

value: spleen

value: CD8+ T cell

value: Cytotoxic T lymphocyte

value: co-cultured with 4T1 cells with acetate


title: CD8+ T cell, co-cultured with 4T1 cells with acetate, Day3, rep2


title: PBMCs, control YTg, replicate 4

description:
Tg_2m_4
10x Genomics


title: SNU719 CAGE 1

description:
Sample 5a
CAGE

source_name: SNU719 cells


title: CD8+ T cell, co-cultured with 4T1 cells with acetate, Day3, rep1


title: Mutu CAGE 2

description:
Sample 4b
CAGE


title: CD8+ T cell, co-cultured with 4T1 cells with acetate, Day3, rep5


title: CD8+ T cell, co-cultured with 4T1 cells, Day3, rep4

value: co-cultured with 4T1 cells


title: CD8+ T cell, co-cultured with 4T1 cells with acetate, Day3, rep4


title: Mutu CAGE 1

description:
Sample 4a
CAGE


title: CD8+ T cell, co-cultured with 4T1 cells, Day3, rep3


title: CD8+ T cell, co-cultured with 4T1 cells, Day3, rep5


title: Akata CAGE 2

description:
Sample 3b
CAGE

source_name: Akata cells


title: CD8+ T cell, co-cultured with 4T1 cells, Day3, rep2


title: Bone marrow cells, Evi1-1

value: Female


title: CD8+ T cell, co-cultured with 4T1 cells, Day3, rep1


title: Akata CAGE 1

description:
Sample 3a
CAGE


title: PBMCs, control YTg, replicate 1

description:
Tg_2m_1
10x Genomics

value: PBMCs


title: mgR, male, scRNAseq

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the  cellranger-6.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Aortic

extract_protocol:
Aortic tissues of each genotype and treatment arm were pooled together, cleaned, minced and digested in Hank’s balanced salt solution containing elastase (0.5 mg/mL) and collagenase A  for 1 h at 37°C and then passed through a 40 μm filter. Single-cell suspensions were incubated with eBioscience 1X RBC Lysis Buffer for 3 min, collected in PBS containing 1% UltraPure BSA .
Library was performed according to the manufacter’s instructions(Chromium Next GEM Single Cell 3’ Reagent Kits v3.1, 10X Genomics).

treatment_protocol: Drug treatment included Fbn1mgR/mgR mice that received either losartan (0.6 g/L; LKT Labs) or vehicle through drinking water from P16.

tag: gender

value: male

value: Aortic

value: mgR


title: WT, male, scRNAseq

description: 10x Genomics


title: mgR-LOS, male, scRNAseq

description: 10x Genomics

value: mgR-LOS


title: Bone marrow cells, WT-1

value: bone marrow cells

value: 2 months


title: YCCEL1 CAGE 1

description:
Sample 6a
CAGE


title: SNU719 CAGE 2

description:
Sample 5b
CAGE


title: Mutu scRNA-seq

description:
Sample 1
single-cell RNA-seq

extract_protocol: Individual cells were isolated with the droplet-based Chromium single-cell 3' platform (10X Genomics). Briefly, cells were isolated in gel beads, RNA from each cell was barcoded and reverse-transcribed, and the barcoded cDNA was amplified in bulk. Libraries were sequenced on Illumina HiSeq 2500 sequencers.


title: LSK cells, Evi1-OE-3

data_processing:
Quality check of raw reads by Pre-alignment QA/QC
STAR V2.6.1d for reads alignment and counts summary
Reads count data were processed using Partek flow CPM method for cpm normalization
Assembly: mm10
Supplementary files format and content: tab-delimited text file: Partek_Tg_evi1-LSK-BMT-Normalization_Normalized_counts.txt

value: 4 months

value: transplanted with Evi1-OE BM cells

tag: sorted cell type

value: LSK cells


title: LSK cells, Evi1-OE-2


title: LSK cells, WT-3

value: transplanted with WT BM cells


title: LSK cells, Evi1-OE-1


title: liver

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

data_processing:
Raw reads were aligned to zebrafish reference genome (genome reference: GRCz11; annotation reference: GRCz11.103) combined with the sequences for DsRedx using the Cell Ranger pipelines (v6.0).
Downstream analysis of unique molecular identifiers (UMI) count matrix was conducted in R using the Seurat pipeline (v4.0.5).
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: liver

extract_protocol:
For each organ, six sex-balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI-mpeg1.1-DsRedx+ cells were sorted into 5 μl collection buffer (4.5 μl 1% BSA/PBS + 0.5 μl RNaseOUT) using BD Influx high-speed Cell Sorter (BD Biosciences).
scRNA-seq was carried out with a 10X Chromium single cell platform (10X Genomics). In brief, after the cell sorting, single-cell suspensions were prepared according to the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single-cell Gel Beads-in-emulsion (GEMs). Libraries were prepared using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System, followed by sequencing on Illumina Novaseq 6000 system (Illumina) for a targeting average depth of around 100,000 read pairs per cell.

value: liver

value: 6 months old

value: mpeg1.1+ cells

value: WT


title: intestine

source_name: intestine

value: intestine


title: heart

source_name: heart

value: heart


title: brain

source_name: brain

value: brain


title: gill

source_name: gill

value: gill


title: epidermis

source_name: epidermis

value: epidermis


title: LSK cells, WT-1

value: Female


title: SNU719 scRNA-seq

description:
Sample 2
single-cell RNA-seq

value: gastric carcinoma

value: EBV


title: scrMedin_3

city: Phoenix

first: Raymond

last: Migrino

state: Arizona

address: 650 E Indian School Rd

institute: Phoenix Veterans Affairs Health Care System

data_processing:
The raw sequencing data was processed using Cutadapt (v4.3) to remove adapter sequences.
The quality of the processed data was checked with FASTQC (v0.12.1).
Processed reads were then mapped to the human reference genome (GRCh38.p13) using STAR (v2.7.10b) with the Ensembl 106 annotation file to obtain the gene counts for each sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: HBMVEC

extract_protocol:
BIO-RAD Aurum Total RNA Mini Kit was using to extract RNA.
RNA sequencing library preparation were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).

value: HBMVEC

value: scrmedin


title: AB_3

value: ab


title: NL_3

value: nl


title: Sox17_HTO

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

description:
10x Genomics
WT Cell hashing oligo sequence: ACCCACCAGTAAGAC, cKO Cell Hashing oligo sequence: GGTCGAGAGCATTCA

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

extract_protocol:
WT and Sox17 cKO lung were digested to generate single cell suspension. 2 million cells from WT and cKO mice were labeled with Cell Hashing antibodies. Equal amount of cells were combined and loaded on 10X Genomics Chromium Controller for single cell RNA sequencing analysis.
follow the protocol provided by 10X Genomics for feature bacording single-cell RNA seq analysis

value: lung

value: 8 weeks old

value: multiplexed sample:WT and Sox17 cKO


title: Sox17_GEX


title: Medin_NL_3


title: Medin_3

value: medin


title: Medin_AB_3


title: AB_2


title: Vehicle_3

value: vehicle


title: scrMedin_2

description: outlier


title: NL_2


title: Medin_2


title: Medin_NL_2


title: Medin_AB_2


title: BJ Fibroblast, HRAS, rep 3

description:
BJ Fibroblast cells transduced with hTERT,  SV40, and HRAS
HRAS3

data_processing:
Reads were trimmed and adapters were removed using cutadapt using the –minimum-length 1 and -q 20 flags. The adapter sequences were -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCCGTCTTCTGCTTG and -A AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT.
Trimmed reads were aligned to hg38 using STAR with the following flags: --sjdbOverhang 100. The GENCODEv21 and RepeatMasker GTF annotation files used for alignment.
To determine gene and TE subfamily-level read counts, TEtranscripts (V. 2.2.1)  was run with the following flags: --format BAM –mode multi –stranded reverse –GTF.
To determine locus-specific TE read counts, Telescope  was run in a Conda environment with the following dependencies: python=3.6 future pyyaml cython=0.29.7 numpy=1.16.3 scipy=1.2.1 pysam=0.15.2 htslib=1.9 intervaltree=3.0.2 The “telescope assign” command was used with default parameters to quantify TE expression.
Assembly: hg38
Supplementary files format and content: TEtranscripts_combined_cntTable.txt - tab delimited file gives raw read counts for each sample from TEtranscrips analysis (gene and TE subfamily-level data)
Supplementary files format and content: telescope_combined_cntTable.txt - tab delimited file gives raw read counts for each sample from Telescope analysis (locus-specific TE data)

source_name: Neonatal Foreskin

extract_protocol:
Total RNA was extracted from cell pellets using Trizol (Thermo Scientific 15596026). Ribosomal RNA was depleted using Ribozero (Illumina)
Libraries were  prepared by following the manufacturer’s protocol for the Illumina TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat kit (P/N 20020596). Custom 10 bp UDI TruSeq-Compatible Duplex Y Adapters from IDT were used to index the libraries (IDT10_UDI_1 through IDT10_UDI_15)

value: Neonatal Foreskin

value: BJ Fibroblast

value: Fibroblast

value: hTERT, SV40, HRAS overexpression


title: LSK cells, WT-2

source_name: Bone marrow cells

value: bone marrow cells

value: 4 months

value: transplanted with WT BM cells

value: LSK cells


title: BJ Fibroblast, HRAS, rep 2

description:
BJ Fibroblast cells transduced with hTERT,  SV40, and HRAS
HRAS2


title: Vehicle_2

value: HBMVEC


title: scrMedin_1

value: scrmedin


title: BJ Fibroblast, HRAS, rep 1

description:
BJ Fibroblast cells transduced with hTERT,  SV40, and HRAS
HRAS1


title: BJ Fibroblast, SV40, rep 3

description:
BJ Fibroblast cells transduced with hTERT and SV40
SV403

value: hTERT, SV40 overexpression


title: Medin_AB_1


title: AB_1

value: ab


title: NL_1

value: nl


title: BJ Fibroblast, SV40, rep 2

description:
BJ Fibroblast cells transduced with hTERT and SV40
SV402


title: BJ Fibroblast, hTERT, rep 3

description:
BJ Fibroblast cells transduced with hTERT
hTERT3

value: hTERT overexpression


title: BJ Fibroblast, SV40, rep 1

description:
BJ Fibroblast cells transduced with hTERT and SV40
SV401


title: Medin_NL_1


title: BJ Fibroblast, hTERT, rep 2

description:
BJ Fibroblast cells transduced with hTERT
hTERT2


title: iNCs

city: Sapporo

first: Atsushi

last: Tomokiyo

state: Hokkaido

address: Kita13 Nishi7, Kita-ku

institute: Hokkaido University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: Human iPS cells-derived neural crest-like cells

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using ExScript RT reagent kit (Takara) according to the manufacturer's instructions.


title: iPDLSCs

source_name: Human iPS cells-derived periodontal ligament stem cell-like cells


title: Medin_1


title: Vehicle_1


title: BJ Fibroblast, hTERT, rep 1

description:
BJ Fibroblast cells transduced with hTERT
hTERT1


title: BJ Fibroblast, EP

description:
Early passage BJ Fibroblast cells
EP

value: WT


title: lung, cultured Schwann cells, LPS treated, replicate3, bulk RNAseq

data_processing:
The fastq sequence files for all RNA-seq samples were filtered for read quality and ribosomal RNA contamination. The remaining reads were then aligned to the mouse reference genome (GRCm38) using the GSNAP alignment tool(19). Alignments were produced using the following GSNAP parameters: ‘-M 2 n 10 -B 2 -i 1 N 1 w 200000 -E 1 –pairmax-rna = 200000 –clip-overlap’. These steps, and the downstream processing of the resulting alignments to obtain read counts and normalized Reads Per Kilobase Million (nRPKMs) per gene (over all exons of RefSeq gene models), are implemented in the Bioconductor package, HTSeqGenie (v 3.12.0). Only uniquely mapped reads were used for further analysis.
Assembly: GRCm38
Supplementary files format and content: The tab-delimited text files contain 4 columns: entrez gene IDs, gene counts, gene length, and RPKM values

source_name: Schwann cells

growth_protocol: SCs were sorted from hGFAP-tdTomato mice by selecting for CD45-EPCAM-CD31-tdTomato high cells, cultured for 8 days in DMEM plus 10% Fetal Bovine Serum (Invitrogen), 1 X Penicillin/Gentamycin (Invitrogen)

extract_protocol:
After stimulations, RNA was harvested using the RNeasy Micro purification column kit (Qiagen). RNA quantification and purity was analyzed with NanoDrop 2000 (Thermo Scientific).
cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara catalog#: 634894). 150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina catalog#: FC-131-1024). Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific catalog#: Q32851) and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies catalog#: 5067-5582).

treatment_protocol: Cultured SCs were then stimulated with PBS or LPS 20ng/mL for 2 hrs.

value: Schwann cells

value: 12-16 weeks

value: female

value: LPS


title: lung, cultured Schwann cells, LPS treated, replicate1, bulk RNAseq


title: lung, cultured Schwann cells, LPS treated, replicate2, bulk RNAseq


title: Patient 3 [50231]

city: Jena

first: Romain

last: Sigaud

address: Am Klinikum 1

department: Pediatrics and Adolescent Medicine

institute: UKJ

data_processing:
Fastq files were  submitted to the RNAseqWorkflow pipeline on the OTP platform for automated reads trimming, mapping to the hg19/GRCh37 human genome, and calculation of TPM per transcript.
Assembly: hg19/GRCh37 human genome
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Brain tumor

extract_protocol:
RNA extraction was performed using the RNeasy Mini Kit (cat. no. 74104, Qiagen) following manufacturer’s protocol.
Library preparation was done using the Agilent SureSelect XT HS2 RNA kit

value: Brain tumor

value: Pilocytic astrocytoma


title: Patient 1 [HSJ-182]

extract_protocol:
RNA was isolated using AllPrep DNA/RNA/miRNA Universal kit (Qiagen), according to manufacturer’s instructions.
Library preparation was done using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs)

value: Juvenile Pilocytic astrocytoma


title: lung, cultured Schwann cells, PBS treated, replicate3, bulk RNAseq

value: PBS


title: Patient 2 [HSJ-169]

value: High grade astrocytoma


title: Patient 1 [38458]

value: Anaplastic pilocytic astrocytoma


title: lung, cultured Schwann cells, PBS treated, replicate2, bulk RNAseq


title: Patient 2 [39150]


title: lung, sorted Schwann cells, replicate2, scRNAseq

description: 10X genomics

source_name: lung

extract_protocol:
Upon CO2 euthanasia, serum was collected, and lungs were perfused with 1X PBS-EDTA, via the right ventricle. All lung samples per cohort were processed at the same time by transferring the lungs in c-tubes (Miltenyi) and adding 5mL of digestion media consisting of 0.05% Liberase, 0.1% DNAse I (Roche), 1% BSA (Sigma), 0.1% Dispase II (Sigma) in RPMI. Samples were digested using MACS Miltenyi Dissociator using lung dissociation settings, and incubating samples at 37 degrees celsius for 30 minutes in a shaker at 120 rpm. After digestion incubation, samples were further homogenized using the lung dissociation settings, the supernatants were obtained and centrifuged for 1600rpm for 5mins. The pelleted supernatants were ACK treated followed by resuspension in 1X PBS and passed through a 40um cell strainer. Samples were pelleted, and resuspended in 1X PBS, stained with LIVE/DEAD fixable dye (Invitrogen) at a 1:1000 dilution, incubated on ice for 15 minutes, washed in 1X PBS, resuspended in FACS buffer (PBS + 2.5mM EDTA + 5% BSA) with FcR block (Miltenyi), and stained with the appropriate conjugated fluro-antibodies. Antibodies used: anti-CD45-BV650 (BD cat. 563410), anti-CD31-BV421 (BD cat. 563356), anti-EPCAM-BUV396 (BD cat. 740281).
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics) were used for library preparation according to the manufacturer’s user guides. The Cell-RT mix was prepared to aim for 10,000 nuclei per sample and applied to the ChromiumTM Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles with v3.1), and library construction according to the user manual. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit and profiled by Bioanalyzer High Sensitivity DNA kit.

value: lung


title: HDF GATA2-MDmut+GF d6 - donor B

city: Lund

first: Ilia

last: Kurochkin

address: BMC A12, Sölvegatan 17

institute: Lund University

data_processing:
The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a hg38 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
The resulting expression matrix was used as input to the Seurat library v4.1.0
Assembly: hg38
Supplementary files format and content: 10x Gene Expression matrix

source_name: Skin

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

tag: donor

value: B

value: Skin

value: Human dermal fibroblasts

value: Fibroblasts

value: wildtype

value: Cells were sorted by FACS

tag: transduction

value: Cells were transducted with MDmut-GATA2 plus GFI1B and FOS

value: Cells were collected 6 days after viral transduction

value: sorted live cells (DAPI-)


title: HDF GATA2-MDmut+GF d6 - donor A

value: A


title: HDF GATA2-MDmut+GF d4 - donor B

value: Cells were collected 4 days after viral transduction


title: lung, sorted Schwann cells, replicate3, scRNAseq

description: 10X genomics

value: 12-16 weeks

value: female


title: lung, sorted Schwann cells, replicate1, scRNAseq

description: 10X genomics


title: HDF GATA2-MD+GF d6 - donor B

value: Cells were transducted with MD-GATA2 plus GFI1B and FOS


title: HDF GATA2-MD+GF d4 - donor B


title: HDF GATA2-MD+GF d6 - donor A


title: HDF GATA2-MD+GF d4 - donor A


title: HDF GATA2-MDmut+GF d4 - donor A


title: lung, cultured Schwann cells, PBS treated, replicate1, bulk RNAseq

value: Schwann cells

value: PBS


title: SBM-I3

city: Qinzhou City

first: Xin

last: Lu

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

institute: Beibu Gulf University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2 . FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples
Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expressiongene (DEGs)
Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar
Based on the hypergeometric distribution,O , KEGG pathway, Retme ,and WikiPathways enrichment analysis of DEGs were performed to screen the signifisignificantlycant enriched term using R (v 3.2.0),r espectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term.
Assembly: ID:15977
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Epinephelus fuscoguttatus x Epinephelus lanceolatus

source_name: Intestinal

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Intestinal

tag: group

value: SBM


title: Drug-I3

value: Drug


title: FM-I2

value: FM


title: FM-I1


title: SBM-I1


title: FM-I3


title: SBM-I2


title: CRC-SC#1 sh71 KDM1A silenced replicate 1

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

description: CRC-SC#1_Sh rep 1

data_processing:
Fastq files were processed with Cutadapt v. 3.5 to trim TruSeq adapters
Trimmed Fastq files were analyzed with RSEM v. 1.3.1 in order to obtain normalized counts of expressed genes in TPM. RSEM has been launched using STAR aligner 2.7.1a
Reads were aligned against the human GRCh38 / hg38 genome (Ensembl_database)
RSEM was launched with the following parameters --strandedness reverse --calc-ci --ci-memory 12288 --estimate-rspd --append-names --paired-end –star
Assembly: human GRCh38 / hg38 annotated with Homo_sapiens.GRCh38.100.gtf (Ensembl_database)
Supplementary files format and content: normalized counts of genes in TPM in all samples obtained by RSEM.

source_name: Stem colorectal Cancer from patient

growth_protocol: Human CRC stem cell lines (CRC-SCs) CRC-SC#1 were cultured in suspension as colonospheres in stem cell medium (DMEM/F12, Gibco, Waltham, MA, USA) supplemented with EGF (10 μg/mL, PeproTech, Cranbury, NJ, USA) and FGF (20 μg/mL, PeproTech, Cranbury, NJ, USA), N2 and B27 (Gibco, Waltham, MA, USA), 1 mmol/L nicotinamide (Sigma-Aldrich, Saint Louis, MO, USA) and 1% antibiotics–antimycotics (penicillin, streptomycin, and amphotericin; Sigma-Aldrich, Saint Louis, MO, USA).

extract_protocol:
Extraction of total RNA from CRC-SC#1 cells was performed using the miRNeasy® Mini Kit (Cat No./ID: 217004 QIAGEN, Venlo, The Netherlands), according to the manufacturer’s instructions.
500ng of high quality RNA (RIN>9) was used to prepare RNA-libraries using TruSeq Stranded Total RNA Kit (Illumina) according to manufacturer’s instructions

treatment_protocol: To generate stable KDM1A-knockdown cell lines we used MISSIONpLKO.1-puro Empty Vector Plasmid DNA (Sigma-Aldrich) harboring either the sequence targeting human LSD1 (TRCN0000046071; here sh71) or a nontargeting short hairpin RNA (shRNA) (SHC002; here shNT). 500 000 CRC-SCs were plated in an ultra-low 24 well plate and transduced with lentiviral particles in the presence of 6µg/ml polybrene (Sigma-Aldrich, Saint Louis, MO, USA). Spinoculation protocol was performed as follows: the plate was centrifuged for 1 hour at 37°C, 1800 rpm. Subsequently, cells were resuspended and incubated for 1 hour (37°C, 5% CO2); lastly, medium containing viral particles was removed, and cells were resuspended in a fresh medium and incubated overnight (37°C, 5% CO2). The following day, 1.5 µg/ml puromycin was added to each well for selection.

value: Human CRC stem cell line (CRC-SCs)

value: shRNA anti-KDM1A (sh71)


title: CRC-SC#1 sh71 KDM1A silenced replicate 2

description: CRC-SC#1_Sh rep 2


title: HDF donor A

value: Skin

tag: cell line

value: Human dermal fibroblasts

value: Fibroblasts

value: wildtype

value: Cells were sorted by FACS


title: Drug-I2


title: Drug-I1


title: CRC-SC#1 shNT replicate 1

description: CRC-SC#1 shNT rep 1

tag: cell type

value: scramble shRNA (shNT)


title: CRC-SC#1 shNT replicate 2

description: CRC-SC#1 shNT rep 2


title: HDF donor B

value: B

tag: tissue

value: sorted live cells (DAPI-)


title: Tyg, replicate 1

city: Wuerzburg

first: Alexander

middle: J

last: Westermann

address: Am Hubland

department: Department of Microbiology, Biocenter

institute: University of Wuerzburg

data_processing:
Sequenced reads were adapter- and quality- trimmed with BBDuk, using the following parameters: k=13 mink=5 rcomp=t lit-eral=ACACTCTTTCCCTACACGACGCTCTTCCGATCT,GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT hdist=1 ktrim=r minlen=100 tbo. Trimmed reads were merged with BBMerge, using parameters mininsert=120 maxloose=t. The abundance of each CRISPRi mutant within the merged reads was determined with a custom Python script.
Assembly: Custom reference of all designed gRNA/array sequences.
Supplementary files format and content: Tab separated file of gRNA/array name and read count
Library strategy: DNA-seq

organism: Bacteroides thetaiotaomicron

source_name: bacterial culture

extract_protocol:
After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The PCR amplified samples were purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and were analyzed by capillary electrophoresis
We incubated the culture at 37°C until it reached the indicated OD, at which point we took a 2 mL aliquot, pelleted it, discarded the supernatant, and stored the bacterial samples at -20°C until further processing.  Bacterial pellets were resuspended in 100 μL of PBS containing 250 μg lysozyme, mixed with 100 μL lysis buffer (100 mM Tris-HCl pH 8.5, 200 mM NaCl, 0.2% SDS, 5 mM EDTA), and lysed by incu-bating at 37°C for 5 min. Proteins were then degraded by addition of 1 μL of Proteinase K (NEB #P8107) and incubation at 56°C for 30 min, following which RNA was digested with 0.5 μL of RNase A (Thermo #EN0531) and incubation at 56°C for 5 min. The remaining gDNA was purified from each sample via phenol-chloroform extraction, followed by ethanol precipitation.  The genomic regions coding for gRNAs and arrays were PCR-amplified in a 50 µL reaction con-taining 100 ng gDNA with oligonucleotides AWO-577/AWO-578 (annealing temperature: 55°C) and AWO-575/AWO-576 (annealing temperature: 63°C).

value: bacterial culture

value: Rich medium (TYG)


title: Tyg, replicate 3


title: Tyg, replicate 2


title: Tyg bile salts, replicate 3

value: Rich medium (TYG) + 0.5 mg/mL bile salts


title: Tyg bile salts, replicate 2


title: Tyg bile salts, replicate 1


title: Arabidopsis, FLAG tag wild type RGA in ga1 dP [FRGAgdP mock 1h-R1 ]

city: Durham

first: Hao

last: Tian

state: North Carolina

address: Science drive 124

department: Biology

institute: Duke University

data_processing:
Basecalls were performed using Illumina platform output.
Quality trimming and adapters removal were performed using Trim Galore v0.6.4.
The reads were mapped to TAIR10 Arabidopsis reference genome using bowtie2 v 2.4.4
Subsequently, the organelle genomes were removed using samtools v1.122. PCR duplicates were discarded from the mapped reads using samblaster v0.1.26
Blacklisted genomic regions and were removed from the mapped BAM files using samtools and the independent biological replicates were merged using samtools
Then, Tn5 hypersensitive sites (THS) were identified using MACS2 with the parameters: --nomodel –shift -100 –extsize 200 -q 0.05.
The accessibility signals were normalized using the bamCoverage from deepTools v3.5.1
The normalized accessibility signals across whole Arabidopsis genome regions were generated using computeMatrix and plotProfile from deepTools
The differential accessibility regions (DARs) were identified using the R package “DiffBind v3.8.4
Assembly: Arabidopsis thaliana
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown in the long day conditions on MS plates for 10 days.

extract_protocol:
Nuclei purification using sucrose sedimentation for ATAC-seq libraries preparation
ATAC-seq libraries were prepared using the protocol from Greenleaf, W. J lab and Kieber, J. J lab with slight modifications.200 mg of ground tissue was used. and 400 μL of chromatin and incubated at 4 °C with rotation for 2 hr.

treatment_protocol: Treated with 1μM GA or mock for 1h

value: seedlings

tag: genotype

value: wild type RGA

value: mock for 1h


title: Arabidopsis, FLAG tag mutant RGA in sly1 dP [Frga11sdP-R1]

value: mutant RGA


title: Arabidopsis, FLAG tag wild type RGA in ga1 dP [FRGAgdP GA 1h-R2]

tag: treatment

value: 1μM GA


title: Arabidopsis, FLAG tag wild type RGA in ga1 dP [FRGAgdP GA 1h-R1 ]


title: Arabidopsis, FLAG tag wild type RGA in ga1 dP [FRGAgdP mock 1h-R2]


title: Arabidopsis, FLAG tag wild type RGA in sly1 dP [FRGAsdP-R2]


title: Ctrl(DMSO)_72h dataset 2

city: Sendai-shi

first: Susumu

last: Suzuki

institute: Tohoku Medical and Pharmaceutical University

description: Affymetrix Clariom™ D Assay human

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).

source_name: NB4 cell

label_protocol: standard Affymetrix protocol

growth_protocol: RPMI containing 10% heat-inactivated fetal bovine serum (FBS) under 5% CO2 at 37°C in a humidified atmosphere.

extract_protocol: RNA extraction was performed using Sepasol®-RNA I Super G (nacali tesque) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 2-3×10^5 cells/ml and treated with DMSO and 10 µM Triciribine (TCN) for 72h.

value: acute promyelocytic leukemia


title: Arabidopsis, FLAG tag mutant RGA in sly1 dP [Frga11sdP-R2]


title: TCN 10 µM_72h dateset 2

description: Affymetrix Clariom™ D Assay human


title: Arabidopsis, control of Frga11 sly1 dP

description: sly1 dP

data_processing:
Basecalls were performed using Illumina platform output.
ChIP-seq reads were trimmed until the final base had a quality score ≥ 30, using Trimmomatic v0.39, discarding reads left with < 20 bp
ChIP-seq reads were aligned to he Arabidopsis reference genome (TAIR10) with bowtie2 (v.2.4.5). Only uniquely mapping reads with at most two mismatches were retained.
Binding peaks were identified using MACS (v.2.2.7.1) with default parameters except for ‘-f BAMPE’ to model peaks from paired-ends ChIP-seq data, comparing FLAG-RGA and FLAG-(rga-11) to their respective controls without FLAG tags (sdQ for FLAG-RGA, and sdP for FLAG-(rga-11)).
After removing peaks from a small number of genomic regions where the mapped ChIP-seq read depth were consistently high across all samples including controls, we selected peaks with q-values < 10−3. Among them, we considered peaks with the fold enrichment values higher than GID1B
The cumulative ratio of FLAG-RGA and FLAG-(rga-11) read depth within 1.5Kb of all high-confidence peaks were visualized using deeptools (v. 3.1.3).
Assembly: TAIR10
Supplementary files format and content: narrowPeak and bed file

growth_protocol: Arabidopsis seedlings were grown in the continuous light on MS plates for 10 days.

extract_protocol:
Tissue were fixed with 1% formaldehyde for 20 minutes. After cell lysis, chromatin was sonicated using Bioruptor (High power, 1 cycle = on-30 sec / off-30 sec).
ChIP-seq libraries were prepared using the protocol in our lab.100-200 mg of ground tissue was used and 400 μL of chromatin and incubated at 4 °C with rotation for 2 hr.

tag: chip antibody

value: FLAG-M2-Agarose beads (Sigma-Aldrich)


title: Arabidopsis, control of FRGA sly1 dP

description: RGA sly1 dQ


title: Arabidopsis, FLAG tag mutant RGA in sly1 dP

description: Frga11 sly1 dP


title: Arabidopsis, FLAG tag wild type RGA in sly1 dP [FRGAsdP-R1 ]


title: Arabidopsis, FLAG tag wild type RGA in sly1 dP

description: FRGA sly1 dP


title: WT, 24h, rep2

city: Freiburg im Breisgau

first: Manuel

last: Brenes-Álvarez

address: Schänzlestraße 1

department: Genetics and Experimental Bioinformatics

institute: University of Freiburg

data_processing:
Quality control was performed using FASTQC
Reads were aligned to Nostoc genome using HISAT2 (parameter –no-spliced-alignment)
Fragments associated to transcriptional units predicted in this study were counted using Htseq (parameter -m union).
Assembly: Reads were aligned to Nostoc genome (GCA_000009705.1) and raw counts were associated to the transcriptional units predicted in this study included in gff file “transcriptional_units.gff”
Supplementary files format and content: tab-delimited text files include raw counts associated to transcriptional units predicted in this study.

organism: Nostoc sp. PCC 7120 = FACHB-418

source_name: bacterial cells

growth_protocol: Cultures of Nostoc sp. PCC 7120 wild type were bubbled with an CO2/air mixture (1% v/v) and grown photoautotrophically at 30ºC in BG11 medium containing ferric citrate instead of ammonium ferric citrate, lacking NaNO3 but containing 6 mM NH4Cl, 10 mM NaHCO3, and 12 mM N-tris (hydroxymethyl) methyl-2-aminoethanesulfonic acid-NaOH buffer (pH 7.5).

extract_protocol:
Total RNA was isolated using hot phenol, phenol-chloroform and chloroform extractions. Total RNA was later treated with Turbo DNAse (Ambion) to eliminate DNA traces.
RNA libraries for RNA-seq were prepared using Illumina Stranded TOTAL RNA preparation RIBO-ZERO PLUS kit following manufacturer's protocols.

treatment_protocol: Nitrogen deficiency was induced by filtering, washing and resuspending cells in nitrogen-free BG11 medium containing 10 mM NaHCO3.

value: bacterial cells

value: WT

value: Nitrogen deficiency

value: 24 hours


title: Liver, 72 h after partial hepatectomy, rep3 [Sample13]

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
FASTQ were aligned to the mouse genome build mm10 using the STAR aligner version 2.7.1a and sorted using samtools version 1.15.1.
BAM files were used to generate a gene-centric read count matrix with the software featureCounts version 1.6.4 using the gencode M6 primary assembly annotation (GTF file) using default parameters.
The count matrix (counts.txt) was imported into the R software (2022-01-07 r81454). The counts from the two sequencing lanes were aggregated for each sample and used for further analysis.
Assembly: mm10
Supplementary files format and content: Tab delimted text file from featureCounts with raw counts per gene.

source_name: Whole liver

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer's instructions.
The Illumina TruSeq stranded mRNA kit was used for multiplexed cDNA library generation using 500 ng of total RNA as input material. The multiplexed library was sequenced across two flowcell lanes.

value: Whole liver

tag: Sex

value: female

value: not-depleted, 72 h after partial hepatectomy


title: WT, 0h, rep2

value: control

tag: time

value: 0 hours


title: Liver, 72 h after partial hepatectomy, rep2 [Sample12]

value: male


title: WT, 9h, rep2

value: 9 hours


title: WT, 24h, rep1


title: Liver, 72 h after partial hepatectomy, rep1 [Sample11]


title: Liver, HSC depleted [Sample10]

description: Liver, HSC depleted, rep4

value: depleted of hepatic stellate cells


title: WT, 0h, rep1


title: Library, replicate 3

source_name: glycerol stock

extract_protocol:
Libraries were prepared using QIAseq Ultralow Input Library Kit according to manufacturer instructions. 10ng input DNA were used and 8 PCR cycles were performed. Libraries were quantified by QubitTM dsDNA HS Assay Kit (3.0 Fluometer; ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent Technologies) before pooling. Sequencing of pooled libraries, spiked with 50% PhiX control library, was performed in paired-end mode with 150 nt read length on the NextSeq 2000 platform (Illumina) with a P1 Kit and 20 Mio reads per library. Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).
We incubated the culture at 37°C until it reached the indicated OD, at which point we took a 2 mL aliquot, pelleted it, discarded the supernatant, and stored the bacterial samples at -20°C until further processing.  Bacterial pellets were resuspended in 100 μL of PBS containing 250 μg lysozyme, mixed with 100 μL lysis buffer (100 mM Tris-HCl pH 8.5, 200 mM NaCl, 0.2% SDS, 5 mM EDTA), and lysed by incu-bating at 37°C for 5 min. Proteins were then degraded by addition of 1 μL of Proteinase K (NEB #P8107) and incubation at 56°C for 30 min, following which RNA was digested with 0.5 μL of RNase A (Thermo #EN0531) and incubation at 56°C for 5 min. The remaining gDNA was purified from each sample via phenol-chloroform extraction, followed by ethanol precipitation.  The genomic regions coding for gRNAs and arrays were PCR-amplified in a 50 µL reaction con-taining 100 ng gDNA with oligonucleotides AWO-577/AWO-578 (annealing temperature: 55°C) and AWO-575/AWO-576 (annealing temperature: 63°C).

value: glycerol stock

tag: strain


title: 15-Control-healthy-G10

city: Gent

first: Anne-Sofie

last: Vermeersch

address: Ottergemsesteenweg 46

country: Belgium

institute: Ghent University

description: Control sample

data_processing:
Quality and length of raw sequencing reads inspection with FastQc (v0.11.7). Fastq_screen was utilized for putative contamination check.
Adaptor and quality trimming with cutadapt (v2.8).
The reads were mapped on the Bos_taurus_ARS-UCD1.2 cow reference genome using splice-aware Spliced Transcripts Alignment to a Reference (STAR) (v2.5.3a) mapper.
Features were counted at the gene and transcript isoform level using rsem_calc_expression (RSEM v1.3.1).
An analysis was done by comparing the healthy samples with the severe lesion samples, using the edgeR package in R.
Assembly: Bos_taurus_ARS-UCD1.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

extract_protocol:
Samples were taken with a biopsy punch tool and flash frozen in liquid nitrogen. RNA isolation was performed using the Qiagen RNeasy Minikit (Qiagen Benelux, Venlo, the NL).
Sequencing libraries were constructed using the ‘QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina’ from Lexogen (Lexogen Inc, Greenland, NH, USA).

value: Skin

tag: breed

value: Holstein-Friesian


title: WT, 9h, rep1


title: Liver, HSC depleted [Sample9]

description: Liver, HSC depleted, rep3


title: 14-Control-healthy-F10

description: Control sample


title: AERD-Aspirin challenge 4hr-6

type: genomic

city: Bucheon

first: Jong Uk

last: Lee

address: 170, Jomaru-ro, Wonmi-gu

institute: Soonchunhyang University Bucheon Hospital

hyb_protocol: genomic DNA was bisulfite-converted using the EZ DNA Methylation kit (Zymo) then assayed by the Illumina Infinium MethylationEPIC BeadChip array that interrogates over 850,000 CpG methylation sites.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Cy5 and Cy3

source_name: PBMC

label_protocol: A total of 50 ng of genomic DNA was used for genome-wide DNA methylation profiling using Illumina’s Infinium MethylationEPIC (HM850K) platform.

extract_protocol: Genomic DNA was extracted from whole blood using QIAamp DNA Blood Mini kit  (Qiagen) following the manufacturer’s instructions. DNA quality and concentration were checked using nanodrop and qubit instruments, respectively.

value: Female

value: Human PBMC

tag: time point

value: Aspirin challenge 4hr

tag: disease state

value: AERD


title: Library, replicate 2


title: Liver, HSC depleted [Sample8]

description: Liver, HSC depleted, rep2


title: Library, replicate 1


title: 13-Control-healthy-E10

description: Control sample


title: AERD-Aspirin challenge 4hr-4

tag: gender


title: AERD-Aspirin challenge 4hr-2


title: AERD-Aspirin challenge 4hr-3


title: 12-Control-healthy-D10

description: Control sample


title: Liver, control [Sample6]

description: Liver, control, rep6

value: not-depleted of hepatic stellate cells


title: AERD-Aspirin challenge 4hr-1


title: Liver, control [Sample5]

description: Liver, control, rep5


title: AERD-Aspirin challenge 0hr-3

value: Aspirin challenge 0hr


title: 11-Control-healthy-C10

description: Control sample


title: AERD-Aspirin challenge 4hr-5

value: Male


title: ATA-Aspirin challenge 4hr-5

value: ATA


title: Acetate, DMS, biol rep 3

city: University Park

first: Elizabeth

last: Jolley

address: 239 Chemistry Bldg, Pennsylvania State University

institute: Pennsylvania State University

data_processing:
All data processing steps were done using StrutureFold2
Library strategy: Structure-seq2

organism: Methanosarcina acetivorans C2A

extract_protocol:
Pelleted cells were resuspended in 1 mL of Trizol, and the RNA was extracted according to the Direct-zol RNA MiniPrep kit (Zymo Research).
DMS-treated total RNA is reverse transcribed using a random hexamer primer to generate cDNA that is prepared for sequencing by ligating a hairpin adapter and then PCR amplifying products while incorporating Illumina sequencing primers. Libraries are size-selected on a denaturing PAGE gel between 200-600 nucleotides and then submitted for sequencing.

value: WT

value: DMS


title: Liver, control [Sample4]

description: Liver, control, rep4

value: Whole liver

value: female


title: Acetate, DMS, biol rep 2


title: Acetate, DMS, biol rep 1


title: AERD-Aspirin challenge 0hr-4


title: 10-Disease-B10

description: Disease sample


title: AERD-Aspirin challenge 0hr-1


title: Liver, HSC depleted [Sample7]

description: Liver, HSC depleted, rep1


title: 9-Disease-A10

description: Disease sample


title: ATA-Aspirin challenge 0hr-6


title: AERD-Aspirin challenge 0hr-6


title: AERD-Aspirin challenge 0hr-2


title: 8-Disease-H9

description: Disease sample


title: Liver, control [Sample3]

description: Liver, control, rep3


title: Methanol, DMS, biol rep 3


title: ATA-Aspirin challenge 4hr-6


title: 7-Disease-G9

description: Disease sample


title: Methanol, DMS, biol rep 2


title: Liver, control [Sample1]

description: Liver, control, rep1

value: male


title: 6-Disease-F9

description: Disease sample


title: Methanol, DMS, biol rep 1


title: ATA-Aspirin challenge 0hr-5


title: Liver, control [Sample2]

description: Liver, control, rep2


title: 5-Disease-E9

description: Disease sample


title: ATA-Aspirin challenge 4hr-2


title: ATA-Aspirin challenge 4hr-4


title: ATA-Aspirin challenge 4hr-3


title: 4-Disease-D9

description: Disease sample


title: Acetate, control, biol rep 2

value: control


title: ATA-Aspirin challenge 4hr-1


title: Sorted tissue lung NK cells, scRNAseq

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger Pipeline v3.0.1
Assembly: GRCh38
Supplementary files format and content: 10X Genomics .h5 file (gene expression matrices)

source_name: Lung

growth_protocol: Newborn MISTRG mice were irradiated and transplanted by intrahepatic injection with human CD34+ HSPCs from umbilical cord blood. MISTRG mice were engrafted with pooled batches of human CD34+ cells to reduce the impact of HSPC donor variability. Two months after transplantation, lung cells were isolated. Before lung harvest, intravascular cell labeling was performed as described below. To obtain enough cells, lungs were pooled from ten MISTRG mice.

extract_protocol:
Human ILCs were purified as live CD45+CD127+CD94-CD3-TCRab-Lin- lymphocytes and divided into intravascular (IV-CD45-PE+) and extravascular (IV-CD45-PE-) ILCs. Human NK cells were purified as live CD45+CD127-CD94+CD3-TCRab-Lin- lymphocytes and divided into intravascular (IV-CD45-PE+) and extravascular (IV-CD45-PE-) NK cells. Lineage (Lin) markers included CD11c, CD14, CD19, CD34 CD123, FceRI. Further processing of sorted ILCs and NK cells (GEM generation, barcoding, cleanup, cDNA amplification) was performed using reagents and protocols from 10x Genomics Chromium Single Cell 3' Reagent kit v2.
Library construction was done using the 10x Genomics Chromium Single Cell 3' Reagent kit v2.

treatment_protocol: Intravascular cell labeling to distinguish vascular from tissue ILCs and NK cells was performed by injecting HSPC-engrafted MISTRG mice intravenously (IV) with a phycoerythrin (PE)-conjugated anti human CD45 antibody 5 minutes before lung harvest without any prior perfusion. Lungs were enzymatically digested, and lymphocytes isolated by density gradient centrifugation. ILCs and NK cells were then purified by immunomagnetic selection and cell sorting.

value: Lung

value: MISTRG humanized mouse

value: Lymphocyte

tag: cell population_characteristic

value: Live human CD45+ TCRab- CD3- Lineage- CD94+ CD127- i.v. CD45-


title: AERD-Aspirin challenge 0hr-5

value: Human PBMC


title: Acetate, control, biol rep 1


title: Sorted intravascular lung NK cells, scRNAseq

description: 10x Genomics

value: Live human CD45+ TCRab- CD3- Lineage- CD94+ CD127- i.v. CD45+