title: Nucleus accumbens, MAN0 female, rep6 [Lib21_S5]

status: Public on Jul 31 2023

type: SRA

city: Charlottesville

first: Joshua

last: Danoff

state: VA

address: 485 McCormick Road

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
TrimGalore: removal of auto-deteted Illumina adapters and trimming of low-quality ends up to a threshold of Q20
MultiQC: quality control
Kallisto: pseudoalignment and transcript quantification
Assembly: Microtus ochrogaster, MichOch v1.0, Ensembl release version 96
Supplementary files format and content: csv; raw counts

molecule: total RNA

organism: Microtus ochrogaster

source_name: Nucleus accumbens

extract_protocol:
Qiagen AllPrep DNA/RNA mini kit
NEBNext Ultra Directional RNA Library Prep Kit with mRNA magnetic isolation

tag: tissue

value: Nucleus accumbens

tag: treatment

tag: Sex

value: F


title: Nucleus accumbens, MAN0 female, rep7 [Lib26_S10]


title: Nucleus accumbens, MAN0 male, rep7 [Lib25_S9]

value: M


title: Nucleus accumbens, MAN1 female, rep6 [Lib24_S8]


title: Nucleus accumbens, MAN1 male, rep5 [Lib20_S4]


title: Nucleus accumbens, MAN1 female, rep5 [Lib19_S3]


title: Nucleus accumbens, MAN0 male, rep6 [Lib22_S6]


title: Nucleus accumbens, MAN0 male, rep5 [Lib18_S2]


title: Nucleus accumbens, MAN0 female, rep5 [Lib17_S1]


title: Nucleus accumbens, MAN1 male, rep4 [Lib15_S15]


title: Nucleus accumbens, MAN1 female, rep3 [Lib12_S12]


title: Nucleus accumbens, MAN1 female, rep4 [Lib16_S16]


title: Nucleus accumbens, MAN0 male, rep4 [Lib13_S13]


title: Nucleus accumbens, MAN1 male, rep3 [Lib11_S11]


title: Nucleus accumbens, MAN0 female, rep4 [Lib14_S14]


title: Nucleus accumbens, MAN0 female, rep3 [Lib10_S10]


title: Nucleus accumbens, MAN1 male, rep2 [Lib06_S6]


title: Nucleus accumbens, MAN1 female, rep2 [Lib05_S5]


title: Nucleus accumbens, MAN0 male, rep1 [Lib04_S4]


title: Nucleus accumbens, MAN0 male, rep2 [Lib08_S8]


title: Nucleus accumbens, MAN0 female, rep1 [Lib03_S3]


title: Nucleus accumbens, MAN0 male, rep3 [Lib09_S9]


title: Nucleus accumbens, MAN1 female, rep1 [Lib01_S1]


title: Nucleus accumbens, MAN1 male, rep1 [Lib02_S2]


title: Nucleus accumbens, MAN0 female, rep2 [Lib07_S7]


title: Skud_24C_BR2

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

data_processing:
Raw reads were first processed using TrimGalore v0.6.10 to remove Illumina sequencing adapters using default settings.
All genomic DNA sequences and GTF files were downloaded from NCBI using the following versions (Saccharomyces cerevisiae: GCF_000146045.2_R64, Saccharomyces kudriavzevii: GCA_947243785.1_Skud-ZP591, Kluyveromyces_marxianus: GCA_001417885.1_Kmar_1.0).
These files were then used by STAR v2.7.10b to generate indices (--sjdbOverhang 99 --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFfeatureExon CDS --sjdbGTFtagExonParentGene gene_id --genomeSAindexNbases 10).
Mapping of the filtered and trimmed fastqs was also done with STAR v2.7.10b (--alignMatesGapMax 20000).
The reads mapping to each gene were quantified using HTSeq v2.0.2 (--stranded=no --type=CDS --idattr=gene_id).
Assembly: GCF_000146045.2_R64, GCA_947243785.1_Skud-ZP591, GCA_001417885.1_Kmar_1.0
Supplementary files format and content: tab-separated value format; includes raw counts
Supplementary files format and content: tab-separated value format; includes TPMs

organism: Saccharomyces kudriavzevii

growth_protocol: Each species (strains BY4742, FM1389, DMKU3-1042) was grown at its optimum growth temperature (33C, 34C, and 37C, respectively) until OD600 was between 0.2-0.4 in YPD with 2% dextrose.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep kit (Zymo cat. no R2052) with Ambion TRI-reagent (Fisher cat. no. AM9738) and Zirconia/Silica 0.5 mm homogenization beads (Biospec cat. no. 11079105Z). Samples were treated with Dnase I (NEB M0303S).
Sequencing libraries were prepared by Novogene (https://www.novogene.com/us-en/). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Paired-end sequencing of the library was then performed on an Illumina instrument.

treatment_protocol: Using cells between OD600 of0.2-0.4: 1.2 mL of cells were transferred to a 1.5 mL tube and treated at either the control temperature (optimal growth temperature) or their maximum heat shock temperature for 8 minutes (BY = 40C, FM = 31C, DMKU = 46C). Cells were then centrifuged at 3,000 g for 1 minute at room temperature, and the supernatant was removed. Cells were flash frozen and stored at -80°C.

tag: strain

tag: temperature

tag: biological replicate


title: Skud_31C_BR2


title: Skud_24C_BR1


title: Skud_31C_BR1


title: G_420F

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Trinity is used to perform the transcriptome assembly. The workflow could be found at: http://trinityrnaseq.github.io. Trinity is developed by  Broad Institute and Hebrew University of Jerusalem. It is a professional transcriptome assembler software (comprising modules entitled Inchworm,  Chrysalis and Butterfly). After that, we use CORSET software to remove the redundance from Trinity results. Hierarchical clustering performs  based on multiple mapping events and expression pattern. The workflow could be found at: https://github.com/Oshlack/Corset/wiki. Finally,  BUSCO was used to attempts to provide a quantitative assessment of the completeness in terms of expected gene content of transcriptome.
Seven databases are used to decipher gene function:  NR (NCBI non-redundant protein sequences): it is the formal protein sequence databases of NCBI, which includes protein sequence  information from GeneBank, PDB (Protein Data Bank), SwissProt, PIR (Protein Information Resource), PRF (Protein Research Foundation)
The abundance of transcript reflects the gene expression level directly. The Corset filtered Trinity reconstructed transcriptome is used as  reference. RSEM (Li et al., 2011) is the software used to do the alignment. FPKM (short for the expected number of Fragments Per Kilobase of  transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects  into consideration of both sequencing depth and gene length on counting of fragments.
The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression  analysis commonly contains three steps:  1) Read counts Normalization;  2) Model dependent p-value estimation;  3) FDR value estimation based on multiple hypothesis testing.  Cluster analysis is used to find genes with similar expression patterns under various experimental conditions. By clustering genes with similar  expression patterns, it is possible to discern unknown functions of previously characterized genes or functions of unknown genes. In hierarchical  clustering, areas of different colors denote different groups (clusters) of genes, and genes within each cluster may have similar functions or take  part in the same biological process. In addition to the FPKM cluster, the H-cluster are used to cluster the log2(ratios). Genes within the same  cluster exhibit the same trends in expression levels under different conditions.  Tips: When the number of gene in Union_for_cluster.xls is between 50 ~30000, we will do analysis of cluster.
Genome_build: de novo
Supplementary_files_format_and_content: excel files containing read count, fpkm, log2 fold change, p-value

organism: Rhinichthys cataractae

source_name: liver

extract_protocol:
Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencng was performed by Novogene.

treatment_protocol: Samples were collected from fish from different river systems.

value: liver

value: female

tag: timepoint

value: day 28

tag: location

value: 5% Pine Creek effluent


title: G_408M

value: male


title: G_401M


title: G_419F


title: Fetal liver Ter-119+ erythroid cells  2

type: RNA

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

hyb_protocol: 100ng of total RNA was hybridized with NanoString Mouse Immunology V1 panel according to the manufacturer's protocols.

scan_protocol: not provided

data_processing: We performed QC on the raw data, performed background thresholding using the (mean of negative controls + 2 SD) + mean of POS_D controls, normalized gene expression using 15 housekeeping genes. We normalized CD71 and Ter-119 Bone marrow erythroid cells separately from the Bone marrow and fetal liver ter-119+ erythroid cells.

label: not provided

organism: Mus musculus

source_name: Fetal liver Ter-119+ erythroid cells

label_protocol: not provided

extract_protocol: We obtained mononucler cells (MNCs) using Ficoll-paque density gradient, then labeled the MNCs with either anti-CD71 or anti-Ter-119-biotin-magnetic bead antibody and sorted the cells using a magnetic separator.

tag: age

value: 12 weeks

value: Fetal Liver


title: Bone Marrow CD71+ erythroid cells  3

source_name: Bone Marrow CD71+ erythroid cells

value: 6 month

value: Adult Bone Marrow


title: Fetal liver Ter-119+ erythroid cells  1


title: Bone Marrow Ter-119+ erythroid cells  3

source_name: Bone Marrow Ter-119+ erythroid cells


title: Bone Marrow Ter-119+ erythroid cells  2

value: 5 month


title: Bone Marrow CD71+ erythroid cells  1

value: 4 month


title: Fetal liver Ter-119+ erythroid cells  3


title: Bone Marrow CD71+ erythroid cells  2


title: Bone Marrow Ter-119+ erythroid cells  1


title: G_395F


title: F_347M

value: Bow River control


title: G_363F


title: G_367F


title: G_384M


title: F_343F


title: F_308M


title: F_344F


title: G_375M


title: G_365M


title: F_355M


title: G_396M


title: G_397F


title: F_317F


title: F_327M


title: F_323F


title: F_321M


title: E_297M

value: day 14


title: F_333F


title: F_329M


title: F_314F


title: E_293M


title: E_286F


title: E_272F


title: D_227F


title: D_209M


title: D_207M


title: D_216F


title: E_252M


title: D_242M


title: E_255M


title: E_289F


title: E_269F


title: D_245M


title: E_256F


title: D_211F


title: D_229F


title: D_223M


title: E_254F


title: D_191F


title: E_270M


title: E_259M


title: C_169M

value: day 7


title: C_167M


title: C_164F


title: D_187F


title: C_152F


title: C_145F


title: C_158F


title: C_180M


title: C_156M


title: C_143M


title: D_190M


title: B_117M


title: C_132M


title: B_100F


title: B_94M


title: B_104M


title: B_74F


title: B_112F


title: B_96F


title: B_93F


title: C_179F


title: B_71M


title: THP1, UNS, rep3

city: Hong Kong

first: Lishi

last: Wang

state: Hong Kong

address: 30-32 Ngan Shing Street, Shatin, NT

department: Surgery

country: China

institute: The Chinese University of Hong Kong

data_processing:
The quality of reads was evaluated by FastQC. The genome assembly and annotation were downloaded from GENCODE (version 40). Raw sequence reads were mapped to the human reference genome (hg38) with STAR, and the quantification of expression levels was performed using RSEM.  Lowly expressed genes (raw count < 1) were filtered out to improve efficiency.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes expected counts for each Sample

organism: Homo sapiens

growth_protocol: Suspension cells were maintained in RPMI medium supplemented with 5% FBS, 25mM HEPES, and 0.1%  2-Mercaptoethanol (GIBCO)

extract_protocol:
Cells were incubated for 24 hours and harvested for RNA using Takara MiniBest Universal RNA Extraction Kit following manufacturer’s instructions. Extracted RNA were stored at -80°C and concentrations were quantified immediately using a NanoDrop spectrophotometer. RNA samples were diluted to obtain a final concentration of 1 - 5 ug/mL to allow for analysis using Bioanalyzer RNA Pico Kit (Agilent). Preparation of RNA samples for analysis using the Bioanalyzer kit was performed according to manufacturer’s instructions to acquire appropriate RIN numbers.
RNA libraries for RNA-seq were prepared following DNBSEQ Strand-Specific Transcriptome Library Construction Protocol

treatment_protocol: THP-1, PMDC05, and CAL-1 cells were seeded at a concentration of 1 x 10^6 cells in a six well plate and allowed to rest overnight. Cells were either unstimulated (UNS) or stimulated with either CL097, LPS, FLA or POLY.

tag: cell line

tag: cell type

value: monocytic leukemia cells

value: UNS


title: THP1, POLY, rep2

value: POLY


title: THP1, POLY, rep1


title: B_110M

value: liver


title: B_69F

value: female


title: THP1, LPS, rep1

value: LPS


title: C_141F

value: 5% Pine Creek effluent


title: THP1, UNS, rep2


title: THP1, POLY, rep3


title: A_55F

value: day 0

value: reference (Bowness Park)


title: THP1, LPS, rep2


title: THP1, UNS, rep1


title: THP1, FLA, rep2

value: FLA


title: A_53F


title: A_37M

value: male


title: A_36M


title: A_39F


title: A_35F


title: A_40M


title: PMDC05, UNS, rep3

value: plasmacytoid dendritic cells


title: A_61M


title: A_34M


title: THP1, CL097, rep3


title: PMDC05, UNS, rep1


title: THP1, FLA, rep3


title: B_64M


title: platelet treated with PBS, rep3

city: Shanghai

first: Tingting

last: Liu

state: Shanghai

address: No. 197 Ruijin Second Road

institute: Shanghai Jiao Tong University

data_processing:
RNA sequencing was performed on the BGISEQ500 platform (BGI-Shenzhen, China) and the sequencing data were filtered with SOAPnuke (v1.5.2).
Clean reads were mapped to the reference genome (Species: Homo_sapiens; Source: NCBI; Version: GCF_000001405.39_GRCh38.p13) using HISAT2 (v2.0.4).
Differential expression genes (DEGs) analysis of two groups ( platelets treated with SARS-CoV-2 and platelets treated with PBS) was carried out by DESeq2 (v1.4.5) with log2foldchange >1.0 and Q value ≤0.05. GO (http://www.geneontology.org/) enrichment analyses of annotated differentially expressed genes were performed. A P value <0.05 was considered statistical significance.
Assembly: reference genome (Species: Homo_sapiens; Source: NCBI; Version: GCF_000001405.39_GRCh38.p13)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: platelet

extract_protocol:
Fresh blood collected was subjected to platelet isolation within 1 hours after blood collection. Platelets were incubated with SARS-CoV-2 E protein or PBS for 1 hour at 37℃. Then the platelet pellets were isolated by two continuous steps of centrifugation, followed by lysis in QIAzol (QIAGEN) and extracted the total RNA using the miRNeasy Mini Kit (QIAGEN). Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, MA, USA).
Totol RNA of platelets was isolated by using the miRNeasy Mini Kit (QIAGEN). Platelet RNA was eluated in 30 μL elution buffer.Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, MA, USA), and included as a quality standard for subsequent experiments only platelet RNA samples with a RIN-value >7 and/or distinctive rRNA curves. The double stranded PCR product from previous step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China).

treatment_protocol: Platelets were isolated from peripheral blood of healthy donors and treated with SARS-CoV-2 E protein or PBS, respectively.

tag: subject status

value: healthy donor

value: platelet

tag: gender

value: Female

value: PBS


title: PMDC05, POLY, rep3


title: platelet treated with PBS, rep1


title: platelet treated with PBS, rep2


title: THP1, FLA, rep1


title: platelet treated with SARS-CoV-2 E protein, rep3

value: SARS-CoV-2 E protein


title: PMDC05, POLY, rep2


title: PMDC05, LPS, rep3


title: PMDC05, POLY, rep1


title: PMDC05, UNS, rep2


title: THP1, CL097, rep2

value: monocytic leukemia cells


title: A_60M


title: THP1, CL097, rep1


title: platelet treated with SARS-CoV-2 E protein, rep1


title: PMDC05, LPS, rep2


title: platelet treated with SARS-CoV-2 E protein, rep2


title: PCI_restenosis-3

city: shijiazhuang

first: haibin

last: li

address: 102 Youyi Bei Dajie, Shijiazhuang, Hebei 050000

institute: The Third Hospital of Hebei Medical University

description:
X3
heart

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity sequence.
Mapped to human reference genome.
Obtain mapped data (reads, etc.) for subsequent transcription assembly and expression count.
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS (coding region), Intron (Intron), Intergenic region and UTR (5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: *.expression_count.xls: Gene/transcript COUNT expression matrices.

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard Illumina protocol.

value: blood

tag: diagnosis


title: PMDC05, FLA, rep3


title: PMDC05, LPS, rep1


title: PCI_restenosis-1

description:
X1
heart


title: PMDC05, FLA, rep1


title: PCI_restenosis-2

description:
X2
heart


title: PCI_non-restenosis-3

description:
Z3
heart


title: PCI_non-restenosis-2

description:
Z2
heart


title: PCI_non-restenosis-1-1

description:
Z1
heart


title: PMDC05, FLA, rep2


title: PMDC05, CL097, rep1


title: PMDC05, CL097, rep2


title: CAL1, UNS, rep3

value: UNS


title: Acute coronary syndrome-1

description:
H1
heart

source_name: Acute coronary syndrome

value: Acute coronary syndrome


title: Acute coronary syndrome-2

description:
H2
heart


title: Normal-3

description:
C3
heart

source_name: Normal

value: Normal


title: Acute coronary syndrome-3

description:
H3
heart


title: Normal-2

description:
C2
heart


title: CAL1, POLY, rep2

value: POLY


title: CAL1, POLY, rep1


title: CAL1, POLY, rep3


title: CAL1, UNS, rep1


title: Normal-1

description:
C1
heart


title: CAL1, LPS, rep3

value: LPS


title: CAL1, LPS, rep2


title: PMDC05, CL097, rep3


title: CAL1, LPS, rep1


title: CAL1, FLA, rep3


title: CAL1, FLA, rep1


title: CAL1, UNS, rep2


title: CAL1, CL097, rep3


title: CAL1, CL097, rep2


title: CAL1, CL097, rep1


title: scRNA-seq for bone marrow mononuclear cells after metoprolol treatment

city: Beijing

first: Yuzhuo

last: Yang

address: Zheng Yutong Building room D311

institute: Tsinghua University

description: Single cell RNA-seq

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix for sample were generated for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Gene-barcode matrix for scRNA-seq dataset was saved as .h5 file.

molecule: polyA RNA

source_name: bone marrow

extract_protocol: Bone marrow  from CAR-T therapy received DLBCL patient were diluted by PBS, and mononuclear cells were isolated by Ficol gradient. PBMC were frozen in FBS with 10% DMSO for preservation. For library construction, cells were thrawed and resuspened, and the single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5’ library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and were further prepared as sequencing library.

treatment_protocol: CAR-T therapy received DLBCL patient was administrated with metoprolol orally from day6-day9 after CAR-T infusion

value: mononuclear cells

tag: disease state

value: Diffuse large B-cell lymphoma

value: metoprolol


title: RNAseq_siTdg_G1_day9_EBs_R2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: RNA-seq experiment

data_processing:
RNA-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using TOPHAT (PubMed ID 22383036) with the option -g 1.
RNA-seq analysis: DESeq2 (PubMed ID 25516281) was used to calculate differential gene expression (pairing samples). The "stat" attribute of DESeq2 output per gene was used to build the preranked gene lists suitable for GSEA analysis.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each *seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome except in the cases in which spike-in information was available to perform the normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
Supplementary_files_format_and_content: Files .rnk (preranked files from RNA-seq for GSEA)

source_name: Embryoid Bodies (EBs) derived from mouse Embryonic Stem Cells (mESCs)

growth_protocol: Briefly, ESCs were growth in serum-free medium N2B27 media (DMEM/F12:Neurobasal 1:1, 0.5x N-2 supplement, 1x B-27 serum-free supplement, 50 µM 2-mercaptoethanol; Bovine Albumin Fraction V 0.033%; 1X Glutamax; 1X MEM non-essential aminoacids; 1X Penicillin-Streptomycin; all from Gibco) supplemented with 1 µM PD0325901 (Tocris), 3 uM CHIR99021 (Tocris) and Leukemia Inhibitory Factor (LIF).

extract_protocol:
RNA-seq: RNA extraction was performed using the RNeasy mini kit (Qiagen) following manufacturer’s instruction. RNA samples were quantified and quality was evaluated using Bioanalyzer (RIN > 9.9). A total of 0.5 ug of RNA was used as starting material for library preparation with rRNA depletion using TruSeq Stranded Total RNA Library Prep kit (Ilumina) following the manufacturer´s instruction.
modified DNA immunoprecipitation followed by sequencing (DIP-seq): DNA extraction and purification was carried out as in (PMID: 30220521). Briefly, DNA was extracted using the Blood & Cell Culture DNA Mini kit (QIAGEN Cat#13323). Purified genomic DNA was sonicated using Covaris to obtain fragments of 200–600 bp. Library preparation was performed using the NEBNext Ultra library prep kit (New England Biolabs Cat#E7370) substituting the NEB hairpin adaptors by full-length barcoded TruSeq adaptors from Illumina (Cat# FC-401-3001). Fragmented DNA with compatible adaptors were pooled together. Pooled DNA was heated for 10 minutes at 99°C, cold down on ice, and incubated overnight with 5-Carboxylcytosine (5-caC) antibody (1 μg Ab/μg DNA; Active Motif Cat#61225) in IP buffer (10 mM Sodium Phosphate buffer, 140 mM NaCl, 0.05% Triton X-100). Immunocomplexes were recovered using pre-equilibrated Protein G/A Dynabeads (Life Technologies Cat#10002D and Cat#10009D respectively) for 2 hr at 4°C. After washing with IP buffer, immunocomplexes were eluted from columns by heating at 55°C for 30 minutes in proteinase digestion buffer [50 mM Tris-HCl pH = 8, 10 mM EDTA, 0.5% SDS, 35 mg Proteinase K (New England Biolabs Cat#P8107S)] and the DNA purified using MinElute PCR Purification kit (QIAGEN Cat#28004). Recovered DNA was amplified by PCR and sequenced in Illumina HiSeq2500.
Libraries were prepared according to Illumina instructions.

value: EBs at different time points from siC/siTdg transfected E14Tg2A


title: scRNA-seq for bone marrow mononuclear cells before metoprolol treatment

description: Single cell RNA-seq


title: ZF_Hypoxia_LowFlow_rep3

city: Montreal

first: R. Thomas

last: Jagoe

state: Quebec

address: Jewish General Hospital, 3755 Cote Ste Catherine

department: Medicine

country: Canada

institute: McGill University

description: Gene expression after 5 days at hypoxic conditions with low flow to prompt similar activity level to controls

hyb_protocol: The arrays were incubated in an Agilent Hybridization oven at 65°C for 17 hours at 10 rpm.

scan_protocol: They were washed and scanned on an Agilent DNA Microarray Scanner C. All these steps were done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, Inc).

data_processing: The scanned images were analysed using Feature Extraction software (Agilent) with deafult parameters (Protocol GE1_107_Sep09, Grid US09473739).  Features were excluded from analysis if failed to achieve the default 'glsWellAboveBkg' threshold for the Agilent Feature Extraction Software.

organism: Danio rerio

source_name: post-anal muscle block, 4kPa, 7cm/sec rep3

label_protocol: Cyanine 3-labeled CTP cRNA was produced with 50 ng of total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc).  The labeled cRNA was then normalized at 1650 ng, fragmented and hybridized on Zebrafish GE Microarray 4x44K.

extract_protocol: Total RNA was further cleaned and purified using Qiagen MinElute RNA cleanup column and quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and integrity checked using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: On 5th day of each experiment, fish were euthanized by stunning and rapid decapitation.  After rapid removal of tail and fins and scales, the post-anal block was dissected, minced and placed in 4ml Trizol solution on ice and then stored at -80C.  After thawing samples were homogenized, spun at 10,000g for 10 minutes.  Chloroform extraction was performed on supernatant and RNA precipitated in isopropyl alcohol.

value: skeletal muscle

value: 4 months

value: unspecified (mixed)


title: RNAseq_siC_G1_day9_EBs_R2

description: RNA-seq experiment


title: RNAseq_siC_SG2M_day9_EBs_R2

description: RNA-seq experiment


title: RNAseq_siTdg_SG2M_day9_EBs_R2

description: RNA-seq experiment


title: CAL1, FLA, rep2

value: plasmacytoid dendritic cells

value: FLA


title: ZF_Hypoxia_HighFlow_rep3

description: Gene expression after 5 days of intermittent high intensity exercise under hypoxic conditions

source_name: post-anal muscle block, 6kPa, 30cm/sec rep3


title: ZF_Hypoxia_LowFlow_rep1

source_name: post-anal muscle block, 4kPa, 7cm/sec rep1


title: y w, Pngl-ex14, Pngl-ex14 replicate 2

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

data_processing:
The raw FASTQ files were trimmed using cutadapt v1.4 with parameters "-A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q 25 -e 0.1 -m 12" was performed.
Alignment to the Drosophila dm6 genome using STAR v2.5.3 with the reference transcriptome derived from Flybase release 6_20.
Statistical testing for significance of differential expression was done using edgeR and custom R scripts.
Assembly: dm6
Supplementary files format and content: tab-delimited text file including raw counts for each sample

organism: Drosophila melanogaster

source_name: midgut

extract_protocol:
For each genotype, 40 midguts were dissected directly in the TRI Reagent (Millipore/Sigma, T9424) and stored at -80°C.
The samples were prepared on a Beckman Fxp using the Illumina TruSeq stranded mRNA chemistry and sequenced on a NextSeq 500 (Mid output flowcell) in paired-end mode.

tag: developmental stage

value: third instar larvae

value: y w

value: midgut

tag: genotype

value: y w; Pngl[ex14]/Pngl[ex14] (homozygous)


title: y w, Pngl-ex14, Pngl-ex14 replicate 1

tag: tissue


title: RNAseq_siC_G1_day9_EBs_R1

description: RNA-seq experiment


title: RNAseq_siTdg_SG2M_day9_EBs_R1

description: RNA-seq experiment


title: ZF_Hypoxia_LowFlow_rep4

source_name: post-anal muscle block, 4kPa, 7cm/sec rep4


title: y w, Pngl-ex14, Pngl-ex14, PBAC replicate 2

value: y w; Pngl[ex14]/Pngl[ex14];PBac{Pngl[wt]Ch322-3O13}VK27 (homozygous with rescue transgene)


title: ZF_Hypoxia_HighFlow_rep1

source_name: post-anal muscle block, 6kPa, 30cm/sec rep1


title: ZF_Normoxia_HighFlow_rep1

description: Gene expression after 5 days of intermittent high intensity exercise

source_name: post-anal muscle block, 20kPa, 35cm/sec rep1


title: ZF_Normoxia_HighFlow_rep3

source_name: post-anal muscle block, 20kPa, 35cm/sec rep3


title: ZF_Normoxia_HighFlow_rep4

source_name: post-anal muscle block, 20kPa, 35cm/sec rep4


title: RNAseq_siC_SG2M_day9_EBs_R1

description: RNA-seq experiment


title: ZF_Hypoxia_LowFlow_rep2

source_name: post-anal muscle block, 4kPa, 7cm/sec rep2


title: y w, Pngl-ex14, Pngl-ex14, PBAC replicate 1


title: RNAseq_siTdg_G1_day9_EBs_R1

description: RNA-seq experiment


title: y w, Pngl-ex14, Cyo replicate 2

value: y w; Pngl[ex14]/CyoKr>GFP (heterozygous)


title: ATACseq_G1

description: ATAC-seq experiment

library_source: genomic

data_processing:
ChIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection at each replicate of the same condition against the Input was performed with MACS (PubMed ID: 18798982) and EaSEQ (PubMed ID:  26926434). DiffBind was next used to generate the final consensus set of peaks (PubMed ID: 22217937). Peaks were reported in BED format.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
RNA-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using TOPHAT (PubMed ID 22383036) with the option -g 1.
RNA-seq analysis: DESeq2 (PubMed ID 25516281) was used to calculate differential gene expression (pairing samples). The "stat" attribute of DESeq2 output per gene was used to build the preranked gene lists suitable for GSEA analysis.
ATAC-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each *seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome except in the cases in which spike-in information was available to perform the normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
Supplementary_files_format_and_content: Files .rnk (preranked files from RNA-seq for GSEA)
Supplementary_files_format_and_content: Files DESEq2 results (statistical values)
Supplementary_files_format_and_content: Files DESEq2 results (RPKMs)

molecule: genomic DNA

source_name: mouse Embryonic Stem Cells (mESCs)

extract_protocol:
RNA-seq: RNA extraction was performed using the RNeasy mini kit (Qiagen) following manufacturer’s instruction. RNA samples were quantified and quality was evaluated using Bioanalyzer (RIN > 9.9). A total of 0.5 ug of RNA was used as starting material for library preparation with rRNA depletion using TruSeq Stranded Total RNA Library Prep kit (Ilumina) following the manufacturer´s instruction.
modified DNA immunoprecipitation followed by sequencing (DIP-seq): DNA extraction and purification was carried out as in (PMID: 30220521). Briefly, DNA was extracted using the Blood & Cell Culture DNA Mini kit (QIAGEN Cat#13323). Purified genomic DNA was sonicated using Covaris to obtain fragments of 200–600 bp. Library preparation was performed using the NEBNext Ultra library prep kit (New England Biolabs Cat#E7370) substituting the NEB hairpin adaptors by full-length barcoded TruSeq adaptors from Illumina (Cat# FC-401-3001). Fragmented DNA with compatible adaptors were pooled together. Pooled DNA was heated for 10 minutes at 99°C, cold down on ice, and incubated overnight with 5-Carboxylcytosine (5-caC) antibody (1 μg Ab/μg DNA; Active Motif Cat#61225) in IP buffer (10 mM Sodium Phosphate buffer, 140 mM NaCl, 0.05% Triton X-100). Immunocomplexes were recovered using pre-equilibrated Protein G/A Dynabeads (Life Technologies Cat#10002D and Cat#10009D respectively) for 2 hr at 4°C. After washing with IP buffer, immunocomplexes were eluted from columns by heating at 55°C for 30 minutes in proteinase digestion buffer [50 mM Tris-HCl pH = 8, 10 mM EDTA, 0.5% SDS, 35 mg Proteinase K (New England Biolabs Cat#P8107S)] and the DNA purified using MinElute PCR Purification kit (QIAGEN Cat#28004). Recovered DNA was amplified by PCR and sequenced in Illumina HiSeq2500.
ATAC-seq was performed as previously described (PMID: 24097267). The standard protocol was used with the following modifications. 100.000 cells were washed once with 100μl PBS and resuspended in 50μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500 g at 4°C, followed by the addition of 50μl transposition reaction mix (25μl TD buffer, 2.5μl Tn5 Transposase and 22.5μl Nuclease Free H2O) (Illumina Cat#FC-121-1030) and incubation at 37°C for 45min. DNA was isolated using MinElute Kit (QIAGEN Cat#28004). Library amplification was done by two sequential PCR reactions (8 and 5 cycles, respectively) using NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs Cat#M0541S). Library quality was checked on a Bioanalyzer using High Sensitivity DNA Analysis Kits (Agilent Cat# 5067-4626), followed by paired-end sequencing (2x50bp) on an Illumina HiSeq2500.
ChIP-seq: mESCs plates were crosslinked by adding parafolmaldehid (PFA) to media at 1% final concentration, for 10 minutes at room temperature. Fixation was stopped by addition of 0.125M glycine (pH=7.4) for 5 minutes at room temperature. Crosslinked cells were then washed 3 times in 1X PBS 1X and collected in 1X ice-cold PBS with protease inhibitors (Roche). Cell were collected by centrifugation at 1250g during 5 min at 4ºC, and were then resuspended in 30x volume of ice-cold IP buffer (1× volume SDS buffer [100 mM NaCl, 50 mM Tris-HCl, pH 8., 5 mM EDTA, pH 8, and 2% SDS] and 0.5 volume Triton dilution buffer (100 mM NaCl, 50 mM Tris-HCl, pH 8.6, 5 mM EDTA, pH 8 and 5% Triton X-100]) with protease inhibitors. Samples were sonicated for 60 cycles using a Bioruptor (Diagenode) at maximum output (30 seconds on/30 seconds off). After sonicaton, cells were centrifuged for 15 minutes at 16,000xg at 4ºC and the supernatant was collected. To check fragmented chromatin size, 1% of de material (input) was reversed-crosslinked in 1X PBS for 3 hours at 65ºC at 1000rpm. DNA was then purified using the PCR purification kit (Qiagen) and 0.5-0.8µg was analyzed in a 1% agarose gel to corroborate chromatin was sheared in 200-500bp fragments. Chromatin equivalent to 50-60µg of DNA was incubated with 5µg of specific antibody in 650ul of total volume overnight at 4ºC in rotation. The following day, 42µl of protein A agarose beads (Diagenode), pre-blocked with 0.05% BSA in IP buffer for 1h at 4ºC, were added to ChIP samples and incubated for 2 hours at 4ºC. After incubation, beads were washed three times with 1 ml of low-salt buffer (140 mM NaCl, 50 mM HEPES, pH 7.5, and 1% Triton X-100) and once with 1 ml high-salt buffer (500 mM NaCl, 50 mM HEPES, pH 7.5, and 1% Triton X-100). All supernatant was removed, and 110 µl of freshly prepared elution buffer (1% SDS, 100 mM NaHCO3) was added per ChIP reaction (including 1% of every input). Samples were de-crosslinked at 65 °C for 3 h in a shaker (1000 rpm). DNA was purified following the PCR purification kit. DNA was eluted with 100 µl of water (with two consecutive elutions of 50 µl). ChIP-seq libraries were prepared with 2 to 10 ng of ChIP DNA material using the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instruction. ChIP-seq libraries were amplified for 10 to 15 PCR cycles. Libraries were sequenced using a HiSeq 2500 sequencer (Illumina).
Libraries were prepared according to Illumina instructions.
ChIP-seq, DIP-seq, RNA-seq, ATAC-seq

tag: chip antibody


title: y w, Pngl-ex14, Cyo replicate 1


title: ZF_Hypoxia_HighFlow_rep2

source_name: post-anal muscle block, 6kPa, 30cm/sec rep2

tag: Sex


title: ZF_Normoxia_LowFlow_rep3

description: Gene expression after 5 days in control conditions

source_name: post-anal muscle block, 20kPa, 0 cm/sec rep3


title: y w, Control replicate 2

tag: strain

value: y w (wildtype for Pngl)


title: ZF_Normoxia_HighFlow_rep2

source_name: post-anal muscle block, 20kPa, 35cm/sec rep2


title: RNAseq_siTdg_G1_R2

description: RNA-seq experiment


title: y w, Control replicate 1


title: ZF_Normoxia_LowFlow_rep1

source_name: post-anal muscle block, 20kPa, 0 cm/sec rep1


title: PBMCs-XCR1neg-R848-1

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

description: reporter code sets (Nanostring Technologies, nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel)

hyb_protocol: Hybridization was performed as described in the manufacturers instruction. Briefly, samples were hybridized with reporter code sets (target-specific Reporter and Capture Probes) for 24h in a thermal cycler at 65°C

scan_protocol: nCounter Prep Station v4.1.0.1 was used. Scanning and image aquisition using the NanoString Digital Analyzer.

data_processing:
NanoString data were analyzed and exported using nSolver software (version 4.0). RUVg method was applied to remove the batch effect and data were normalized using NanoStringNorm according to 14 control genes and 40 housekeeping spikes genes. Differential gene expression analysis were conducted using edgeR
normalized signal intensity (log2 transformed)

source_name: isolated from PBMCs XCR1- R848

label_protocol: Labeling was performed as described in the manufacturers instruction (NanoString Technologies). Briefly, samples were labeled with reporter code sets (nCounter_Hs_Myeloid_Innate_Immunity_V2 Panel) consisting of many RNA capture probes targeting specific mRNAs. Each probe is labeled with a unique combination of fluorochromes (molecular barcode).

growth_protocol: Blood DCs were enriched from PBMCs of healthy donors using the EasySep Pan-DC Pre-Enrichment Kit. XCR1- and XCR1+ cDC1 were sorted.

extract_protocol: Cell pellets were lysed using 1/3 RLT buffer and sample mRNAs were stored at -80°C

treatment_protocol: Cells were stimulated with 5µg/ml R848 (TLR7-ligand) or control treated for 3h

value: PBMCs

tag: diseasse state

value: healthy donor


title: RNAseq_siC_G1_R2

description: RNA-seq experiment


title: RNAseq_siTdg_G2M_R1

description: RNA-seq experiment


title: PBMCs-XCR1neg-R848-2


title: ZF_Hypoxia_HighFlow_rep4

source_name: post-anal muscle block, 6kPa, 30cm/sec rep4


title: ZF_Normoxia_LowFlow_rep2

source_name: post-anal muscle block, 20kPa, 0 cm/sec rep2


title: RNAseq_siC_G2M_R2

description: RNA-seq experiment


title: RNAseq_siTdg_G1_R1

description: RNA-seq experiment


title: PBMCs-XCR1-R848-2

source_name: isolated from PBMCs XCR1+ R848


title: PBMCs-XCR1neg-2

source_name: isolated from PBMCs XCR1-


title: PBMCs-XCR1neg-1


title: RNAseq_siC_G1_R1

description: RNA-seq experiment


title: ZF_Normoxia_LowFlow_rep4

source_name: post-anal muscle block, 20kPa, 0 cm/sec rep4


title: RNAseq_siC_G2M_R1

description: RNA-seq experiment


title: PBMCs-XCR1-R848-1


title: RNAseq_siTdg_G2M_R2

description: RNA-seq experiment


title: RNAseq_siTdg_96h_R2

description: RNA-seq experiment


title: RNAseq_siC_96h_R2

description: RNA-seq experiment


title: PBMCs-XCR1-1

source_name: isolated from PBMCs XCR1+


title: PBMCs-XCR1-2


title: RNAseq_siTdg_96h_R1

description: RNA-seq experiment


title: RNAseq_siC_48h_R2

description: RNA-seq experiment


title: RNAseq_siTdg_48h_R1

description: RNA-seq experiment


title: RNAseq_siTdg_48h_R2

description: RNA-seq experiment


title: RNAseq_siC_48h_R1

description: RNA-seq experiment


title: RNAseq_siC_96h_R1

description: RNA-seq experiment


title: Mr PB microglia-like cells

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

description: HAMINUS

data_processing:
STAR
Cellranger
Genome_build: UCSC_mm10
Supplementary_files_format_and_content: tar archive of clusters and mtx,tsv files

source_name: Brain microglia-like cells

extract_protocol:
Cells were harvested by FACS, followed by the library preparation via 10x genomics protocol.
Followed the manufacture's protocol of 10x genomics.

value: Brain

tag: microglia replacement method

value: microglia replacement by peripheral blood


title: Mr BMT microglia-like cells

description: BAPLUS

value: bone marrow transplantation


title: RNAseq_EB_day11_siTdg_R1

description: RNA-seq experiment

source_name: Embryoid Bodies (EBs) derived from mouse Embryonic Stem Cells (mESCs)

value: EBs at different time points from siC/siTdg transfected E14Tg2A


title: Mr MT microglia

source_name: Brain microglia

value: microglia transplantation


title: RNAseq_EB_day11_siTdg_R2

description: RNA-seq experiment


title: RNAseq_EB_day11_siC_R1

description: RNA-seq experiment


title: Normal microglia


title: DIPseq_Input_siTdg_96h

description: DIP-seq experiment


title: Paip1_1: Paip1 mutant replicate 1

city: Hangzhou

first: Wanzhong

last: Ge

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Basic reads quality check was performed with FastQC
Reads were mapped to the Drosophila melanogaster reference genome assembly (version dm6.09, 2016) using TopHat and gene quantification was carried out using RSEM.
Differential expression analysis was performed using DEseq.

source_name: third instar larval wing imaginal discs

extract_protocol:
RNA extractions was performed using Trizol.
Libraries were prepared according to the Illumina protocol and sequenced on an Illumina HiSeq 4000 platform

value: larval wing imaginal discs

value: third instar

tag: genotype/variation

value: Paip1 mutant


title: control_1: y w control replicate 1

value: control (y w)


title: DIPseq_Input_siTdg_48h

description: DIP-seq experiment


title: DIPseq_Input_siC_96h

description: DIP-seq experiment


title: DIPseq_Input_siC_48h

description: DIP-seq experiment


title: Old.

first: Yehua

last: Li

address: shengmingkexueyuanlu7hao, changping

institute: NIBS

description: All pituitary cells

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned mm10 whole genome, filtered, de-duplicted, and converted into a digital count matrix using Cell Ranger 2.2.0 (10XGenomics)
Assembly: mm10
Supplementary files format and content: The processed files are combined digital expression matrix divided in three files. The matrix.mtx file contains the values, barcodes.tsv contains the cell barcodes detected, and genes.tsv contains the list of genes detected.

source_name: Pituitary

growth_protocol: Wild-type C57BL/6 mice were housed at the animal center in the National Institute of Biological Sciences in a Specific Pathogen Free (SPF) facility within individually ventilated cages as well as the controlled temperature, humidity and light-dark cycle, and a regular rodent chow diet.

extract_protocol:
For the young and old pituitary sample, anesthetized mice were perfused via the aorta with cold PBS and dissected pituitary was placed into an enzyme mix containing 0.5% w/v collagenase type 2, 0.25% trypsin, in Hanks balanced salt solution for 2-3 hours at 37°C. The tissue and cells were gently triturated and pelleted at 900g for 3 minutes, and resuspended for further single cell sorting. All live cells from young or old pituitary negative for DAPI  staining were sorted for further scRNA-seq.
Libraries were prepared for sequencing using standard Illumina protocols

value: Pituitary

value: 18-24 months

value: WT


title: Igha-Cre.

description: ZsGreen+ pituitary cells

value: 4-8 months


title: Young.

description: All pituitary cells

value: 2-3 months


title: DIPseq_5caC_siC_96h

description: DIP-seq experiment

source_name: mouse Embryonic Stem Cells (mESCs)

value: 61225, Active Motif


title: DIPseq_5caC_siTdg_96h

description: DIP-seq experiment


title: RNAseq_EB_day11_siC_R2

description: RNA-seq experiment


title: Paip1_2: Paip1 mutant replicate 2


title: control_2: y w control replicate 2


title: DIPseq_5caC_siTdg_48h

description: DIP-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection at each replicate of the same condition against the Input was performed with MACS (PubMed ID: 18798982) and EaSEQ (PubMed ID:  26926434). DiffBind was next used to generate the final consensus set of peaks (PubMed ID: 22217937). Peaks were reported in BED format.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
RNA-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using TOPHAT (PubMed ID 22383036) with the option -g 1.
RNA-seq analysis: DESeq2 (PubMed ID 25516281) was used to calculate differential gene expression (pairing samples). The "stat" attribute of DESeq2 output per gene was used to build the preranked gene lists suitable for GSEA analysis.
ATAC-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each *seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome except in the cases in which spike-in information was available to perform the normalization.
The UCSC genome browser (PubMed ID 36420891) was used to generate screenshots of the *seq experiments (ChIP-seq of Tdg: windowing function mean, smoothing window 3; ChIP-seq of p53: windowing function mean, smoothing window 14; DIP-seq 5 caC: windowing function mean, smoothing window 14).
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
Supplementary_files_format_and_content: Files .rnk (preranked files from RNA-seq for GSEA)
Supplementary_files_format_and_content: Files DESEq2 results (statistical values)
Supplementary_files_format_and_content: Files DESEq2 results (RPKMs)


title: THP1, LPS, rep3

value: monocytic leukemia cells

tag: treatment

value: LPS


title: DIPseq_5caC_siC_48h

description: DIP-seq experiment


title: liver tissue from MDA 12

city: Bunkyo

first: Tadahaya

last: Mizuno

state: Tokyo

address: 7-3-1, Hongo, Pharmaceutical Sciences, Sogo-kenkyuto 8th floor, Dotai

department: Pharmaceutical Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Quality control of all reads was performed using PINSEQ++ (version 1.2.4) with the indicated parameters (trim_left = 5, trim_tail_right = 5, trim_qual_right = 30, ns_max_n = 20, min_len = 30) (https://peerj.com/preprints/27553/).
The expression of transcripts was quantified using Salmon (version 1.6.0) and gencode.vM28.transcripts obtained from GENCODE (https://www.gencodegenes.org/) with the indicated parameters (validation Mappings, gcBias, seqBias) and decoy-aware index created using Salmon and GRCm39.primary_assembly.genome obtained from GENCODE.
Transcripts per kilobase million (TPM) data were obtained using tximport, which is implemented in the software package Bioconductor with R (version 4.1.3) from quant.sh files created by Salmon.
Assembly: GRCm39
Supplementary files format and content: Files with gene raw counts and transcripts per millions (TPM)

source_name: liver

extract_protocol:
We euthanized animals 24 hrs after administration, and perfused liver samples and blood were harvested. For the obtained liver, a portion of the outer left lateral lobe of the liver was subjected to RNA isolation, and the remaining tissue was subjected to flow cytometry analysis. Total RNA was prepared using Isogen II and purified using an RNeasy Plus Mini Kit with gDNA elimination by an RNase-Free DNase Set, following the manufacturer’s protocols.
RNA-Seq libraries were prepared with a TruSeq Stranded mRNA Sample Preparation kit. The libraries were sequenced for single-end reading using a NovaSeq 6000 (Illumina).

treatment_protocol: Six-week-old mice acclimatized for one week were used for the experiments. Seven compounds, alpha-naphthyl isothiocyanate (ANIT), acetaminophen (APAP), CCl4 (CCl4), concanavalin A (ConA), galactosamine (GAL), 4,4'-methylene dianiline (MDA), and thioacetamide (TAA), were administered after 12 hrs of fasting. Depending on the compound to be administered, the vehicle was selected from 0.5% methylcellulose solution, saline, and corn oil. As a control group, 0.5% methylcellulose solution was used for oral administration, and saline was used for tail vein and intraperitoneal administration. The dose was 10 µL/kg for all groups.

value: male

value: liver

value: 4,4'-methylene dianiline (MDA)

tag: route

value: gavage

tag: time

value: 24 hr


title: liver tissue from TAA 7

value: thioacetamide (TAA)


title: liver tissue from TAA 1


title: liver tissue from TAA 8


title: liver tissue from MDA 8


title: liver tissue from TAA 3


title: liver tissue from TAA 6


title: liver tissue from MDA 7


title: liver tissue from MDA 4


title: ChIPseq_Tdg-shTdg

description: ChIP-seq experiment

tag: cell line

value: TDG Polyclonal ab PA5-29140 ThermoFisher


title: ChIPseq_Input

description: ChIP-seq experiment


title: ChIPseq_p53_R1

description: ChIP-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
ChIP-seq analysis: Peak detection at each replicate of the same condition against the Input was performed with MACS (PubMed ID: 18798982) and EaSEQ (PubMed ID:  26926434). DiffBind was next used to generate the final consensus set of peaks (PubMed ID: 22217937). Peaks were reported in BED format.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
RNA-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using TOPHAT (PubMed ID 22383036) with the option -g 1.
RNA-seq analysis: DESeq2 (PubMed ID 25516281) was used to calculate differential gene expression (pairing samples). The "stat" attribute of DESeq2 output per gene was used to build the preranked gene lists suitable for GSEA analysis.
ATAC-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
DIP-seq analysis: Alignment: Sequence of the reads of the samples  were mapped to the mouse genome (mm9) using BOWTIE (PubMed ID 19261174) with the option -m 1.
SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each *seq experiment. Height of the profiles was normalized by the total number of reads mapped over the mouse genome except in the cases in which spike-in information was available to perform the normalization.
The UCSC genome browser (PubMed ID 36420891) was used to generate screenshots of the *seq experiments (ChIP-seq of Tdg: windowing function mean, smoothing window 3; ChIP-seq of p53: windowing function mean, smoothing window 14; DIP-seq 5 caC: windowing function mean, smoothing window 14)
Genome_build: mm9
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)
Supplementary_files_format_and_content: Files .rnk (preranked files from RNA-seq for GSEA)
Supplementary_files_format_and_content: Files DESEq2 results (statistical values)
Supplementary_files_format_and_content: Files DESEq2 results (RPKMs)

value: NCL-L-p53-CM5 (Leica)


title: ChIPseq_Tdg_R2

description: ChIP-seq experiment


title: liver tissue from MDA 3


title: liver tissue from MDA 2


title: liver tissue from MDA 1


title: ChIPseq_Tdg_R1

description: ChIP-seq experiment


title: genomic DNA from MB0120PT01

type: genomic

city: Goyang

first: Seong-min

last: Park

address: Ilsan-ro

country: South Korea

institute: NCC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Beadchip using standard Illumina protocol

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

data_processing: BeadStudio, Lumi, BMIQ

label: Cy5 and Cy3

source_name: primary medulloblastoma MB0120PT01

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from medulloblastoma samples using MagNA Pure 24 Total NA Isolation kit (Roche, Switzerland) or Allprep DNA/RNA Mini Kit (Qiagen, Germany) according to standard instructions

tag: sample

value: primary medulloblastoma

tag: type

value: primary


title: genomic DNA from MB0121PT01

source_name: primary medulloblastoma MB0121PT01


title: liver tissue from GAL 4

value: galactosamine (GAL)


title: liver tissue from GAL 8

value: WT


title: liver tissue from GAL 7


title: genomic DNA from MB0115PT01

source_name: primary medulloblastoma MB0115PT01


title: ChIPseq_p53_R2

description: ChIP-seq experiment


title: genomic DNA from MB0109PT01

source_name: primary medulloblastoma MB0109PT01


title: genomic DNA from MB0109RT01

source_name: recurrent medulloblastoma MB0109RT01

value: recurrent medulloblastoma

value: recurrent


title: liver tissue from GAL 2


title: liver tissue from Ctrl 18

value: 0.5 % methylcellulose


title: liver tissue from Ctrl 16


title: genomic DNA from MB0083PT01

source_name: primary medulloblastoma MB0083PT01


title: genomic DNA from MB0062PT01_3

source_name: primary medulloblastoma MB0062PT01_3


title: liver tissue from Ctrl 17


title: genomic DNA from MB0086PT01

source_name: primary medulloblastoma MB0086PT01


title: genomic DNA from MB0087PT01

source_name: primary medulloblastoma MB0087PT01


title: genomic DNA from MB0015PT01

source_name: primary medulloblastoma MB0015PT01


title: genomic DNA from MB0077PT01_2

source_name: primary medulloblastoma MB0077PT01_2


title: liver tissue from Ctrl 10


title: liver tissue from Ctrl 12


title: genomic DNA from MB0107PT02

source_name: primary medulloblastoma MB0107PT02


title: genomic DNA from MB0109PT02

source_name: primary medulloblastoma MB0109PT02


title: liver tissue from Ctrl 15


title: genomic DNA from MB0123PT01

source_name: primary medulloblastoma MB0123PT01


title: liver tissue from Ctrl 7


title: liver tissue from Ctrl 8


title: liver tissue from Ctrl 4


title: liver tissue from Ctrl 9


title: genomic DNA from MB0004PT01

source_name: primary medulloblastoma MB0004PT01


title: genomic DNA from MB0100PT01

source_name: primary medulloblastoma MB0100PT01


title: genomic DNA from MB0082PT01

source_name: primary medulloblastoma MB0082PT01


title: genomic DNA from MB0075PT01

source_name: primary medulloblastoma MB0075PT01


title: genomic DNA from MB0073PT01

source_name: primary medulloblastoma MB0073PT01


title: liver tissue from Ctrl 1

source_name: liver


title: liver tissue from ConA 11

value: concanavalin A (ConA)


title: liver tissue from ConA 12


title: liver tissue from Ctrl 2


title: genomic DNA from MB0072PT01

source_name: primary medulloblastoma MB0072PT01


title: liver tissue from ConA 8


title: genomic DNA from MB0032PT01

source_name: primary medulloblastoma MB0032PT01


title: genomic DNA from MB0043PT01

source_name: primary medulloblastoma MB0043PT01


title: genomic DNA from MB0031PT01

source_name: primary medulloblastoma MB0031PT01


title: genomic DNA from MB0119PT01

source_name: primary medulloblastoma MB0119PT01


title: liver tissue from ConA 2


title: liver tissue from ConA 3


title: liver tissue from ConA 4


title: genomic DNA from MB0118PT01

source_name: primary medulloblastoma MB0118PT01


title: liver tissue from Ctrl 3


title: genomic DNA from MB0077PT01

source_name: primary medulloblastoma MB0077PT01


title: genomic DNA from MB0117PT01

source_name: primary medulloblastoma MB0117PT01


title: genomic DNA from MB0060PT01_2

source_name: primary medulloblastoma MB0060PT01_2


title: liver tissue from CIP 8

value: 0.9% saline


title: liver tissue from CIP 7

value: male


title: liver tissue from CIV 7

value: liver


title: liver tissue from CCl4 12


title: genomic DNA from MB0097RT01

source_name: recurrent medulloblastoma MB0097RT01


title: liver tissue from ConA 5


title: liver tissue from CCl4 10


title: liver tissue from CCl4 11


title: liver tissue from CIV 8


title: genomic DNA from MB0112PT01

source_name: primary medulloblastoma MB0112PT01


title: genomic DNA from MB0111PT01

source_name: primary medulloblastoma MB0111PT01


title: liver tissue from CCl4 6


title: genomic DNA from MB0070PT01

source_name: primary medulloblastoma MB0070PT01


title: genomic DNA from MB0112RT01

source_name: recurrent medulloblastoma MB0112RT01


title: genomic DNA from MB0062PT01_2

source_name: primary medulloblastoma MB0062PT01_2


title: liver tissue from CCl4 8


title: liver tissue from CCl4 5


title: genomic DNA from MB0111RT01

source_name: recurrent medulloblastoma MB0111RT01


title: genomic DNA from MB0107PT01

source_name: primary medulloblastoma MB0107PT01


title: liver tissue from CCl4 1

source_name: liver


title: liver tissue from APAP 8

value: acetaminophen (APAP)


title: liver tissue from APAP 11

value: gavage


title: liver tissue from APAP 6

value: 24 hr


title: liver tissue from APAP 2


title: genomic DNA from MB0103RT01

source_name: recurrent medulloblastoma MB0103RT01


title: genomic DNA from MB0103PT01

source_name: primary medulloblastoma MB0103PT01


title: genomic DNA from MB0107RT01

source_name: recurrent medulloblastoma MB0107RT01


title: genomic DNA from MB0105RT01

source_name: recurrent medulloblastoma MB0105RT01


title: liver tissue from APAP 4


title: genomic DNA from MB0099RT01

source_name: recurrent medulloblastoma MB0099RT01


title: genomic DNA from MB0105PT01

source_name: primary medulloblastoma MB0105PT01


title: genomic DNA from MB0097PT01

source_name: primary medulloblastoma MB0097PT01


title: liver tissue from ANIT 3

value: alpha-naphthyl isothiocyanate (ANIT)


title: liver tissue from ANIT 2


title: liver tissue from ANIT 4


title: liver tissue from APAP 1


title: liver tissue from ANIT 1


title: genomic DNA from MB0096RT01

source_name: recurrent medulloblastoma MB0096RT01


title: genomic DNA from MB0092RT01

source_name: recurrent medulloblastoma MB0092RT01


title: genomic DNA from MB0092PT01

source_name: primary medulloblastoma MB0092PT01


title: genomic DNA from MB0080PT01

source_name: primary medulloblastoma MB0080PT01


title: genomic DNA from MB0078PT01

source_name: primary medulloblastoma MB0078PT01


title: genomic DNA from MB0089PT01

source_name: primary medulloblastoma MB0089PT01


title: RNAseq_MEPs_VhlcKO_2

city: Merced

first: Betsabel

last: Chicana

state: CA

address: 5200 Lake Rd

institute: University of California Merced

data_processing:
Sequencing data quality was checked using fastQC
UMIs, adapters and linkers were trimmed from Read 2 using Trimmomatic
Reads were then mapped to mouse genome (mm10) using STAR
read counts per gene were determined using “featureCounts” from Rsubread package
Differentially expressed genes (DEGs) were identified using limma after voom normalization
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone marrow

extract_protocol:
MEPs (live, negative for F4/80, CD3, CD4, CD5, CD8, CD19, NK1.1, Ter119 and Gr1; CD45+ cKIT+ Sca1- CD34- CD16/32-) from pooled bone marrow of control and VhlcKO mice were isolated by flow cytometric sorting on the FACS Aria3 and stored in RLT lysis buffer (Qiagen, Redwood City, CA, USA) supplemented with β-mercaptoethanol at -80C until RNA isolation.
Library construction was performed with the SMARTer® Stranded Total RNA-Seq Kit v3

value: pooled male and female

tag: pooled mice_info

value: 4M 1F

tag: age

value: 24 weeks

tag: cell type

value: Vhl fl/fl; Dmp1-Cre+

value: bone marrow


title: RNAseq_MEPs_Control_2

value: 2M 2F

tag: genotype

value: Vhl fl/fl; Dmp1-Cre-


title: RNAseq_MEPs_VhlcKO_1

value: 3M 3F

tag: tissue


title: RNAseq_MEPs_Control_1

value: 1M 4F


title: genomic DNA from MB0088PT01

source_name: primary medulloblastoma MB0088PT01

value: primary medulloblastoma

value: primary


title: genomic DNA from MB0099PT01

source_name: primary medulloblastoma MB0099PT01


title: genomic DNA from MB0096PT01

source_name: primary medulloblastoma MB0096PT01


title: genomic DNA from MB0068PT01

source_name: primary medulloblastoma MB0068PT01


title: genomic DNA from MB0035PT01

source_name: primary medulloblastoma MB0035PT01


title: BMC_3

city: Shanghai,

first: Ting

last: Jiang

address: Quxi Road No. 500

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

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1)
Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: the complete medium αMEM (Sigma, MO, USA) containing 10% fetal bovine serum (FBS, Gibco, USA) was added to the culture system. Cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen) as per manufacturer instructions. Samples for RNA-seq were further cleaned up by RNeasy Mini Kit (QIAGEN). RNAseq libraries were prepared with Illumina TruSeq Stranded mRNAseq Sample Prep kit (Illumina), polyadenylated mRNAs were captured with oligodT beads
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

value: wild type

value: cultered on BMC membrane


title: BMC+L_2

value: cultered on BMC membrane stimulated by LIPUS


title: BMC+L_1


title: genomic DNA from MB0067PT01

source_name: primary medulloblastoma MB0067PT01


title: BMC+L_3


title: BMC_1


title: control_1

value: blank control


title: RELACS_Histone_K2-iKO-WT_H4K12ac_Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
The data processing, quality control, trimming, mapping and H3-Normalized coverage file were performed using snakePipes DNA-mapping and ChIP-seq pipeline (Bhardwaj et al., 2019).
Assembly: mm10
Supplementary files format and content: BigWig file , H3 normalized

source_name: Mouse Embryonic Fibroblasts

extract_protocol:
Cells were fixed with 1% PFA for 10 minutes at RT , Nuclei extraction, quantification and ChIP was performed using the published RELACS (Arrigoni et al, 2018)
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645)

value: Mouse Embryonic Fibroblasts

value: KANSL2 inducible Knockout

value: 4 Hydroxyltamoxifen for 4 days in culture, infected with "KANSL2-WT" Lentivirus and selected with blasticidin for 2 days in culture

tag: chip antibody

value: H4K12ac (Millipore, 07595)


title: genomic DNA from MB0065PT01

source_name: primary medulloblastoma MB0065PT01


title: genomic DNA from MB0066PT01

source_name: primary medulloblastoma MB0066PT01


title: genomic DNA from MB0064PT01

source_name: primary medulloblastoma MB0064PT01


title: control_3


title: control_2


title: BMC_2


title: RELACS_Histone_K2-iKO-WT_H3_Rep2


title: RELACS_Histone_K2-iKO-WT_H4K5ac_Rep2

value: H4K5ac (Activ Motif, 39169


title: genomic DNA from MB0063PT01

source_name: primary medulloblastoma MB0063PT01


title: RELACS_Histone_K2-iKO-WT_H4K5ac_Rep1


title: RELACS_Histone_K2-iKO-WT_H3_Rep1


title: genomic DNA from MB0085PT01

source_name: primary medulloblastoma MB0085PT01


title: RELACS_Histone_K2-iKO-Vector_H4K12ac_Rep2

value: 4 Hydroxyltamoxifen for 4 days in culture, infected with "Vector control" Lentivirus and selected with blasticidin for 2 days in culture


title: genomic DNA from MB0057PT01

source_name: primary medulloblastoma MB0057PT01


title: genomic DNA from MB0058PT01

source_name: primary medulloblastoma MB0058PT01


title: genomic DNA from MB0071PT01

source_name: primary medulloblastoma MB0071PT01


title: genomic DNA from MB0059PT01

source_name: primary medulloblastoma MB0059PT01


title: RELACS_Histone_K2-iKO-Vector_H3_Rep2


title: RELACS_Histone_K2-iKO-Vector_H4K12ac_Rep1


title: genomic DNA from MB0053PT01

source_name: primary medulloblastoma MB0053PT01


title: genomic DNA from MB0056PT01

source_name: primary medulloblastoma MB0056PT01


title: genomic DNA from MB0050PT01

source_name: primary medulloblastoma MB0050PT01


title: RELACS_Histone_K2-iKO-Vector_H4K5ac_Rep1


title: RELACS_Histone_K2-iWT-Vector_H4K12ac_Rep2

value: WT (Kansl2 floxed)


title: genomic DNA from MB0048PT01

source_name: primary medulloblastoma MB0048PT01


title: genomic DNA from MB0062PT01

source_name: primary medulloblastoma MB0062PT01


title: genomic DNA from MB0047PT01

source_name: primary medulloblastoma MB0047PT01


title: RELACS_Histone_K2-iKO-Vector_H4K5ac_Rep2


title: genomic DNA from MB0049PT01

source_name: primary medulloblastoma MB0049PT01


title: RELACS_Histone_K2-iKO-Vector_H3_Rep1

source_name: Mouse Embryonic Fibroblasts


title: genomic DNA from MB0052PT01

source_name: primary medulloblastoma MB0052PT01


title: RELACS_Histone_K2-iWT-Vector_H4K12ac_Rep1


title: RELACS_Histone_K2-iWT-Vector_H4K5ac_Rep2


title: genomic DNA from MB0045PT01

source_name: primary medulloblastoma MB0045PT01


title: RELACS_Histone_K2-iWT-Vector_H4K5ac_Rep1


title: genomic DNA from MB0060PT01

source_name: primary medulloblastoma MB0060PT01


title: RELACS_Histone_K2-iKO-WT_H4K12ac_Rep1


title: genomic DNA from MB0042PT01

source_name: primary medulloblastoma MB0042PT01


title: RELACS_Histone_K2-iWT-Vector_H3_Rep1


title: genomic DNA from MB0044PT01

source_name: primary medulloblastoma MB0044PT01


title: genomic DNA from MB0041PT01

source_name: primary medulloblastoma MB0041PT01


title: LNP-empty 6dpi biol rep3

city: Chongqing

first: Xiaoyan

last: Ding

address: No. 30, Gao Tan Yan Zheng Street， Shapingba District

institute: Army Medical University

data_processing:
After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).
Reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 version 2.1.0(15) software.
Assembly: The mapped reads of each sample were assembled by StringTie version 2.1.2 in a reference-based approach
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted from the brain tissues using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen, USA) and genomic DNA was removed using DNase I (TaKaRa, Japan).    from Illumina (San Diego, CA) using 1μg of total RNA.
RNA-seq librariy was prepared following TruSeqTM RNA sample preparation Kit  from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: 20 PFU DENV-2 were mixed with 2 ug LNP-Cnpy3 and LNP-empty, separately. Then, mixture was infected three-day-old suckling mice by intracranial injection (total volume 20 μL each).

value: Brain

value: LNP-empty and DENV2 mix injiection


title: LNP-empty 6dpi biol rep2

value: LNP-empty and DENV2 mix injiection for 1 day


title: genomic DNA from MB0040PT01

source_name: primary medulloblastoma MB0040PT01


title: LNP-Cnpy3 6dpi biol rep3

value: LNP-Cnpy3 and DENV2 mix injiection


title: LNP-empty 6dpi biol rep1


title: genomic DNA from MB0039PT01

source_name: primary medulloblastoma MB0039PT01

value: primary medulloblastoma


title: genomic DNA from MB0046PT01

source_name: primary medulloblastoma MB0046PT01

value: primary


title: genomic DNA from MB0038PT01

source_name: primary medulloblastoma MB0038PT01


title: RELACS_Histone_K2-iWT-Vector_H3_Rep2


title: genomic DNA from MB0036PT01

source_name: primary medulloblastoma MB0036PT01


title: LNP-Cnpy3 6dpi biol rep2


title: LNP-empty 1dpi biol rep2

description: LNPB


title: genomic DNA from MB0037PT01

source_name: primary medulloblastoma MB0037PT01


title: LNP-empty 1dpi biol rep1

description: LNPA


title: LNP-Cnpy3 6dpi biol rep1


title: genomic DNA from MB0029PT01

source_name: primary medulloblastoma MB0029PT01


title: genomic DNA from MB0034PT01

source_name: primary medulloblastoma MB0034PT01


title: LNP-empty 1dpi  biol rep3

description: LNPC


title: LNP-Cnpy3 1dpi biol rep3


title: LNP-Cnpy3 1dpi biol rep2


title: genomic DNA from MB0025PT01

source_name: primary medulloblastoma MB0025PT01


title: LNP-Cnpy3 1dpi biol rep1


title: genomic DNA from MB0024PT01

source_name: primary medulloblastoma MB0024PT01


title: genomic DNA from MB0026PT01

source_name: primary medulloblastoma MB0026PT01


title: genomic DNA from MB0023PT01

source_name: primary medulloblastoma MB0023PT01


title: LGG+GEMys-IL2 2

city: Columbus

first: Alessandro

last: Canella

state: OH

address: 700 Children’s Drive

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

description: 60-80M read pairs

data_processing:
Low-quality reads (q<10), and adaptor sequences were eliminated from raw reads using bbduk version 37.64
Features were identified from the GFF file that came with the assembly from Gencode (V28).
Feature coverage counts were calculated using featureCounts
Normalized (TPM) quantification for each sample was done using salmon counts
Assembly: GRCm38.p6 assembly of theMus musculus reference from NCBI
Supplementary files format and content: comma separated file that includes the aggregated normalized salmon TPM counts for all samples

source_name: brain

growth_protocol: DF1-PDGF and DF1-CRE cells were injected intracranially in the right hemisphere of RCAS mice at the age of 2 days. Low-grade glioma (LGG) animals were randomized at day 21

extract_protocol:
Total RNA from tumor-infiltrating immune cells was isolated using the Qiagen miRNeasy Micro kit (Qiagen) and eluted with 14uL H2O. The quality and quantity of RNA was checked with Bioanalyzer.
Total RNA-seq by Illumina NovaSeq6000

treatment_protocol:
LGG animals were treated with one dose of Vehicle (80μl of PBS, n=3), or 8x106 GEMys-IL2 (80μl, n=3) by retro-orbital intravenous injection.
To Isolate the tumor-infiltrating immune cells: the brain tissue was mechanically dissociated on a 70μm cell strainer and collected in DPBS supplemented with the 10% of FBS (Corning). Cells were washed and resuspended with RBC buffer (Biolegend) on ice for 5 minutes to lyse the red blood cells. RBC solution was quenched with 5x DPBS+10% FBS and cells isolated by centrifugation. The stratification with 25% Percoll (GE Healthcare) was performed to deplete the myelin layer at 500g for 20 minutes at 18°C in absence of break.

value: brain

value: Tumor infiltrating immune cells

value: Day 3


title: LGG+GEMys-IL2 3

description: 60-80M read pairs


title: LGG+GEMys-IL2 1

description: 60-80M read pairs


title: LGG 3

description: 60-80M read pairs

value: PBS


title: genomic DNA from MB0030PT01

source_name: primary medulloblastoma MB0030PT01


title: genomic DNA from MB0019PT01

source_name: primary medulloblastoma MB0019PT01


title: genomic DNA from MB0017PT01

source_name: primary medulloblastoma MB0017PT01


title: genomic DNA from MB0022PT01

source_name: primary medulloblastoma MB0022PT01


title: genomic DNA from MB0020PT01

source_name: primary medulloblastoma MB0020PT01


title: genomic DNA from MB0018PT01

source_name: primary medulloblastoma MB0018PT01


title: genomic DNA from MB0016PT01

source_name: primary medulloblastoma MB0016PT01


title: genomic DNA from MB0028PT01

source_name: primary medulloblastoma MB0028PT01


title: LGG 1

description: 60-80M read pairs


title: genomic DNA from MB0014PT01

source_name: primary medulloblastoma MB0014PT01


title: genomic DNA from MB0012PT01

source_name: primary medulloblastoma MB0012PT01


title: genomic DNA from MB0010PT01

source_name: primary medulloblastoma MB0010PT01


title: WT3

city: La Jolla

first: Olivia

last: Osborn

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Quality control of fastq file using FastQC v0.11.8
Sequence trimming using Trimmomatic V0.38
Alignment using STAR aligner v2.5.1a
Data quantification using RSEM v1.3.0 and Ensembl release 98 notation
limma-voom method for differential expression analaysis using edgeR and limma
Assembly: GRCm38p6
Supplementary files format and content: clic1ko_rnaseq_differential_expression_KOvsWT_AllGenes.csv

source_name: Hypothalamus

extract_protocol:
RNA extraction using Qiagen RNAeasy and RNA integrity using Tapestation 2200
TruSeq library preparation kit

treatment_protocol: Frozen perigonadal adipose tissue

value: Hypothalamus

tag: Sex

value: male

value: WT


title: KO6

tag: strain

value: Clic1 Knockout


title: WT9


title: KO8


title: KO4


title: WT11


title: LGG 2

description: 60-80M read pairs


title: BMO 2% B.breve midlog growth 3

city: Davis

first: David

middle: A

last: Mills

address: One Shields ave

department: Dept. of Food Science and Technology

institute: University of California Davis

data_processing:
Raw sequence files were uploaded in to CLC genomic work bench 12.0 (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-genomics-workbench/). Data quality was checked and then the RNAseq analysis was conducted by aligining the sequence read in to to the genome of B. breve 1107E in CLC genomic work bench.
Assembly: B. breve SW 1107E genome is deposited in the JGI/IMG database and will be released upon manuscript submission.
Supplementary files format and content: Processed files are obtained from CLC genomic work bench and each file was exported as tab limited txt file. Processed files cotain the gene ID and the expression in RPKM

organism: Bifidobacterium breve

source_name: bacterial cells

growth_protocol: Grown in the anaerobic hood at 37 degrees celcius. Growth media is basal MRS and 2% Lactose or 3SL or BMO as the energy source

extract_protocol:
RNA was collected to RNA protect and Qiagen RNA easy kit was used. Before Qiagen protocol Mutanolysin and Protnase K was used.to open the cells
Ribodepletion was conducted using RiboZero plus kit and illumina prokaryotic RNA seq library was constructed

treatment_protocol: Three different carbon sources as energy - Lactose, 3SL or BMO

value: bacterial cells

value: BMO


title: genomic DNA from MB0008PT01

source_name: primary medulloblastoma MB0008PT01


title: BMO 2% B.breve midlog growth 1


title: genomic DNA from MB0105RT02

source_name: recurrent medulloblastoma MB0105RT02

value: recurrent medulloblastoma

value: recurrent


title: genomic DNA from MB0006PT01

source_name: primary medulloblastoma MB0006PT01


title: Flt3–CD48–LSK cells, CreERT2+Regnase-1fl/flRegnase-3–/–

city: Kyoto

first: Takuya

last: Uehata

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto university

description: scATAC-seq

data_processing:
scATAC-seq base call files  were processed into FASTQ files and count data using cellranger-atac mkfastq and cellranger-atac count (10X Genomics, version 2.0.0).
Data for the four samples were merged using cellranger-atac aggr.
Assembly: version mm10-2020-A-2.0.0 (the 10X Genomics website)
Supplementary files format and content: output files of cellranger-atac aggr

source_name: bone marrow

extract_protocol:
Nuclei isolation for single-cell ATAC sequencing was performed according to “Nuclei Isolation for Single Cell ATAC Sequencing Demonstrated Protocol”
Nuclei suspension was mixed with the tagmentation mix and incubated for 1 hr at 37°C. After mixing with a barcoding mix, the nuclei were loaded into a 10x chip H together with barcoded beads and partitioning oil (Chromium Next GEM Chip H Single Cell Kit v1.1, Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1, 10x Genomics) and encapsulated using the Chromium controller (10x Genomics). The Gel Bead-In EMulsions (GEMs) was transferred into a PCR tube and amplified for 12 cycles in a thermocycler. The barcoded DNA was purified and subjected to an index PCR for 11 cycles.

treatment_protocol: Mice were intraperitonially injected with tamoxifen for 5 consecutive days. BM cells were freshly prepared followed by magnetic isolation of Kit+ cells. Using FACS sorting, Flt3–CD48–LSK cells were isolated from the Kit+ cells of CreERT2+Regnase-1fl/flRegnase-3–/–, CreERT2+Regnase-1fl/flRegnase-3–/–Nfkbizfl/fl, CreERT2+Nfkbizfl/fl, or control mice.

value: bone marrow

value: HSCs

value: Regnase-1/Regnase-3 DKO


title: WT10


title: 3SL 2% B.breve midlog growth 2


title: 3SL  2% B.breve midlog growth 1


title: genomic DNA from MB0013PT01

source_name: primary medulloblastoma MB0013PT01

value: primary medulloblastoma


title: Lactose 2% B.breve midlog growth 2

value: Lactose


title: WT1


title: Flt3–CD48–LSK, CreERT2+Nfkbizfl/fl

description: scATAC-seq

value: Nfkbiz KO


title: genomic DNA from MB0005PT01

source_name: primary medulloblastoma MB0005PT01

value: primary


title: genomic DNA from MB0009PT01

source_name: primary medulloblastoma MB0009PT01


title: Lactose 2% B.breve midlog growth 1


title: KO2


title: genomic DNA from MB0011PT01

source_name: primary medulloblastoma MB0011PT01


title: Flt3–CD48–LSK cells, control

description: scATAC-seq

value: control


title: genomic DNA from MB0003PT01

source_name: primary medulloblastoma MB0003PT01


title: Lactose 2% B.breve midlog growth 3


title: genomic DNA from MB0002PT01

source_name: primary medulloblastoma MB0002PT01


title: Flt3–CD48–LSK cells, CreERT2+Regnase-1fl/flRegnase-3–/–Nfkbizfl/fl

description: scATAC-seq

value: Regnase-1/Regnase-3/Nfkbiz TKO


title: Non-GVHD

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
We use Seurat(v4.0.2) to determine clusters,dimensionality reduction was performed using PCA and the first twenty principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: thymus

extract_protocol:
A certain number of thymic lymphocytes from WT (C57BL/6 mice without BMT), non-GVHD (BMT F1 mice without cGVHD) and GVHD (BMT F1 mice with cGVHD) group were taken and centrifuged. Resuspend cell pellet and stain with CD8-FITC antibody. Wash cells to remove unbound antibody and centrifuge the samples. The cell precipitation was suspended and anti-FITC MicroBeads were added for incubation. Apply cell suspension onto the separation column, and then collect unlabeled cells which pass through. TCRβ+ CD1d-tetramer+ CD24- NK1.1- cells were sorted by flow cytometry after cell surface staining.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3'/5’ Library and Gel Bead Kit, Single Cell V(D)J Enrichment Kit.The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: thymus

value: NKT

value: 16w (9w after BMT)


title: GVHD

description: 10x Genomics


title: MBH, Emulsifier, Rep5

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

institute: IDIBAPS

data_processing:
Quality control of samples was performed using FastQC v0.11.9
Transcript quantification was done using Kallisto v0.46.1 with default parameters
normalized log2 CPM TMM gene values for all samples were obtained using edgeR v3.40.1
Assembly: mm10
Supplementary files format and content: Sample abundance tab-delimited text files include TPM values for the corresponding Sample
Supplementary files format and content: CPM_allsamples tab-delimited text file includes log2 CPM TMM gene values for all samples

source_name: Mediobasal hypothalamus

growth_protocol: Offspring mice were kept with their dams until weaning at P21.

extract_protocol:
mRNA strand-specific RNA libraries were generated using 200 ng of total RNA using the Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions
Libraries were sequenced on an Illumina NextSeq2000 (Illumina) in paired-end mode with a read length of 2×50 bp. Around 40 million of paired-end reads were generated for each sample/condition.

treatment_protocol: After weaning, the offspring were subdivided into control (drinking water without supplementation) and emulsifier group (CMC+P80; 1% in drinking water), ending up with four different conditions:  maternal control - offspring control (CTRL – CTRL); maternal control - offspring emulsifiers (CTRL – Emul); maternal emulsifiers - offspring control (Emul – CTRL) and maternal emulsifiers - offspring emulsifiers (Emul – Emul).

value: Mediobasal hypothalamus

value: wild-type C57Bl/6

value: Emulsifiers (1% CMC + 1% P80)

value: P21, after weaning


title: 3SL 2% B.breve midlog growth 3

value: bacterial cells


title: genomic DNA from MB0001PT01

source_name: primary medulloblastoma MB0001PT01


title: MBH, Emulsifier, Rep2


title: MBH, Emulsifier, Rep4


title: WT

description: 10x Genomics


title: MBH, Emulsifier, Rep3


title: MBH, Emulsifier, Rep1


title: BM adipo and stroma 2, snRNAseq

city: New York

first: Lei

state: NY

institute: Conlumbia University Irving Medical Center

description: 10x Genomics

data_processing:
The sequencing data were demultiplexed and converted to FASTQ format using the Cell Ranger pipeline (10x Genomics).
Assembly: mm10
Supplementary files format and content: H5

source_name: Bone marrow

extract_protocol:
Collected bone marrow adipocytes and sorted CD45/Ter119/CD31- cells from the bone marrow of Plin1-creER; tdTomato mice 5 weeks after sublethal irradiation were kept frozen until nuclei isolation. Frozen cell pellets were resuspended in TST buffer (10 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA) and incubated for 10 min on ice. After adding ST buffer (10 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM CaCl2, 21 mM MgCl2), solution was filtered through a 40 µm nylon mesh, and then centrifuged (500 g, 5 min) to obtain nuclei. We analyzed 4 Plin1-creER; tdTomato mice (two were pooled together for a total of two samples).
Isolated nuclei were loaded into the 10X Chromium system and libraries were constructed using Chromium Single Cell 3’ Reagent Kit (v3) according to the manufacturer’s protocol. Libraries were subsequently sequenced on a NovaSeq 6000 Sequencing System (Illumina).

value: Adipocytes and stromal cells

value: Bone marrow

value: Plin1-CreER; tdTomato

value: 13-15 weeks old


title: MBH, Control, Rep4

value: Control


title: BM adipo and stroma 1, snRNAseq

description: 10x Genomics


title: MBH, Control, Rep2


title: MBH, Control, Rep3


title: 123994

city: Ann Arbor

first: Joanna

last: Spencer-Segal

address: 205 Zina Pitcher PI

department: Michigan Neuroscience Institute

institute: University of Michgan

data_processing:
Alignment & Generation of Count Summaries: the RNA-Seq reads were aligned to the mouse genome (GRCm38) using the Subread aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) with multi-mapping enabled. The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl release 95). The counts were then filtered. Genes with counts per million of less than 0.5 in ten or fewer samples were filtered out.
Quality Control: Quality control was performed in R (v.3.6.1) and included visualization of the overall log CPM gene expression across all subjects via boxplots and MDS plots. Outlier samples were detected and removed at this stage. We also noted that all samples from batch 3 were contaminated and were removed in the subsequent analysis. A list of which samples were removed is below in the RAW FILES section.
Differential Expression Analysis was performed using the limma-voom workflow provided by the limma package (v 3.42.0). Contrasts were developed for each comparison and interaction term of interest.
Assembly: GRCm38
Supplementary files format and content: Gene level unfiltered raw counts using ENSEMBL annotation

source_name: Brain

extract_protocol:
mRNA was isolated from dorsal and ventral hippocampi using the Qiagen RNAeasy kit in five batches, with groups counterbalanced across batches. RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA).
Samples with RINs (RNA Integrity Numbers) of 8 or greater were prepared using theKAPA mRNA Hyper prep (KAPA/Roche #KK8581) according to the protocol using 400ng input and 11 cycles PCR. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).
The samples were pooled and sequenced on 50% of an Illumina NovaSeq S4 Paired-end 50bp, according to the manufacturer's recommended protocols.

tag: animal id

value: Brain

tag: brain region

value: DHC

value: CORT

tag: surgery

value: SHAM

value: Female

value: Adult

tag: batch

tag: passed qc

value: Yes

tag: adrenal weight

tag: max weight loss

tag: cort baseline

tag: acth baseline


title: 123995

value: VHC

tag: treatment


title: 123993

tag: age


title: Pt-14_GEX

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

description:
single-cell 5' Gene Expression
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.

source_name: FNA

extract_protocol:
Live immune cells were sorted by EpCAM- /CD45+ (Biolegend, # clone 2D1 and 9C4) on a Sony SH800 cell sorter, stained with AO/PI (acridine orange / propidium iodide, Nexcelom ViaStain), and checked for viability > 80% using a Countess FL II Automated Cell Counter.
Gene expression (GEX) and V(D)J BCR libraries were constructed according to the manufacturer’s instructions (Single Cell 5’ Gene Expression V1 protocol, 10x Genomics). Libraries were sequenced on a combination of Illumina NextSeq500 (for GEX and V(D)J) and MiSeq (for V(D)J) flow cells.

tag: patient diagnosis

value: PDAC

value: FNA


title: Pt-14_BCR

description:
single-cell BCR
10x Genomics

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the human reference genome version gex-GRCh38-2020-A, while V(D)J reads were mapped to vdj-GRCh38-alts-ensembl-7.0.0, both available from the 10X Genomics website. Matrices from each separate sample were aggregated without read-depth normalization using the Cell Ranger aggr (v6.0.0) pipeline using the “normalize=None”.
Secondary analysis was carried out primarily using Loupe Browser (10X Genomics). Dead cells (% mitochondrial reads > 10%) and cells with the number of genes expressed less than 200 were also filtered out. Doublets were removed using a R package ‘Scrublet’. ScRNA-Seq Data was normalized, logarithm transformed and scaled. Principle component analysis (PCA) was run with 50 components using the top 4000 genes of each sample. The nearest neighbor algorithm was run with 50 PCAs and clustered in UMAP projections using Leiden clustering. All additional analyses were performed using Loupe Browser (10X Genomics) and the Python toolkit Scanpy. Immune cells clusters were defined using the set of markers and UMAP clusters: T cells (CD3+, TCR+, NCAM-), NK cells (CD3-, NCAM+), B cells (CD20+, CD79A+, IgKC low), PCs (JChainhi, IgKChi), myeloid cells (CD14+, CSF1R+), mast cells (CPA3+, GATA2+), fibroblasts (FAP+, ACTA2+, PDGFRA1+), epithelial cells (CK19+, CK18+, CK5+, CK14+).
Assembly: GRCh38
Supplementary files format and content: Gene expression: Single cell 5' cell/gene matrices in .mtx format generated by Cell Ranger for individual samples and for all samples aggregated.  V(D)J analysis: annotated contig files in .csv format and assembled contig sequences in FASTA format for all detected BCR sequences output by cellranger vdj.
Library strategy: scBCR-seq


title: Pt-20_BCR

description:
single-cell BCR
reads also produced on Illumina NextSeq 500
10x Genomics

source_name: resection

value: resection


title: Pt-20_GEX

description:
single-cell 5' Gene Expression
reads also produced on Illumina NextSeq 500
10x Genomics