title: E17.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep2

city: New Haven

first: James

last: Noonan

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
c16-p7
10x Genomics, v2 chemistry, single-indexed

data_processing:
Reads were mapped to the mm10 reference genome with STAR v2.7.9a, using recommended settings to generate genome indices (cellranger reference 2020-A; parameters: --outSAMtype BAM Unsorted --outSAMattributes NH HI AS nM CR CY UR UY GX GN --outSAMprimaryFlag AllBestScore --outSAMmultNmax 10 --outBAMcompression 10 --sjdbOverhang 99 --genomeSAsparseD 3). Reads mapping to more than 10 loci or with more than one best-scoring alignment were discarded. Droplet filtering and generation of cell-by-gene count matrices was performed using STARsolo (STAR v2.7.9a; parameters: --soloType CB_UMI_Simple  --soloCBwhitelist 737K-august-2016.txt --soloBarcodeReadLength 1 --soloCBmatchWLtype 1MM_multi --soloInputSAMattrBarcodeSeq CR UR --soloInputSAMattrBarcodeQual CY UY  --soloMultiMappers Unique --soloUMIdedup 1MM_CR --soloUMIfiltering - --soloCellFilter CellRanger2.2 3000 0.99 10).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, which constitute outputs from STARsolo

source_name: dorsal telencephalon

extract_protocol:
The dorsal telencephalon was dissected from four litter- and sex-matched pairs of wild type and Chd8+/- embryos at four time points: embryonic day (E) 12.5, E14.5, E16.0, and E17.5. The medial dorsal telencephalon was removed to avoid capturing the hippocampal primordium. Freshly dissected tissue was immediately dissociated into single cells, then loaded onto the 10x Genomics Chromium Controller for single cell capture.
Libraries were generated and indexed using the 10x Chromium Next GEM Single-Cell 3' kit with v2 chemistry, then sequenced using standard Illumina protocols on an Illumina HiSeq 2500, with 26 cycles for read 1 and 98 cycles for read 2.

tag: time point

value: dorsal telencephalon

value: female

value: Chd8 het


title: lean4 MeRIP-m6A

status: Public on Aug 14 2024

type: SRA

city: Shanghai

first: Yunchen

last: Luo

address: shanghai hongkou

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Assembly: MM10
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: methylation sites and enrichment information of all samples.
Library strategy: MeRIP-m6A

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: All mice were raised under Specific Pathogen Free conditions with a 12-hour dark/light cycle, 20–22 °C and 45–65% humidity with water and food provided ad libitum.

extract_protocol:
Total RNAs were obtained from db/db mice and lean control mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
Fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

tag: tissue

value: liver

tag: Sex

value: male

tag: strain


title: breast cancer single cell A053

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

country: USA

institute: UT health Science Center at San Antonio

library_source: genomic

data_processing:
The raw reads of scHi-C were first aligned to human HG19 genome, then filtered by HiC-Pro to get the valid pairs.
Genome_build: HG19
Supplementary_files_format_and_content: the column headers of *allValidPairs are:
read_name, chromosome of first locus, read position of first locus (currently middle of the reads), strand of first locus, chromosome of second locus, read position of second locus, strand of second locus, DNA fragment length, name of first restriction fragment, name of second restiction fragment, mapping quality of first read, mapping quality of second read, allele-specific analysis

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Routine cell media for all cell lines, respectively.

extract_protocol:
Extraction of cell nucleus and DNA were performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).
single-cell Hi-C was performed as described (Flyamer et al. 2017, doi:10.1038/nature21711).

treatment_protocol: Untreated

tag: cell line

tag: cell type

value: immortalized breast epithelial cell line

tag: treatment

value: untreated

tag: analysis

value: single-cell Hi-C


title: breast cancer single cell A054


title: E17.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep2

department: Genetics

description:
c17-p5
10x Genomics, v2 chemistry, single-indexed

library_source: transcriptomic single cell

molecule: polyA RNA

tag: genotype


title: Super-enhancer 66 replicate 1

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

institute: UNC Lineberger Cancer Center

description:
HF66R1
RNA-seq

data_processing:
Merge multiple FASTQs together
Map the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
Perform QC by running Picard 2.22.4 CollectRnaSeqMetrics, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: salmon_gene.matrix

growth_protocol: MDA-MB-436 TNBC cells expressing dCas9-KRAB were routinely grown and replated in T75 flasks in Dulbecco's modified eagle media supplemented with 10% fetal bovine serum and 1% pen-strep

extract_protocol:
RNA was extracted and purified from cells 48 hrs post-transfection using the Zymo RNA miniprep kit (Cat# R1054). Transfection replicates 1, 3, and 4 were used to construct RNA-seq libraries for experimental samples. Four replicates were used for positive controls (both CSF1 gene promoter and CSF1 enhancer). Three replicates were used for each of two scrambled negative controls for six total negative control replicates.
RNA-seq libraries were constructed by Novogene. 250~300 bp insert cDNA library,PolyA selected, non-strand specific

treatment_protocol: Cells were seeded into 6-well plates and transiently transfected via Fugene 6 (Promega) with unique guide RNA plasmids to target dCas9-KRAB to the region of interest.

value: Triple-negative breast cancer

value: dCas9-KRAB expressing

tag: sgrna pool_target


title: lean3 Input

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (UCSC MM10) by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts.
Assembly: MM10
Supplementary files format and content: Methylated_RNA_sites.mRNA.xlsx: methylation sites and enrichment information of all samples.


title: breast cancer single cell A051


title: lean3 MeRIP-m6A


title: breast cancer single cell A052


title: E17.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep1

description:
p6
10x Genomics, v2 chemistry, single-indexed


title: E17.5 dorsal telencephalon, wild type female, scRNA-seq, rep1

description:
p5
10x Genomics, v2 chemistry, single-indexed

value: WT


title: breast cancer single cell A056


title: lean2 Input


title: Super-enhancer 83 replicate 3

description:
HF83R3
RNA-seq


title: breast cancer single cell A050


title: Super-enhancer 30 replicate 3

description:
HF30R3
RNA-seq


title: lean2 MeRIP-m6A


title: E17.5 dorsal telencephalon, wild type male, scRNA-seq, rep2

description:
c17-p9
10x Genomics, v2 chemistry, single-indexed


title: E17.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep1

description:
p2
10x Genomics, v2 chemistry, single-indexed


title: lean1 Input


title: lean4 Input


title: breast cancer single cell A048


title: lean1 MeRIP-m6A


title: E17.5 dorsal telencephalon, wild type male, scRNA-seq, rep1

description:
p3
10x Genomics, v2 chemistry, single-indexed


title: Super-enhancer 83 replicate 1

description:
HF83R1
RNA-seq


title: breast cancer single cell A049


title: Super-enhancer 30 replicate 1

description:
HF30R1
RNA-seq


title: E16.0 dorsal telencephalon, Chd8 het female, scRNA-seq, rep2

description:
c7-p4
10x Genomics, v2 chemistry, single-indexed


title: E17.5 dorsal telencephalon, wild type female, scRNA-seq, rep2

description:
c16-p3
10x Genomics, v2 chemistry, single-indexed


title: breast cancer single cell A047


title: lean4

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Assembly: MM10
Supplementary files format and content: Gene Expression Profiling.xlsx: raw counts, normalized counts and annotations of all samples of the gene.

extract_protocol:
Total RNAs were obtained from db/db mice and lean control mice using TRIzol reagent (catalog T9108, Takara) according to the manufacturer's protocol.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).


title: Super-enhancer 52 replicate 4

description:
HF52R4
RNA-seq


title: Super-enhancer 66 replicate 3

description:
HF66R3
RNA-seq


title: breast cancer single cell A046


title: Super-enhancer 52 replicate 1

description:
HF52R1
RNA-seq


title: lean3


title: E16.0 dorsal telencephalon, Chd8 het female, scRNA-seq, rep1

description:
c7-p11
10x Genomics, v2 chemistry, single-indexed


title: E16.0 dorsal telencephalon, Chd8 het male, scRNA-seq, rep2

description:
c6-p9
10x Genomics, v2 chemistry, single-indexed


title: breast cancer single cell A045


title: Super-enhancer 52 replicate 3

description:
HF52R3
RNA-seq


title: Super-enhancer 30 replicate 4

description:
HF30R4
RNA-seq


title: breast cancer single cell A044


title: lean1


title: breast cancer single cell A043


title: E16.0 dorsal telencephalon, Chd8 het male, scRNA-seq, rep1

description:
c6-p2
10x Genomics, v2 chemistry, single-indexed


title: Super-enhancer 77 replicate 4

description:
HF77R4
RNA-seq


title: lean2


title: breast cancer single cell A042


title: E16.0 dorsal telencephalon, wild type male, scRNA-seq, rep2

description:
c6-p6
10x Genomics, v2 chemistry, single-indexed


title: breast cancer single cell A041


title: db4

value: db/db


title: db2


title: E16.0 dorsal telencephalon, wild type female, scRNA-seq, rep2

description:
c7-p7
10x Genomics, v2 chemistry, single-indexed


title: E16.0 dorsal telencephalon, wild type female, scRNA-seq, rep1

description:
c7-p10
10x Genomics, v2 chemistry, single-indexed


title: Super-enhancer 54 replicate 3

description:
HF54R3
RNA-seq


title: Super-enhancer 77 replicate 3

description:
HF77R3
RNA-seq


title: db1


title: Super-enhancer 54 replicate 1

description:
HF54R1
RNA-seq


title: db3


title: Super-enhancer 77 replicate 1

description:
HF77R1
RNA-seq


title: breast cancer single cell A040


title: E16.0 dorsal telencephalon, wild type male, scRNA-seq, rep1

description:
c6-p3
10x Genomics, v2 chemistry, single-indexed


title: E14.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep2

description:
c24-p2
10x Genomics, v2 chemistry, single-indexed


title: Super-enhancer 54 replicate 4

description:
HF54R4
RNA-seq


title: breast cancer single cell A039


title: E14.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep2

description:
rm5
10x Genomics, v2 chemistry, single-indexed


title: Brain, BCAS+TBI biol rep 2

city: Morgantown

first: Zachary

last: Weil

state: WV

address: 108 Biomedical Road, 313 BMRC

institute: WVU

description: 10x Genomics

data_processing:
Raw reads were processed usingCell Ranger, and FASTQ files were mapped to the GRCm38/mm10 reference genome
Seurat R objects were created in the Seurat R softward package
Seurat objects were loaded into BbrowserX (Bioturing) for downstream analysis
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Flash frozen tissues were received at Azenta, South Plainfield, NJ, USA in dry-ice and stored upon receipt -80°C until further processing. Nuclei extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec, Auburn, CA, USA) following manufacturer’s guidelines with gentle MACS Dissociation and C tubes. Upon isolation, the nuclei were counted using trypan blue with Thermo Fisher Countess III automated cell counter
3’ RNA Library preparation and Sequencing Single nuclei RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). Loading onto the Chromium Controller was performed to target capture of ~3,000 GEMs per sample for downstream analysis and processed through the Chromium Controller following the standard manufacturer’s specifications. The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Pooled libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to sequencing using Illumina 2 x 150bp at a target death of 50,000 pair-end end reads per cell at a configuration compatible with the recommended guidelines as outlined by 10X Genomics.
snRNA-seq

value: brain

value: Swiss Webster

tag: age

value: 10 weeks old

tag: injury

value: BCAS+TBI


title: E14.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep1

description:
c12_5-p2
10x Genomics, v2 chemistry, single-indexed


title: Brain, BCAS+TBI biol rep 1

description: 10x Genomics


title: Brain, TBI only biol rep 2

description: 10x Genomics

value: TBI


title: Positive control CSF1 enhancer replicate 3

description:
HFE1R3
RNA-seq

value: Positive control CSF1 enhancer


title: Brain, control biol rep 2

description: 10x Genomics

value: contol


title: Positive control CSF1 enhancer replicate 1

description:
HFE1R1
RNA-seq


title: Positive control CSF1 enhancer replicate 4

description:
HFE1R4
RNA-seq


title: Brain, BCAS only biol rep 2

description: 10x Genomics

value: BCAS


title: Super-enhancer 32 replicate 3

description:
HF32R3
RNA-seq


title: E14.5 dorsal telencephalon, wild type female, scRNA-seq, rep1

description:
c12_5-p1
10x Genomics, v2 chemistry, single-indexed

value: dorsal telencephalon

value: female


title: breast cancer single cell A034

value: immortalized breast epithelial cell line


title: breast cancer single cell A038

value: untreated


title: E14.5 dorsal telencephalon, wild type female, scRNA-seq, rep2

description:
c24-p1
10x Genomics, v2 chemistry, single-indexed


title: breast cancer single cell A035

value: single-cell Hi-C


title: Super-enhancer 32 replicate 1

description:
HF32R1
RNA-seq

value: Triple-negative breast cancer


title: E14.5 dorsal telencephalon, wild type male, scRNA-seq, rep2

description:
rm7
10x Genomics, v2 chemistry, single-indexed

value: male


title: Brain, TBI only biol rep 1

description: 10x Genomics


title: breast cancer single cell A037


title: breast cancer single cell A033


title: Super-enhancer 32 replicate 4

description:
HF32R4
RNA-seq

value: dCas9-KRAB expressing


title: E14.5 dorsal telencephalon, wild type male, scRNA-seq, rep1

description:
rm3
10x Genomics, v2 chemistry, single-indexed

value: WT


title: Brain, control biol rep 1

description: 10x Genomics

value: brain


title: E14.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep1

description:
rm4
10x Genomics, v2 chemistry, single-indexed

value: Chd8 het


title: breast cancer single cell A032


title: Donor 2 N4-RT12-2

type: other

city: Philadelphia

first: Huasheng

last: Yu

state: PENNSYLVANIA

address: 3610 Hamilton Walk

department: Neuroscience

institute: University of Pennsylvania

description:
selected 100 RNA
XETG00171__0018220__Region_4

hyb_protocol: Xenium In Situ Protocol

scan_protocol: Xenium In Situ Analyzer

data_processing:
Cell segmentation was performed manually based on the clustering expression of pan-neuronal marker gene PGP9.5, satellite glia cell marker FABP7, and the corresponding H.E. staining. Each transcript was mapped back to the new segmentation for downstream analysis.
hDRG_gene_expression_matrix.csv contains raw signal intensity

label: not applicable

molecule: other

source_name: dorsal root ganglia

label_protocol: Xenium In Situ Protocol

growth_protocol: not applicable

extract_protocol: Fresh frozen tissue were OCT embeded, and 10 μm frozen sections were cut with cryostat

treatment_protocol: not applicable

value: dorsal root ganglia

tag: level

value: thoracic 12

tag: donor id

tag: section type

value: fresh frozen section

tag: section thickness

value: 10 μm


title: Brain, BCAS only biol rep 1

description: 10x Genomics

value: Swiss Webster

value: 10 weeks old


title: breast cancer single cell A036


title: E12.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep2

description:
c10-p7
10x Genomics, v2 chemistry, single-indexed

value: dorsal telencephalon


title: Super-enhancer 84 replicate 4

description:
HF84R4
RNA-seq


title: breast cancer single cell A031


title: breast cancer single cell A030


title: Super-enhancer 84 replicate 1

description:
HF84R1
RNA-seq


title: Donor 2 N4-RT12-1

description:
selected 100 RNA
XETG00171__0018220__Region_3


title: Super-enhancer 84 replicate 3

description:
HF84R3
RNA-seq


title: E12.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep2

description:
c15-p6
10x Genomics, v2 chemistry, single-indexed


title: Donor 2 N4-RL3

description:
selected 100 RNA
XETG00171__0018220__Region_2

value: lumbar 3


title: breast cancer single cell A029

value: immortalized breast epithelial cell line


title: Super-enhancer 86 replicate 4

description:
HF86R4
RNA-seq


title: breast cancer single cell A028

value: untreated


title: Donor 1 N3-LL3

description:
selected 100 RNA
XETG00171__0018220__Region_1

value: female


title: Super-enhancer 86 replicate 3

description:
HF86R3
RNA-seq

value: Triple-negative breast cancer


title: E12.5 dorsal telencephalon, wild type female, scRNA-seq, rep2

description:
c10-p3
10x Genomics, v2 chemistry, single-indexed


title: breast cancer single cell A027

value: single-cell Hi-C


title: E12.5 dorsal telencephalon, wild type female, scRNA-seq, rep1

description:
c10-p2
10x Genomics, v2 chemistry, single-indexed


title: Super-enhancer 39 replicate 4

description:
HF39R4
RNA-seq

value: dCas9-KRAB expressing


title: Super-enhancer 86 replicate 1

description:
HF86R1
RNA-seq


title: breast cancer single cell A026


title: breast cancer single cell A025


title: E12.5 dorsal telencephalon, Chd8 het female, scRNA-seq, rep1

description:
c10-p6
10x Genomics, v2 chemistry, single-indexed


title: Cadenza_rep3

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

data_processing:
RNA-seq was performed by Novogene Bioinformatics Technology Co. Ltd. (Cambridge, UK). Paired reads were trimmed to remove adaptor sequences and for quality using Trimmomatic 0.39 software (Bolger et al., 2014) (SLIDINGWINDOW:4:20; MINLEN:50). The raw FASTQ files were mapped to wheat IWGSC RefSeq v2.1 genome assembly using STAR 2.7.8a (Dobin et al., 2013) (outFilterMismatchNmax 6; -- alignIntronMax 10000). Raw mapped reads were counted using HTSeq 0.11.3 (Putri et al., 2022) and converted to TPMs (transcripts per million). Differential expression between each mutant genotype and TaBRI1-NS was performed using DESeq2 (Love et al., 2014) in RStudio version 4.1.1717 (RStudioTeam, 2015). Genes with >two-fold change in expression and FDR-adjusted p value of ≤0.05 were classified as DEGs. PCA plot were generated using Bioconductor package pheatmap version 1.0.12 (Kolde, R.Pheatmap: pretty heatmaps. R Package Version 1.0.12.https://CRAN.R-project.org/package=pheatmap(2012). Differential expression was visualised by generating heatmaps for the BR-pathway genes as reported in Ptošková et al., 2022 and Hou et al., 2019 using Heatmapper (Babicki et al., 2016, http://www.heatmapper.ca/). Venny2.1 (Oliveros JC 2007, https://csbg.cnb.csic.es/BioinfoGP/venny.html) was used to produce Venn diagrams for the genes co-expressed in the tabri1 mutants compared to TaBRI1-NS. g:Profiler (http://biit.cs.ut.ee/gprofiler/, Reimand et al., 2016) was used to visualize gene ontology (GO) terms.
Assembly: Reads were aligned to the Triticum aestivum hexaploid wheat reference genome IWGSC v2.1
Supplementary files format and content: Microsoft excel file containing TPM values for all annotated wheat gene models in each RNA-seq library

organism: Triticum aestivum

source_name: Entire above ground tissue at two-leaf seedling stage

growth_protocol: For RNA-seq experiments, germinated seeds of genotypes were transferred to damp vermiculite in a controlled environment (CE) chamber (Constant 21 ℃ and 24 h photoperiod using fluorescent light source set at 300 μmolm-2s-1 PAR).

extract_protocol:
The total RNA was extracted from the entire above ground tissue on the above stated genotypes when they reached at 2nd leaf stage using Monarch® Total RNA Miniprep Kit (New England Biolabs, Ipswich, Massachusetts, USA) according to the manufacturer’s instructions and including DNase treatment. To assess RNA concentration and quality, Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA) and Agilent 6000 Nano RNA Kit (Agilent, Santa Clara, California, USA) was used according to the manufacturer’s instructions.
Paired-end Illumina libraries were constructed by Novogene Bioinformatics Technology Co. Ltd. (Cambridge UK).

value: Cadenza


title: Super-enhancer 39 replicate 1

description:
HF39R1
RNA-seq


title: Cadenza_rep2

value: Entire above ground tissue at two-leaf seedling stage


title: Cadenza _rep4


title: breast cancer single cell A024


title: Super-enhancer 39 replicate 3

description:
HF39R3
RNA-seq


title: Cadenza_rep1


title: E12.5 dorsal telencephalon, wild type male, scRNA-seq, rep1

description:
c10-p1
10x Genomics, v2 chemistry, single-indexed

value: male

value: WT


title: E12.5 dorsal telencephalon, wild type male, scRNA-seq, rep2

description:
c15-p9
10x Genomics, v2 chemistry, single-indexed


title: LECs_KO_Rep2

city: Berlin

first: Pedro

last: Vallecillo García

state: Berlin

address: Augustenburger Platz 1

department: Hematology and Oncology

country: Germany

institute: Charité Berlin

data_processing:
Obtained fastq data were further analysed using the platform Galaxy Europe (https://usegalaxy.eu)
53-81 million of reads were obtained and mapped using STAR (PMID: 23104886)
Quantification of aligned reads at the gene level was conducted using featureCounts (PMID: 24227677)
Differential gene expression analysis was performed using DESeq2 (PMID: 25516281). Transcript per million (TPM) abundances were calculated using normalised gene counts from DESeq2 analysis of E13.5 Osr1GCE/GCE LECs samples
Genes with an absolute log2 fold change of at least 0.3, a Benjamini-Hochberg adjusted p-value (padj) below 0.05, and TPM value higher than 1, were considered as being differentially expressed between E13.5 Osr1cantrols and Osr1GCE/GCE LECs
Assembly: mm10
Supplementary files format and content: Feature_counts. Raw read counts for each gene

source_name: Trunk peripheral tissues devoid of cranial, limb, tail tissues and inner organs

extract_protocol:
Total RNA was isolated using Direct-zol RNA Microprep (ZYMO RESEARCH) following manufacturer´s protocol. Total RNA was measured using a Qubit 4 Fluorometer and RNA quality was assessed using an Agilent RNA 6000 Nano kit prior library preparation
Library preparation was conducted according to Illumina instructions TruSeq Library Preparation Kit V2.

treatment_protocol: To obtain the total RNA amount necessary for RNA-seq, we pooled LECs from 8-10 E13.5 Osr1cantrols embryos and 8-10 Osr1GCE/GCE embryos per sample. E13.5 LECs were isolated by FACS.

tag: developmental stage

value: Lymphatic endothelial cell


title: breast cancer single cell A023


title: LECs_KO_Rep1

value: Trunk peripheral tissues devoid of cranial, limb, tail tissues and inner organs


title: TaBRI1-NS_rep4


title: HECT_MB-436_4_inter_30

description: Hi-C-seq replicate 4

data_processing:
A modified version of the Juicer Hi-C pipeline (https://github.com/EricSDavis/dietJuicer) with default parameters as previously described (Durand et al. 2016)
MboI was used as the restriction enzyme, and reads were aligned to the hg19 human reference genome with bwa (version 0.7.17). Four biological replicates were aligned and merged.
Assembly: hg19
Supplementary files format and content: .hic files

growth_protocol: MDA-MB-436 triple-negative breast cancer cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma cat. #30-2002) supplemented with 10% fetal bovine serum (FBS) (Sigma) and 1% penicillin/streptomycin (Corning) at 37°C and passaged as required.

extract_protocol: In situ Hi-C was performed as previously described (Rao et al. 2014, https://doi.org/10.1016/j.cell.2014.11.021)

value: Wildtype


title: TaBRI1-NS_rep3


title: E12.5 dorsal telencephalon, Chd8 het male, scRNA-seq, rep1

description:
c10-p8
10x Genomics, v2 chemistry, single-indexed

tag: time point

value: Chd8 het


title: HECT_MB-436_3_inter_30

description: Hi-C-seq replicate 3


title: LECs_Control_Rep2

tag: tissue


title: LECs_Control_Rep1


title: TaBRI1-NS_rep2


title: HECT_MB-436_2_inter_30

description: Hi-C-seq replicate 2


title: breast cancer single cell A021


title: breast cancer single cell A020


title: HECT_MB-436_1_inter_30

description: Hi-C-seq replicate 1


title: TaBRI1-NS_rep1


title: tabri1-bd_rep4


title: A375 cell, Olive oil, 6h_2

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Hokkaido university

data_processing:
RNA-seq reads were preprocessed with bcl2fastq and FastQC software (v. 0.11.7) and aligned to hg38 reference genome with HISAT2 (v. 2.1.0)
StringTie algorithm (v.1.3.4d) was then used with default parameter settings to assemble RNA-Seq alignments into annotated transcripts to estimate their expression using the UCSC annotated human genome (hg38) assembly files.
Transcript expression was normalized using the transcripts per million (TPM) algorithms. For differential expression analysis, we used the R package (edgeR).
For analysis and interpretation, we used SAMtools (v.1.9), BEDTools (v.2.27.1), Seqkit (version 0.13.2), RSeQC (v.3.0.1), and Ngsplot (v.2.6.3).
Assembly: hg38
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Skin

growth_protocol: A375 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-aldrich) contained 10% fetal bovine serum (FBS; cosmobio) at 37℃ in humidified 5% CO2/95% air atmosphere.

extract_protocol:
Total mRNA was extracted by using Tri reagent (Trizol; Sigma-aldrich) according to manufacturer's protocol
RNA libraries for RNA-seq were constructed by using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer's manual. After which library quality was further assessed using the TapeStation 4200 with High sensitivity D1000 Screen Tape (Agilent Technologies).

treatment_protocol: Cells were cultured in presence of 0.01% ozonated olive oil or olive oil for 6h.

value: Skin

value: Melanoma

value: olive oil-treated for 6h


title: breast cancer single cell A019

value: immortalized breast epithelial cell line


title: MKs, Day 9+6, C [MKD9+6C]

city: Guangzhou

first: Chuxin

last: Chen

address: Xiaoguwei Street

institute: South China University of Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.23.2 (parameter- Quality phred: 20)
Trimmed sequence reads were mapped to GRCh38 using hista2 2.2.1
Read count extraction and normalization were performed using featureCounts 2.0.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: human embryonic stem cells

extract_protocol:
RNA was harvested using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

tag: source cell type

value: human embryonic stem cells

value: Megakaryocytic differentiation

value: Day 9+6


title: A375 cell, Ozonated olive oil, 6h_1

value: ozonated olive oil-treated for 6h


title: tabri1-bd_rep3


title: breast cancer single cell A018

value: untreated

value: single-cell Hi-C


title: breast cancer single cell A022


title: A375 cell, Olive oil, 6h_1


title: breast cancer single cell A016


title: breast cancer single cell A017


title: MKs, Day 9+2, C [MKD9+2C]

value: Day 9+2


title: tabri1-bd_rep1

value: Entire above ground tissue at two-leaf seedling stage


title: MKs, Day 9+6, A [MKD9+6A]

value: WT


title: breast cancer single cell A015


title: MKs, Day 9+2, B [MKD9+2B]


title: tabri1-a3bd_rep4


title: tabri1-a3bd_rep3


title: breast cancer single cell A014


title: breast cancer single cell A013


title: MKs, Day 9+2, A [MKD9+2A]


title: MKs, Day 9+6, B [MKD9+6B]


title: tabri1-bd_rep2


title: breast cancer single cell A012


title: A375 cell, Ozonated olive oil, 6h_2


title: HPT3, Pt1_R, scRNAseq, TCR

city: Newport

first: Jillian

middle: F

last: Wise

state: Rhode Island

address: 100 Ochre Point Ave

department: Biology and Biomedical Sciences

institute: Salve Regina University

description:
TCR_HPT3_S2
10X Genomics

data_processing:
Raw sequencing reads were aligned, and samples aggregated without normalization (Cell Ranger (v6.1.1))
Cells with fewer than 150 genes or 15% of UMIs mapped to mitochondrial genes were filtered (Seurat (v3))
Potential doublets were filtered using DoubletFinder (chris-mcginnis-ucsf/DoubletFinder).
Filtered TCR alpha and beta contigs were then integrated by barcode with scRepertoire (ncborcherding/scRepertoire) based on VDJC genes and CDR3 nucleotide sequence.
Principal component analysis used 2000 highly variable genes from scaled and log normalized expression matrices. Clustering utilized the first 40 principal components with a Louvain algorithm.
Assembly: hg38
Supplementary files format and content: tab separated files and matrix files

source_name: Tongue

extract_protocol:
All tumors were dissociated using the Human Tumor Dissociation kit (Miltenyi Biotec; Cat#130-095-929) within 30 minutes after surgery. Briefly, minced fragments were incubated with DMEM, enzyme H, enzyme R, and enzyme A and vortexed for 15 minutes at 400 rpm, 37°C. Tissue was filtered (50µm filter, Sysmex; Cat# 04-004-2327), washed, minced with a 1mL syringe plunger, and re-washed. Dissociated cells were then filtered and spun again (30µm filter, Sysmex; Cat# 04-004-2326) at 1500 rpm at 4°C for 5 minutes. Next, incubation with ACK buffer (Gibco, cat#A1049201) was performed followed by removal of the ACK buffer. In all cases, the viability of dissociated single-cell suspensions was increased to >=90% by using a modified protocol of the EasySep Dead Cell Removal (Annexin V) kit (STEMCELL; cat#17899). Gene expression (GEX) and TCR libraries were generated using the 10x Genomics Chromium NextGEM Single Cell V(D)J Reagents kits v1.1 (PN-1000165; PN-1000020; PN-1000005; PN-1000120) according to the manufacturer instructions.
Gene expression (GEX) and TCR libraries were generated using the 10x Genomics Chromium NextGEM Single Cell V(D)J Reagents kits v1.1 (PN-1000165; PN-1000020; PN-1000005; PN-1000120) according to the manufacturer instructions.

treatment_protocol: Briefly, fresh tumor tissue biopsies were collected before two doses of anti-PD1 inhibitor (nivolumab) and four doses of toll-like receptor 8 (TLR8) agonist (Motolimod). The tumor was then resected on days 22, 30, and 28 for patient 1 (Pt1_R), patient 2 (Pt2_R) and patient 3 (Pt3_NR), respectively.

value: Tongue

tag: subject status

value: head and neck squamous cell carcinoma patient

value: Motolimod and Nivolumab


title: HPT6, Pt3_NR, scRNAseq, TCR

description:
TCR_HPT6_S5
10X Genomics

value: pre-treatment


title: HPT5, Pt2_R, scRNAseq, TCR

description:
TCR_HPT5_S4
10X Genomics

source_name: Larynx

value: Larynx


title: HPT4, Pt2_R, scRNAseq, TCR

description:
TCR_HPT4_S3
10X Genomics


title: MKs, Day 9+0, B [MKD9+0B]

value: Day 9+0


title: MKs, Day 9+0, C [MKD9+0C]


title: HPT7, Pt3_NR, scRNAseq, TCR

description:
TCR_HPT7_S6
10X Genomics


title: tabri1-a2bd_rep4


title: breast cancer single cell A011

tag: cell line


title: HPT1, Pt1_R, scRNAseq, TCR

description:
TCR_HPT1_S1
10X Genomics


title: tabri1-a2bd_rep3


title: MKs, Day 9, C [MKD9C]

value: Day 9


title: tabri1-a3bd_rep1


title: HPT7, Pt3_NR, scRNAseq, GEX

description:
HPT7_S6
10X Genomics


title: MKs, Day 9, B [MKD9B]


title: tabri1-a2bd_rep2


title: HPT6, Pt3_NR, scRNAseq, GEX

description:
HPT6_S5
10X Genomics


title: breast cancer single cell A008

tag: cell type

value: immortalized breast epithelial cell line


title: breast cancer single cell A009

tag: treatment


title: tabri1-a3bd_rep2


title: MKs, Day 9, A [MKD9A]

value: human embryonic stem cells


title: HPT5, Pt2_R, scRNAseq, GEX

description:
HPT5_S4
10X Genomics


title: MKs, Day 6, C [MKD6C]

value: Megakaryocytic differentiation

value: Day 6


title: breast cancer single cell A007

tag: analysis


title: tabri1-a1bd_rep3

tag: genotype


title: breast cancer single cell A010


title: HPT4, Pt2_R, scRNAseq, GEX

description:
HPT4_S3
10X Genomics


title: MKs, Day 9+0, A [MKD9+0A]


title: breast cancer single cell A004


title: breast cancer single cell A005


title: MKs, Day 6, B [MKD6B]


title: MKs, Day 6, A [MKD6A]


title: HPT3, Pt1_R, scRNAseq, GEX

description:
HPT3_S2
10X Genomics


title: tabri1-a1bd_rep2


title: MKs, Day 2, B [MKD2B]

value: Day 2


title: breast cancer single cell A003

value: untreated


title: HPT1, Pt1_R, scRNAseq, GEX

description:
HPT1_S1
10X Genomics


title: breast cancer single cell A006

value: single-cell Hi-C


title: MKs, Day 2, C [MKD2C]


title: tabri1-a2bd_rep1


title: MKs, Day 2, A [MKD2A]


title: breast cancer single cell A001


title: tabri1-a1bd_rep1


title: Itga9-Lyz2-cHet PD, scRNAseq

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

description: 10x Genomics

data_processing:
scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp  with default parameter filtering the adaptor sequence and removed the low quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we used STARsolo  (version 2.7.10a) along with mouse genome mm10 (ensembl annotation version 100).
Assembly: mm10
Supplementary files format and content: matrix files（barcodes.tsv.gz、features.tsv.gz、matrix.mtx.gz）

source_name: Gingival tissue

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 0.5mg/mL collagenase I, 0.5mg/mL collagenase II, 1mg/mL dispase II and 50 U/mL DNase I for 20 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 400g for 5 min. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.

value: Gingival tissue

value: Primary cells

value: Gingival cells

value: PD


title: Itga9-Lyz2-cHet control, scRNAseq

description: 10x Genomics

value: Control


title: Itga9-Lyz2-cKO control, scRNAseq

description: 10x Genomics


title: Itga9-Lyz2-cKO PD, scRNAseq

description: 10x Genomics


title: iASC_pos_7_c_male

status: Public on Aug 13 2024

city: Huddinge

first: Martin

middle: Verner

last: Uhrbom

address: Hälsovägen 7C

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institute

description: iASC_pos_7_c_male_control_S263_L008_R1_001

data_processing:
bcl2fastq - demultiplexing
Individual fastq-files were mapped to the mouse reference genome (mm10-build94) with the STAR aligner, and raw reads for each gene was quantified using Salmon.
As technical controls, 92 ERCC RNAs were spiked in the lysis buffer and included in the mapping.
Bulk RNA-seq samples with fewer than 250 000 total reads were filtered out. Samples that had fewer than 8000 genes expressed and that had a high percent of the reads mapped to the mitochondrial genome (>15%) or to the ERCCs (>1%) were removed from the dataset.
Assembly: mm10-build94
Supplementary files format and content: Space-delimited text files as expression matrices including non-normalized counts of all samples.

source_name: iWAT

growth_protocol: FACS sorted cells for bulk RNA sequencing.

extract_protocol:
Qiagen’s RNeasy Micro kit (Cat. No. 74004) was used for isolation of RNA from FACS-sorted ASC cells (5000 cells per sample).
RNA libraries were prepared using standard SmartSeq2 protocol. RNA from approxiimately 300 cells were used for cDNA synthesis.

treatment_protocol: Collagenase/Dispase treatment of tissue pieces for 30 min.

value: iWAT

tag: Sex

value: male

tag: mouse

tag: replicate

value: c


title: iASC_pos_8_b_male

description: iASC_pos_8_b_male_control_S136_L008_R1_001

value: b


title: iASC_pos_8_a_male

description: iASC_pos_8_a_male_control_S8_L008_R1_001

value: a


title: iASC_pos_7_b_male

description: iASC_pos_7_b_male_control_S135_L008_R1_001


title: iASC_pos_7_a_male

description: iASC_pos_7_a_male_control_S7_L008_R1_001


title: iASC_pos_6_b_male

description: iASC_pos_6_b_male_control_S134_L008_R1_001


title: iASC_pos_6_c_male

description: iASC_pos_6_c_male_control_S262_L008_R1_001


title: iASC_pos_6_a_male

description: iASC_pos_6_a_male_control_S6_L008_R1_001


title: iASC_pos_4_b_male

description: iASC_pos_4_b_male_control_S132_L008_R1_001


title: iASC_pos_4_a_male

description: iASC_pos_4_a_male_control_S4_L008_R1_001


title: iASC_pos_2_c_male

description: iASC_pos_2_c_male_control_S258_L008_R1_001


title: breast cancer single cell A002

value: immortalized breast epithelial cell line


title: iASC_pos_3_c_male

description: iASC_pos_3_c_male_control_S259_L008_R1_001


title: iASC_pos_2_a_male

description: iASC_pos_2_a_male_control_S2_L008_R1_001


title: iASC_pos_24_c_female

description: iASC_pos_24_c_female_control_S296_L008_R1_001

value: female


title: iASC_pos_24_a_female

description: iASC_pos_24_a_female_control_S40_L008_R1_001


title: iASC_pos_3_b_male

description: iASC_pos_3_b_male_control_S131_L008_R1_001


title: iASC_pos_23_a_female

description: iASC_pos_23_a_female_control_S39_L008_R1_001


title: iASC_pos_1_b_male

description: iASC_pos_1_b_male_control_S129_L008_R1_001


title: iASC_pos_20_a_female

description: iASC_pos_20_a_female_control_S36_L008_R1_001


title: iASC_pos_20_b_female

description: iASC_pos_20_b_female_control_S164_L008_R1_001


title: iASC_pos_21_a_female

description: iASC_pos_21_a_female_control_S37_L008_R1_001


title: iASC_pos_21_b_female

description: iASC_pos_21_b_female_control_S165_L008_R1_001


title: iASC_pos_19_c_female

description: iASC_pos_19_c_female_control_S291_L008_R1_001


title: iASC_pos_20_c_female

description: iASC_pos_20_c_female_control_S292_L008_R1_001


title: iASC_pos_19_b_female

description: iASC_pos_19_b_female_control_S163_L008_R1_001


title: iASC_pos_18_c_female

description: iASC_pos_18_c_female_control_S290_L008_R1_001


title: iASC_pos_18_a_female

description: iASC_pos_18_a_female_control_S34_L008_R1_001


title: iASC_pos_17_c_female

description: iASC_pos_17_c_female_control_S289_L008_R1_001


title: iASC_pos_18_b_female

description: iASC_pos_18_b_female_control_S162_L008_R1_001


title: iASC_pos_17_a_female

description: iASC_pos_17_a_female_control_S33_L008_R1_001


title: iASC_neg_8_c_male

description: iASC_neg_8_c_male_control_S280_L008_R1_001


title: iASC_pos_2_b_male

description: iASC_pos_2_b_male_control_S130_L008_R1_001


title: iASC_neg_8_b_male

description: iASC_neg_8_b_male_control_S152_L008_R1_001


title: iASC_neg_7_c_male

description: iASC_neg_7_c_male_control_S279_L008_R1_001


title: iASC_pos_21_c_female

description: iASC_pos_21_c_female_control_S293_L008_R1_001


title: iASC_pos_1_c_male

description: iASC_pos_1_c_male_control_S257_L008_R1_001


title: iASC_neg_7_a_male

description: iASC_neg_7_a_male_control_S23_L008_R1_001


title: iASC_neg_8_a_male

description: iASC_neg_8_a_male_control_S24_L008_R1_001


title: iASC_neg_6_c_male

description: iASC_neg_6_c_male_control_S278_L008_R1_001


title: iASC_neg_6_b_male

description: iASC_neg_6_b_male_control_S150_L008_R1_001


title: iASC_neg_6_a_male

description: iASC_neg_6_a_male_control_S22_L008_R1_001


title: iASC_pos_19_a_female

description: iASC_pos_19_a_female_control_S35_L008_R1_001


title: iASC_neg_4_b_male

description: iASC_neg_4_b_male_control_S148_L008_R1_001


title: iASC_neg_4_a_male

description: iASC_neg_4_a_male_control_S20_L008_R1_001


title: iASC_neg_5_c_male

description: iASC_neg_5_c_male_control_S277_L008_R1_001


title: iASC_neg_5_a_male

description: iASC_neg_5_a_male_control_S21_L008_R1_001


title: iASC_neg_5_b_male

description: iASC_neg_5_b_male_control_S149_L008_R1_001


title: iASC_neg_3_b_male

description: iASC_neg_3_b_male_control_S147_L008_R1_001


title: iASC_neg_3_c_male

description: iASC_neg_3_c_male_control_S275_L008_R1_001


title: iASC_neg_4_c_male

description: iASC_neg_4_c_male_control_S276_L008_R1_001


title: iASC_neg_2_c_male

description: iASC_neg_2_c_male_control_S274_L008_R1_001


title: iASC_pos_17_b_female

description: iASC_pos_17_b_female_control_S161_L008_R1_001


title: iASC_neg_2_a_male

description: iASC_neg_2_a_male_control_S18_L008_R1_001


title: iASC_neg_3_a_male

description: iASC_neg_3_a_male_control_S19_L008_R1_001


title: iASC_neg_24_c_female

description: iASC_neg_24_c_female_control_S312_L008_R1_001


title: iASC_neg_23_a_female

description: iASC_neg_23_a_female_control_S55_L008_R1_001


title: iASC_neg_23_c_female

description: iASC_neg_23_c_female_control_S311_L008_R1_001


title: iASC_neg_24_a_female

description: iASC_neg_24_a_female_control_S56_L008_R1_001


title: iASC_neg_22_c_female

description: iASC_neg_22_c_female_control_S310_L008_R1_001


title: iASC_neg_7_b_male

description: iASC_neg_7_b_male_control_S151_L008_R1_001


title: iASC_neg_22_a_female

description: iASC_neg_22_a_female_control_S54_L008_R1_001


title: iASC_neg_21_a_female

description: iASC_neg_21_a_female_control_S53_L008_R1_001


title: iASC_neg_21_b_female

description: iASC_neg_21_b_female_control_S181_L008_R1_001


title: iASC_neg_20_b_female

description: iASC_neg_20_b_female_control_S180_L008_R1_001


title: iASC_neg_1_c_male

description: iASC_neg_1_c_male_control_S273_L008_R1_001


title: iASC_neg_20_a_female

description: iASC_neg_20_a_female_control_S52_L008_R1_001


title: iASC_neg_20_c_female

description: iASC_neg_20_c_female_control_S308_L008_R1_001


title: iASC_neg_19_a_female

description: iASC_neg_19_a_female_control_S51_L008_R1_001


title: iASC_neg_17_b_female

description: iASC_neg_17_b_female_control_S177_L008_R1_001


title: iASC_neg_17_a_female

description: iASC_neg_17_a_female_control_S49_L008_R1_001


title: iASC_neg_19_c_female

description: iASC_neg_19_c_female_control_S307_L008_R1_001


title: iASC_neg_17_c_female

description: iASC_neg_17_c_female_control_S305_L008_R1_001


title: iASC_neg_19_b_female

description: iASC_neg_19_b_female_control_S179_L008_R1_001


title: gASC_pos_8_c_male

description: gASC_pos_8_c_male_control_S328_L008_R1_001

source_name: pgWAT

value: pgWAT


title: iASC_neg_1_a_male

description: iASC_neg_1_a_male_control_S17_L008_R1_001


title: gASC_pos_7_b_male

description: gASC_pos_7_b_male_control_S199_L008_R1_001


title: gASC_pos_7_c_male

description: gASC_pos_7_c_male_control_S327_L008_R1_001


title: gASC_pos_6_c_male

description: gASC_pos_6_c_male_control_S326_L008_R1_001


title: gASC_pos_8_b_male

description: gASC_pos_8_b_male_control_S200_L008_R1_001


title: gASC_pos_7_a_male

description: gASC_pos_7_a_male_control_S71_L008_R1_001


title: gASC_pos_6_a_male

description: gASC_pos_6_a_male_control_S70_L008_R1_001


title: gASC_pos_5_c_male

description: gASC_pos_5_c_male_control_S325_L008_R1_001


title: gASC_pos_4_c_male

description: gASC_pos_4_c_male_control_S324_L008_R1_001


title: gASC_pos_4_b_male

description: gASC_pos_4_b_male_control_S196_L008_R1_001


title: gASC_pos_4_a_male

description: gASC_pos_4_a_male_control_S68_L008_R1_001


title: iASC_neg_1_b_male

description: iASC_neg_1_b_male_control_S145_L008_R1_001


title: gASC_pos_5_a_male

description: gASC_pos_5_a_male_control_S69_L008_R1_001


title: gASC_pos_3_c_male

description: gASC_pos_3_c_male_control_S323_L008_R1_001


title: gASC_pos_3_b_male

description: gASC_pos_3_b_male_control_S195_L008_R1_001


title: gASC_pos_23_a_female

description: gASC_pos_23_a_female_control_S103_L008_R1_001


title: gASC_pos_8_a_male

description: gASC_pos_8_a_male_control_S72_L008_R1_001


title: gASC_pos_22_c_female

description: gASC_pos_22_c_female_control_S358_L008_R1_001


title: gASC_pos_23_b_female

description: gASC_pos_23_b_female_control_S231_L008_R1_001


title: gASC_pos_1_b_male

description: gASC_pos_1_b_male_control_S193_L008_R1_001


title: gASC_pos_21_a_female

description: gASC_pos_21_a_female_control_S101_L008_R1_001


title: gASC_pos_21_c_female

description: gASC_pos_21_c_female_control_S357_L008_R1_001


title: gASC_pos_1_c_male

description: gASC_pos_1_c_male_control_S321_L008_R1_001


title: gASC_pos_19_a_female

description: gASC_pos_19_a_female_control_S99_L008_R1_001


title: gASC_pos_1_a_male

description: gASC_pos_1_a_male_control_S65_L008_R1_001


title: gASC_pos_18_a_female

description: gASC_pos_18_a_female_control_S98_L008_R1_001


title: gASC_pos_22_b_female

description: gASC_pos_22_b_female_control_S230_L008_R1_001


title: gASC_pos_5_b_male

description: gASC_pos_5_b_male_control_S197_L008_R1_001


title: iASC_neg_24_b_female

description: iASC_neg_24_b_female_control_S184_L008_R1_001


title: gASC_neg_6_c_male

description: gASC_neg_6_c_male_control_S342_L008_R1_001


title: gASC_neg_6_a_male

description: gASC_neg_6_a_male_control_S86_L008_R1_001


title: gASC_neg_5_c_male

description: gASC_neg_5_c_male_control_S341_L008_R1_001


title: gASC_pos_18_c_female

description: gASC_pos_18_c_female_control_S354_L008_R1_001


title: gASC_neg_5_b_male

description: gASC_neg_5_b_male_control_S213_L008_R1_001


title: gASC_neg_4_b_male

description: gASC_neg_4_b_male_control_S212_L008_R1_001


title: gASC_neg_4_c_male

description: gASC_neg_4_c_male_control_S340_L008_R1_001


title: gASC_neg_7_c_male

description: gASC_neg_7_c_male_control_S343_L008_R1_001


title: iASC_neg_21_c_female

description: iASC_neg_21_c_female_control_S309_L008_R1_001


title: gASC_neg_3_c_male

description: gASC_neg_3_c_male_control_S339_L008_R1_001


title: gASC_neg_3_a_male

description: gASC_neg_3_a_male_control_S83_L008_R1_001


title: gASC_neg_2_c_male

description: gASC_neg_2_c_male_control_S338_L008_R1_001


title: gASC_neg_2_b_male

description: gASC_neg_2_b_male_control_S210_L008_R1_001


title: gASC_pos_22_a_female

description: gASC_pos_22_a_female_control_S102_L008_R1_001


title: gASC_pos_18_b_female

description: gASC_pos_18_b_female_control_S226_L008_R1_001


title: gASC_pos_17_b_female

description: gASC_pos_17_b_female_control_S225_L008_R1_001


title: gASC_neg_23_b_female

description: gASC_neg_23_b_female_control_S247_L008_R1_001


title: gASC_neg_22_b_female

description: gASC_neg_22_b_female_control_S246_L008_R1_001


title: gASC_neg_21_a_female

description: gASC_neg_21_a_female_control_S117_L008_R1_001


title: gASC_neg_2_a_male

description: gASC_neg_2_a_male_control_S82_L008_R1_001


title: gASC_pos_17_a_female

description: gASC_pos_17_a_female_control_S97_L008_R1_001


title: gASC_neg_23_a_female

description: gASC_neg_23_a_female_control_S119_L008_R1_001


title: gASC_neg_22_a_female

description: gASC_neg_22_a_female_control_S118_L008_R1_001


title: gASC_neg_22_c_female

description: gASC_neg_22_c_female_control_S374_L008_R1_001


title: gASC_neg_20_a_female

description: gASC_neg_20_a_female_control_S116_L008_R1_001


title: gASC_neg_1_a_male

description: gASC_neg_1_a_male_control_S81_L008_R1_001


title: gASC_neg_5_a_male

description: gASC_neg_5_a_male_control_S85_L008_R1_001


title: gASC_neg_1_b_male

description: gASC_neg_1_b_male_control_S209_L008_R1_001


title: gASC_neg_19_c_female

description: gASC_neg_19_c_female_control_S371_L008_R1_001


title: gASC_neg_4_a_male

description: gASC_neg_4_a_male_control_S84_L008_R1_001


title: gASC_neg_18_b_female

description: gASC_neg_18_b_female_control_S242_L008_R1_001


title: gASC_neg_17_c_female

description: gASC_neg_17_c_female_control_S369_L008_R1_001


title: gASC_neg_17_b_female

description: gASC_neg_17_b_female_control_S241_L008_R1_001


title: gASC_neg_19_a_female

description: gASC_neg_19_a_female_control_S115_L008_R1_001


title: gASC_neg_18_a_female

description: gASC_neg_18_a_female_control_S114_L008_R1_001


title: gASC_neg_17_a_female

description: gASC_neg_17_a_female_control_S113_L008_R1_001


title: gASC_neg_23_c_female

description: gASC_neg_23_c_female_control_S375_L008_R1_001


title: pgWAT_SVF_plate_042_female_CD31neg_PDGFRBpos

data_processing:
bcl2fastq - demultiplexing
Individual fastq-files were mapped to the mouse reference genome (mm10-build94) with the STAR aligner, and raw reads for each gene was quantified using Salmon.
As technical controls, 92 ERCC RNAs were spiked in the lysis buffer and included in the mapping.
Cells with fewer than 150 000 total reads and more than 5 000 000 reads were filtered out. Cells that had fewer than 1000 genes expressed and that had a high percent of the reads mapped to the mitochondrial genome (>17.5%) or to the ERCCs (>20%) were removed from the dataset.
Genes that had less than 10 reads in no more than three cells were removed.
Assembly: mm10-build94
Supplementary files format and content: Tab-delimited txt file as expression matrix including non-normalized counts of all samples.

source_name: pgwat

growth_protocol: FACS sorted cells for single cell RNA sequencing.

extract_protocol:
Smartseq2
RNA libraries were prepared using standard SmartSeq2 protocol.

treatment_protocol: PdgfrbGFP (Genesat.org, Tg(Pdgfrb-eGFP)) mouse strain that have been backcrossed to the C57BL6/J background (The Jackson Laboratory, C57B16/J).

value: pgwat

value: Stromal vascular fraction

tag: plate

tag: facs sort

tag: mouse id


title: pgWAT_SVF_plate_874_female_PDGFRBneg_CD31pos


title: pgWAT_SVF_plate_129_female_PDGFRBpos

value: PDGFRBpos


title: pgWAT_SVF_plate_843_female_PDGFRBpos


title: pgWAT_SVF_plate_344_male_PDGFRBpos_and_CD31pos


title: pgWAT_SVF_plate_709_female_PDGFRBpos_DPP4pos


title: pgWAT_SVF_plate_171_male_CD31pos


title: pgWAT_SVF_plate_875_female_CD31neg_Dpp4neg_PDGFRBpos


title: iWAT_Adipocyte_male_8_a

description: iWAT_adipocyte_8_a_male_control_S80_L002_R1_001

data_processing:
bcl2fastq - demultiplexing
Individual fastq-files were mapped to the mouse reference genome (mm10-build94) with the STAR aligner, and raw reads for each gene was quantified using Salmon.
As technical controls, 92 ERCC RNAs were spiked in the lysis buffer and included in the mapping.
Bulk RNA-seq samples with fewer than 250 000 total reads were filtered out. Samples that had fewer than 8000 genes expressed and that had a high percent of the reads mapped to the mitochondrial genome (>15%) or to the ERCCs (>1%) were removed from the dataset.
Assembly: mm10-build94
Supplementary files format and content: Space-delimited text file as expression matrix including non-normalized counts of all samples.
Supplementary files format and content: Space-delimited text file as expression matrix including averaged non-normalized counts.

growth_protocol: Bulk RNA sequencing of adipocytes.

extract_protocol:
QIAzol lysis reagent (Cat. No. 79306) was first used followed by addition of chloroform and subsequent integration of the RNA containing aqueous phase with the workflow of the RNeasy clean up (Qiagen’s RNeasy Micro kit (Cat. No. 74004).
RNA libraries were prepared using standard SmartSeq2 protocol. RNA samples were diluted to 3 ng/µl and 5 ng of RNA was used for cDNA synthesis.

treatment_protocol: Collagenase/Dispare treatment of tissue pieces for 30 min.

value: Adipocyte


title: pgWAT_SVF_plate_172_male_PDGFRBpos


title: gASC_neg_20_b_female

description: gASC_neg_20_b_female_control_S244_L008_R1_001


title: iWAT_Adipocyte_male_7_b

description: iWAT_adipocyte_7_b_male_control_S271_L002_R1_001


title: pgWAT_SVF_plate_043_female_PDGFRBneg_CD31pos_and_viceversa


title: iWAT_Adipocyte_male_6_b

description: iWAT_adipocyte_6_b_male_control_S270_L002_R1_001


title: pgWAT_SVF_plate_131_male_PDGFRBpos


title: iWAT_Adipocyte_male_8_b

description: iWAT_adipocyte_8_b_male_control_S272_L002_R1_001


title: iWAT_Adipocyte_male_5_b

description: iWAT_adipocyte_5_b_male_control_S269_L002_R1_001


title: iWAT_Adipocyte_male_5_a

description: iWAT_adipocyte_5_a_male_control_S77_L002_R1_001


title: iWAT_Adipocyte_male_6_a

description: iWAT_adipocyte_6_a_male_control_S78_L002_R1_001


title: iWAT_Adipocyte_male_4_b

description: iWAT_adipocyte_4_b_male_control_S268_L002_R1_001


title: iWAT_Adipocyte_male_3_b

description: iWAT_adipocyte_3_b_male_control_S267_L002_R1_001


title: iWAT_Adipocyte_male_3_a

description: iWAT_adipocyte_3_a_male_control_S75_L002_R1_001


title: iWAT_Adipocyte_male_4_a

description: iWAT_adipocyte_4_a_male_control_S76_L002_R1_001


title: iWAT_Adipocyte_male_2_b

description: iWAT_adipocyte_2_b_male_control_S266_L002_R1_001


title: iWAT_Adipocyte_male_2_a

description: iWAT_adipocyte_2_a_male_control_S74_L002_R1_001


title: iWAT_Adipocyte_female_24_b

description: iWAT_adipocyte_24_b_female_control_S304_L002_R1_001


title: iWAT_Adipocyte_female_23_b

description: iWAT_adipocyte_23_b_female_control_S303_L002_R1_001


title: iWAT_Adipocyte_female_24_a

description: iWAT_adipocyte_24_a_female_control_S112_L002_R1_001


title: iWAT_Adipocyte_female_23_a

description: iWAT_adipocyte_23_a_female_control_S111_L002_R1_001


title: iWAT_Adipocyte_female_21_b

description: iWAT_adipocyte_21_b_female_control_S301_L002_R1_001


title: iWAT_Adipocyte_female_21_a

description: iWAT_adipocyte_21_a_female_control_S109_L002_R1_001


title: iWAT_Adipocyte_male_7_a

description: iWAT_adipocyte_7_a_male_control_S79_L002_R1_001


title: iWAT_Adipocyte_female_20_b

description: iWAT_adipocyte_20_b_female_control_S300_L002_R1_001


title: iWAT_Adipocyte_male_1_b

description: iWAT_adipocyte_1_b_male_control_S265_L002_R1_001


title: iWAT_Adipocyte_female_22_b

description: iWAT_adipocyte_22_b_female_control_S302_L002_R1_001


title: iWAT_Adipocyte_female_19_b

description: iWAT_adipocyte_19_b_female_control_S299_L002_R1_001


title: iWAT_Adipocyte_female_19_a

description: iWAT_adipocyte_19_a_female_control_S107_L002_R1_001


title: iWAT_Adipocyte_female_18_a

description: iWAT_adipocyte_18_a_female_control_S106_L002_R1_001


title: pgWAT_Adipocyte_male_8_b

description: gWAT_adipocyte_8_b_male_control_S328_L002_R1_001


title: pgWAT_Adipocyte_male_8_a

description: gWAT_adipocyte_8_a_male_control_S136_L002_R1_001


title: iWAT_Adipocyte_female_17_a

description: iWAT_adipocyte_17_a_female_control_S105_L002_R1_001


title: pgWAT_Adipocyte_male_6_b

description: gWAT_adipocyte_6_b_male_control_S326_L002_R1_001


title: pgWAT_Adipocyte_male_7_a

description: gWAT_adipocyte_7_a_male_control_S135_L002_R1_001


title: pgWAT_Adipocyte_male_7_b

description: gWAT_adipocyte_7_b_male_control_S327_L002_R1_001


title: pgWAT_Adipocyte_male_5_b

description: gWAT_adipocyte_5_b_male_control_S325_L002_R1_001


title: pgWAT_Adipocyte_male_4_b

description: gWAT_adipocyte_4_b_male_control_S324_L002_R1_001


title: iWAT_Adipocyte_female_17_b

description: iWAT_adipocyte_17_b_female_control_S297_L002_R1_001


title: iWAT_Adipocyte_female_22_a

description: iWAT_adipocyte_22_a_female_control_S110_L002_R1_001


title: iWAT_Adipocyte_female_20_a

description: iWAT_adipocyte_20_a_female_control_S108_L002_R1_001


title: iWAT_Adipocyte_male_1_a

description: iWAT_adipocyte_1_a_male_control_S73_L002_R1_001


title: pgWAT_Adipocyte_male_6_a

description: gWAT_adipocyte_6_a_male_control_S134_L002_R1_001


title: pgWAT_Adipocyte_male_5_a

description: gWAT_adipocyte_5_a_male_control_S133_L002_R1_001


title: pgWAT_Adipocyte_male_3_b

description: gWAT_adipocyte_3_b_male_control_S323_L002_R1_001


title: pgWAT_Adipocyte_female_21_b

description: gWAT_adipocyte_21_b_female_control_S357_L002_R1_001


title: pgWAT_Adipocyte_female_22_a

description: gWAT_adipocyte_22_a_female_control_S166_L002_R1_001


title: pgWAT_Adipocyte_female_22_b

description: gWAT_adipocyte_22_b_female_control_S358_L002_R1_001


title: pgWAT_Adipocyte_female_21_a

description: gWAT_adipocyte_21_a_female_control_S165_L002_R1_001


title: pgWAT_Adipocyte_male_2_a

description: gWAT_adipocyte_2_a_male_control_S130_L002_R1_001


title: pgWAT_Adipocyte_female_24_b

description: gWAT_adipocyte_24_b_female_control_S360_L002_R1_001


title: pgWAT_Adipocyte_female_23_a

description: gWAT_adipocyte_23_a_female_control_S167_L002_R1_001


title: pgWAT_Adipocyte_female_23_b

description: gWAT_adipocyte_23_b_female_control_S359_L002_R1_001


title: pgWAT_Adipocyte_female_24_a

description: gWAT_adipocyte_24_a_female_control_S168_L002_R1_001


title: pgWAT_Adipocyte_male_1_b

description: gWAT_adipocyte_1_b_male_control_S321_L002_R1_001


title: pgWAT_Adipocyte_female_20_a

description: gWAT_adipocyte_20_a_female_control_S164_L002_R1_001


title: pgWAT_Adipocyte_male_1_a

description: gWAT_adipocyte_1_a_male_control_S129_L002_R1_001


title: pgWAT_Adipocyte_female_19_b

description: gWAT_adipocyte_19_b_female_control_S355_L002_R1_001


title: pgWAT_Adipocyte_female_20_b

description: gWAT_adipocyte_20_b_female_control_S356_L002_R1_001


title: pgWAT_Adipocyte_female_18_a

description: gWAT_adipocyte_18_a_female_control_S162_L002_R1_001


title: pgWAT_Adipocyte_female_19_a

description: gWAT_adipocyte_19_a_female_control_S163_L002_R1_001


title: pgWAT_Adipocyte_female_18_b

description: gWAT_adipocyte_18_b_female_control_S354_L002_R1_001


title: pgWAT_Adipocyte_female_17_b

description: gWAT_adipocyte_17_b_female_control_S353_L002_R1_001


title: pgWAT_Adipocyte_female_17_a

description: gWAT_adipocyte_17_a_female_control_S161_L002_R1_001


title: pgWAT_Adipocyte_male_3_a

description: gWAT_adipocyte_3_a_male_control_S131_L002_R1_001


title: Hippocampus-BXD28-rep3

type: RNA

first: Rupert

middle: W

last: Overall

address: Philippstraße 13

institute: Humboldt University of Berlin

hyb_protocol: Hybridisation was carried out on an Affymetrix Fluidics Station following the manufacturer's protocols for the Mouse Gene ST 1.0.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000.

data_processing: Data were processed to transcript-level gene expression estimates using the Robust Multichip Average (RMA) method. The log-transformed data were then rescaled using a z-scoring procedure to set the mean of each sample at eight expression units with an SD of two units.

label: biotin

source_name: Dissected hippocampal tissue

label_protocol: Samples were biotin labelled following the manufacturer's protocol.

growth_protocol: Mice were housed in a temperature-controlled facility the the UTHSC, Memphis, TN, USA with a 12-h light/dark cycle and ad libitium access to food and water.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufactures’ procedure.

tag: strain

value: M

tag: age

tag: batch


title: Hippocampus-BXD25-rep3


title: Hippocampus-BXD27-rep2

value: F


title: Hippocampus-BXD27-rep1


title: Hippocampus-BXD28-rep2


title: Hippocampus-BXD25-rep2


title: Hippocampus-BXD28-rep1


title: Hippocampus-BXD24-rep4


title: Hippocampus-BXD24-rep5


title: Hippocampus-BXD23-rep1


title: Hippocampus-BXD24-rep2


title: Hippocampus-BXD23-rep3


title: Hippocampus-BXD22-rep2


title: Hippocampus-BXD25-rep1


title: Hippocampus-BXD23-rep2


title: Hippocampus-BXD22-rep1


title: Hippocampus-BXD22-rep3


title: Hippocampus-BXD21-rep1


title: Hippocampus-BXD19-rep1


title: Hippocampus-BXD20-rep2


title: Hippocampus-BXD19-rep2


title: Hippocampus-BXD20-rep1


title: Hippocampus-BXD24-rep3


title: Hippocampus-BXD18-rep2


title: Hippocampus-BXD18-rep1


title: Hippocampus-BXD16-rep3


title: Hippocampus-BXD16-rep2


title: Hippocampus-BXD14-rep2


title: Hippocampus-BXD16-rep1


title: Hippocampus-BXD12-rep5


title: Hippocampus-BXD24-rep1


title: Hippocampus-BXD12-rep3


title: Hippocampus-BXD12-rep2


title: Hippocampus-BXD11-rep2


title: Hippocampus-BXD12-rep4


title: gASC_pos_19_c_female

description: gASC_pos_19_c_female_control_S355_L008_R1_001

tag: tissue


title: Hippocampus-BXD12-rep1


title: Hippocampus-BXD9-rep1


title: Hippocampus-BXD11-rep1


title: Hippocampus-BXD11-rep4


title: Hippocampus-BXD9-rep2


title: Hippocampus-BXD11-rep3


title: Hippocampus-BXD8-rep1


title: gASC_pos_20_a_female

description: gASC_pos_20_a_female_control_S100_L008_R1_001


title: Hippocampus-BXD9-rep3


title: Hippocampus-BXD8-rep3


title: Hippocampus-BXD2-rep4


title: Hippocampus-BXD2-rep3


title: Hippocampus-BXD8-rep2


title: Hippocampus-BXD2-rep1


title: Hippocampus-BXD2-rep2


title: Hippocampus-BXD2-rep5


title: Hippocampus-BXD14-rep1


title: Hippocampus-BXD1-rep3


title: Hippocampus-BXD1-rep1


title: Hippocampus-D2B6F1-rep1


title: Hippocampus-BXD1-rep2


title: Hippocampus-D2-rep2


title: Hippocampus-D2-rep3


title: Hippocampus-B6-rep-rep3


title: Hippocampus-D2-rep1


title: Hippocampus-B6-rep1


title: Hippocampus-B6-rep4


title: Hippocampus-BXD101-rep3


title: Hippocampus-B6-rep2


title: Hippocampus-BXD101-rep1


title: Hippocampus-BXD100-rep5


title: Hippocampus-BXD100-rep3


title: Hippocampus-BXD6-rep1


title: Hippocampus-BXD99-rep2


title: Hippocampus-BXD100-rep2


title: Hippocampus-BXD100-rep4


title: Hippocampus-BXD98-rep3


title: Hippocampus-BXD100-rep1


title: Hippocampus-BXD101-rep2


title: Hippocampus-BXD98-rep1


title: Hippocampus-BXD95-rep2


title: Hippocampus-BXD95-rep1


title: Hippocampus-D2B6F1-rep2


title: Hippocampus-BXD95-rep3


title: Hippocampus-BXD90-rep3


title: Hippocampus-BXD89-rep2


title: Hippocampus-BXD89-rep1


title: Hippocampus-BXD87-rep5


title: Hippocampus-BXD90-rep1


title: Hippocampus-BXD90-rep2


title: Hippocampus-BXD87-rep4


title: Hippocampus-BXD87-rep3


title: Hippocampus-BXD86-rep1


title: Hippocampus-BXD84-rep2


title: Hippocampus-BXD87-rep2


title: Hippocampus-BXD85-rep1


title: Hippocampus-BXD87-rep1


title: Hippocampus-BXD83-rep2


title: Hippocampus-BXD85-rep4


title: Hippocampus-BXD85-rep2


title: Hippocampus-BXD84-rep4


title: Hippocampus-BXD83-rep1


title: Hippocampus-BXD83-rep3


title: Hippocampus-BXD86-rep2


title: Hippocampus-BXD84-rep5


title: Hippocampus-BXD84-rep3


title: Hippocampus-BXD85-rep3


title: Hippocampus-BXD81-rep3


title: Hippocampus-BXD99-rep1


title: Hippocampus-BXD81-rep1


title: Hippocampus-BXD79-rep2


title: Hippocampus-BXD86-rep3


title: Hippocampus-BXD77-rep3


title: Hippocampus-BXD76-rep3


title: Hippocampus-BXD77-rep1


title: Hippocampus-BXD98-rep2


title: Hippocampus-BXD84-rep1


title: Hippocampus-BXD79-rep1


title: Hippocampus-BXD77-rep2


title: Hippocampus-BXD76-rep1


title: Hippocampus-BXD73a-rep3


title: Hippocampus-BXD73a-rep4


title: Hippocampus-BXD73-rep4


title: Hippocampus-BXD81-rep2


title: Hippocampus-BXD79-rep3


title: Hippocampus-BXD73a-rep2


title: Hippocampus-BXD73-rep2


title: Hippocampus-BXD71-rep4


title: Hippocampus-BXD73-rep1


title: Hippocampus-BXD73-rep3


title: Hippocampus-BXD71-rep1


title: Hippocampus-BXD70-rep3


title: Hippocampus-BXD71-rep2


title: Hippocampus-BXD76-rep2


title: Hippocampus-BXD73a-rep1


title: pgWAT_Adipocyte_male_4_a

description: gWAT_adipocyte_4_a_male_control_S132_L002_R1_001


title: Hippocampus-BXD70-rep4


title: Hippocampus-BXD69-rep1


title: Hippocampus-BXD69-rep2


title: Hippocampus-BXD69-rep3


title: Hippocampus-BXD68-rep4


title: Hippocampus-BXD70-rep2


title: Hippocampus-BXD75-rep1


title: Hippocampus-BXD68-rep2


title: Hippocampus-BXD68-rep3


title: Hippocampus-BXD74-rep1


title: Hippocampus-BXD71-rep3


title: Hippocampus-BXD68-rep1


title: Hippocampus-BXD67-rep5


title: Hippocampus-BXD67-rep3


title: Hippocampus-BXD67-rep2


title: Hippocampus-BXD67-rep4


title: Hippocampus-BXD67-rep1


title: Hippocampus-BXD66-rep1


title: Hippocampus-BXD66-rep3


title: Hippocampus-BXD65a-rep4


title: Hippocampus-BXD66-rep4


title: Hippocampus-BXD65-rep3


title: Hippocampus-BXD65a-rep3


title: Hippocampus-BXD70-rep1


title: Hippocampus-BXD65-rep2


title: Hippocampus-BXD65-rep1


title: Hippocampus-BXD64-rep2


title: Hippocampus-BXD65a-rep2


title: Hippocampus-BXD65a-rep1


title: Hippocampus-BXD63-rep3


title: Hippocampus-BXD63-rep2


title: Hippocampus-BXD63-rep1


title: Hippocampus-BXD62-rep3


title: Hippocampus-BXD62-rep2


title: Hippocampus-BXD62-rep1


title: Hippocampus-BXD61-rep2


title: Hippocampus-BXD65b-rep1


title: Hippocampus-BXD66-rep2


title: Hippocampus-BXD60-rep2


title: Hippocampus-BXD61-rep1


title: Hippocampus-BXD56-rep2


title: Hippocampus-BXD60-rep1


title: Hippocampus-BXD56-rep1


title: Hippocampus-BXD55-rep2


title: Hippocampus-BXD51-rep3


title: Hippocampus-BXD51-rep2


title: Hippocampus-BXD55-rep3


title: Hippocampus-BXD50-rep1


title: Hippocampus-BXD56-rep3


title: Hippocampus-BXD55-rep4


title: Hippocampus-BXD50-rep2


title: Hippocampus-BXD50-rep3


title: Hippocampus-BXD48a-rep4


title: Hippocampus-BXD48a-rep5


title: Hippocampus-BXD64-rep1


title: Hippocampus-BXD48a-rep3


title: Hippocampus-BXD51-rep1


title: Hippocampus-BXD48a-rep1


title: Hippocampus-BXD48-rep4


title: Hippocampus-BXD48-rep3


title: Hippocampus-BXD45-rep2


title: Hippocampus-BXD48-rep1


title: Hippocampus-BXD55-rep1


title: Hippocampus-BXD45-rep1


title: Hippocampus-BXD48-rep2


title: Hippocampus-BXD44-rep4


title: Hippocampus-BXD44-rep3


title: Hippocampus-BXD44-rep2


title: Hippocampus-BXD44-rep5


title: Hippocampus-BXD43-rep3


title: Hippocampus-BXD43-rep2


title: Hippocampus-BXD43-rep1


title: Hippocampus-BXD44-rep1


title: Hippocampus-BXD42-rep2


title: Hippocampus-BXD48a-rep2


title: Hippocampus-BXD42-rep1


title: Hippocampus-BXD40-rep4


title: Hippocampus-BXD40-rep2


title: Hippocampus-BXD42-rep3


title: Hippocampus-BXD39-rep4


title: Hippocampus-BXD40-rep3


title: Hippocampus-BXD40-rep1


title: Hippocampus-BXD38-rep4


title: Hippocampus-BXD39-rep1


title: Hippocampus-BXD38-rep3


title: Hippocampus-BXD48a-rep6


title: Hippocampus-BXD38-rep1


title: Hippocampus-BXD34-rep2


title: Hippocampus-BXD33-rep4


title: Hippocampus-BXD34-rep3


title: Hippocampus-BXD33-rep5


title: Hippocampus-BXD33-rep3


title: Hippocampus-BXD40-rep6


title: Hippocampus-BXD33-rep2


title: Hippocampus-BXD32-rep1


title: Hippocampus-BXD29-rep1


title: Hippocampus-BXD34-rep4


title: Hippocampus-BXD39-rep3


title: Hippocampus-BXD40-rep5


title: Hippocampus-BXD31-rep1


title: Hippocampus-BXD34-rep1


title: grp2_DEN_WT_8m_T__bio_rep_1

city: SAN DIEGO

first: Xinyi

state: California

address: 9500 Gilman Dr, La Jolla

department: Pathology

institute: University of California, San Diego

description: group2 sequencing

data_processing:
Raw reads generated by RNA-seq experiments were mapped to the GRCm38 mouse reference genome using STAR(2.7.10a).
The raw counts generated using htseq-count(2.0.2).
We retained 16590 genes that had a non-zero expression level in 105 samples for the following analyses.
Differentially expressed genes between mutant and WT livers at different time points were identified using R package DESeq2(1.32.0).
We set the threshold value of foldchange as 2 and p-adjust value as 0.05.
Assembly: mm10
Supplementary files format and content: Values normalized by rlog and then transformed by CPM
Supplementary files format and content: Gene symbol were provided as the genename for each record

extract_protocol:
Total RNAs were extracted from liver tissues using MAPS in Fu Lab, and RNA-sequencing (RNA-seq) was performed using the Illumina Hiseq2000 machine
Total RNAs were extracted from liver tissues using MAPS in Fu Lab, and RNA-sequencing (RNA-seq) was performed using the Illumina Hiseq2000 machine

value: liver

value: Tumor

value: WT

value: DEN


title: Hippocampus-BXD31-rep3


title: Hippocampus-BXD39-rep2


title: Hippocampus-BXD31-rep2


title: grp2_DEN_WT_8m_T__bio_rep_3

description: group2 sequencing


title: grp2_DEN_WT_5m__bio_rep_1

description: group2 sequencing

value: Normal


title: grp2_DEN_WT_8m_NT__bio_rep_3

description: group2 sequencing


title: grp2_DEN_WT_8m_T__bio_rep_2

description: group2 sequencing


title: grp2_DEN_WT_8m_NT__bio_rep_1

description: group2 sequencing


title: grp2_DEN_WT_8m_NT__bio_rep_2

description: group2 sequencing


title: grp2_DEN_WT_3m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_WT_5m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_WT_3m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_WT_1m__bio_rep_3

description: group2 sequencing


title: Hippocampus-BXD33-rep1


title: grp2_DEN_WT_3m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_WT_1m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_WT_1m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_MKO_8m_T__bio_rep_1

description: group2 sequencing

value: cMet KO


title: grp2_DEN_MKO_8m_T__bio_rep_3

description: group2 sequencing


title: grp2_DEN_MKO_8m_NT__bio_rep_3

description: group2 sequencing


title: grp2_DEN_MKO_8m_NT__bio_rep_2

description: group2 sequencing


title: grp2_DEN_MKO_5m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_MKO_5m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_MKO_8m_NT__bio_rep_1

description: group2 sequencing


title: grp2_DEN_WT_5m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_MKO_5m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_MKO_3m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_MKO_3m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_MKO_3m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_BKO_8m_T__bio_rep_3

description: group2 sequencing

value: beta catenin KO


title: grp2_DEN_MKO_1m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_MKO_1m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_BKO_8m_NT__bio_rep_3

description: group2 sequencing


title: grp2_DEN_MKO_1m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_BKO_8m_T__bio_rep_1

description: group2 sequencing


title: grp2_DEN_BKO_8m_NT__bio_rep_2

description: group2 sequencing


title: grp2_DEN_BKO_8m_NT__bio_rep_1

description: group2 sequencing


title: grp2_DEN_BKO_5m__bio_rep_2

description: group2 sequencing


title: grp2_DEN_MKO_8m_T__bio_rep_2

description: group2 sequencing


title: grp2_DEN_BKO_3m__bio_rep_3

description: group2 sequencing


title: grp2_DEN_BKO_5m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_BKO_3m__bio_rep_1

description: group2 sequencing


title: grp2_DEN_BKO_1m__bio_rep_3

description: group2 sequencing


title: grp1_DEN_WT_8m_T__bio_rep_4

description: group1 sequencing


title: grp2_DEN_BKO_3m__bio_rep_2

description: group2 sequencing


title: grp1_DEN_WT_8m_T__bio_rep_1

description: group1 sequencing


title: grp1_DEN_WT_8m_T__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_8m_NT__bio_rep_2

description: group1 sequencing


title: grp2_DEN_BKO_1m__bio_rep_2

description: group2 sequencing


title: grp1_DEN_WT_8m_NT__bio_rep_1

description: group1 sequencing


title: grp2_DEN_BKO_8m_T__bio_rep_2

description: group2 sequencing


title: grp1_DEN_WT_8m_NT__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_8m_NT__bio_rep_4

description: group1 sequencing


title: grp1_DEN_WT_5m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_WT_5m__bio_rep_2

description: group1 sequencing


title: grp2_DEN_BKO_1m__bio_rep_1

description: group2 sequencing


title: grp1_DEN_WT_3m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_WT_3m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_5m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_WT_1m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_3m__bio_rep_2

description: group1 sequencing


title: grp2_DEN_BKO_5m__bio_rep_3

description: group2 sequencing


title: grp1_DEN_WT_1m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_WT_1m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_WT_1m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_8m_T__bio_rep_3

description: group1 sequencing

value: Shp2 KO


title: grp1_DEN_SKO_8m_T__bio_rep_4

description: group1 sequencing


title: grp1_DEN_WT_8m_T__bio_rep_2

description: group1 sequencing


title: grp1_DEN_SKO_8m_NT__bio_rep_4

description: group1 sequencing


title: grp1_DEN_SKO_8m_T__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_8m_NT__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_5m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_SKO_5m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_SKO_8m_NT__bio_rep_2

description: group1 sequencing


title: grp1_DEN_SKO_8m_NT__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_5m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_SKO_3m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_SKO_3m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_SKO_5m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_WT_3m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_SKO_3m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_3m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_SKO_1m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_SKO_1m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_SKO_5m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_1m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_8m_T__bio_rep_2

description: group1 sequencing

value: Ikk KO


title: grp1_DEN_IKO_8m_T__bio_rep_3

description: group1 sequencing


title: grp1_DEN_SKO_1m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_IKO_8m_T__bio_rep_4

description: group1 sequencing


title: grp1_DEN_IKO_8m_NT__bio_rep_3

description: group1 sequencing


title: grp1_DEN_IKO_8m_T__bio_rep_1

description: group1 sequencing


title: grp1_DEN_SKO_8m_T__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_8m_NT__bio_rep_1

description: group1 sequencing


title: grp1_DEN_IKO_8m_NT__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_5m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_IKO_5m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_IKO_5m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_IKO_5m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_3m__bio_rep_4

description: group1 sequencing


title: grp1_DEN_IKO_3m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_IKO_3m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_IKO_3m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_1m__bio_rep_2

description: group1 sequencing


title: grp1_DEN_IKO_1m__bio_rep_3

description: group1 sequencing


title: grp1_DEN_IKO_1m__bio_rep_1

description: group1 sequencing


title: grp1_DEN_IKO_8m_NT__bio_rep_4

description: group1 sequencing


title: grp1_DEN_IKO_1m__bio_rep_4

description: group1 sequencing


title: DD1C_Day65_VPA_repl1

city: Uppsala

first: Xingqi

address: Husargata

department: Immunology, Genetics and Pathology

institute: uppsala university

data_processing:
adaptors were trimmed.
All reads were aligned to hg38 using bowtie2 with the following parameters  "--end-to-end --very-sensitive -I 10 -X 700"
The aligned BAM files were sorted and filtered with alignment quality of  >Q2 using samtools v.1.9
The bigwig file were generated from BAM file using deeptools with the parameters "bamCoverage –normalizeUsing CPM"
MACS2
Assembly: hg38
Supplementary files format and content: bigwig

source_name: induced pluripotent stem cells (iPSCs)

extract_protocol:
ATAC-Seq libraries were prepared following. In brief, two technical replicates per sample containing 50,000 nuclei each were collected at 500 x g for 5 min at 4°C. Nuclei were resuspended in lysis buffer (10 mM Tris-Cl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Igepal CA-630) and centrifuged at 500 x g for 10 min. The supernatant was removed and each nuclei pellet was resuspended in tagmentation buffer (25 μL 2 × TD buffer) with 2.5 μl Tn5 transposome and incubated at 37°C for 30 min. An equal volume of 2 x reverse crosslinking buffer (50 mM Tris-Cl, 1mM EDTA, 1% SDS, 0.2M NaCl, 5 ng/ml Proteinase K) was added to each sample and incubated at 65°C with agitation at 1200 rpm for overnight. DNA was isolated using a MinElute PCR Purification Kit (Qiagen). Sequencing libraries were prepared following described standard protocol. All libraries were sequenced on an Illumina Nova-seq platform at Novogene Europe.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Cell cultures were sampled at days 0 (D0), D19, D35 and D65, respectively, by harvesting cells with TryplE and collecting by centrifugation (300 x g, 3 min). Harvested cells were counted and assessed for viability using trypan blue staining and an automated EVE cell counter (NanoEntek).Samples with a viability of>90% were selected for ATAC-Seq library preparation (see below).Additionally, neuronal cell cultures at D65 were treated with valproic acid (VPA; 0,5 mM) for 6 days and subsequently harvested for analysis. Harvested cells were resuspended in 1 ml of 1 x PBS and fixed by adding an equal amount of 2% formaldehyde for 10 min at room temperature. The reaction was quenched by adding 100 ul 2,5 M glycine solution. Fixed cells were collected by centrifugation and washed twice with 1 x PBS. Cells where then resuspended in 1 x PBS, counted using an EVE automatic cell counter (NanoEntek) with Trypan Blue, and subsequently 50’000 cells/sample were processed for library preparation for ATAC sequencing.

value: induced pluripotent stem cells (iPSCs)

tag: group

tag: time point


title: Ctl8F_Day65_VPA_repl2

tag: cell line


title: Ctl8F_Day65_VPA_repl1


title: DD1C_Day65_VPA_repl2


title: Ctl1B_Day65_VPA_repl1


title: Ctl7C_Day65_VPA_repl2


title: DD5A_Day65_VPA_repl1


title: DD5A_Day65_VPA_repl2


title: Ctl7C_Day65_VPA_repl1


title: Ctl1B_Day65_VPA_repl2


title: DD1C_Day65_repl1


title: DD1C_Day65_repl2


title: DD5A_Day35_repl1


title: DD5A_Day35_repl2


title: Ctl8F_Day65_repl1


title: Ctl8F_Day65_repl2


title: DD5A_Day65_repl2


title: DD5A_Day65_repl1


title: Ctl1B_Day65_repl1


title: Ctl7C_Day65_repl1


title: Ctl7C_Day65_repl2


title: DD1C_Day35_repl2


title: Ctl7C_Day35_repl1


title: Ctl7C_Day35_repl2


title: DD4A_Day35_repl1


title: Ctl8F_Day35_repl2


title: Ctl8F_Day35_repl1


title: DD4A_Day35_repl2


title: DD5A_Day19_repl2


title: Ctl1B_Day35_repl1


title: DD5A_Day19_repl1


title: Ctl1B_Day65_repl2


title: DD5A_Day0_repl2


title: DD1C_Day19_repl1


title: DD4A_Day19_repl2


title: DD5A_Day0_repl1


title: DD4A_Day19_repl1


title: DD4A_Day0_repl2


title: DD4A_Day0_repl1


title: DD1C_Day0_repl1


title: Ctl1B_Day35_repl2


title: DD1C_Day0_repl2


title: Ctl8F_Day19_repl2


title: Ctl8F_Day19_repl1


title: Methylation - Patient 42

type: genomic

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Quality control of Infinium MethylationEPIC BeadChips was performed via the Genome Studio Methylation Module (Illumina). Subset-quantile Within Array Normalization (SWAN) was performed on the Infinium MethylationEPIC BeadChip IDAT files via the R package “minfi”.

label: cy3, cy5

source_name: Peripheral blood mononuclear cells

label_protocol: standard protocol

extract_protocol: Genomic DNA was isolated and checked for quality by standard protocols. 1 µg genomic DNA then underwent bisulfite treatment using the TrueMethyl oxBS Module (Tecan Genomics, Männedorf, Switzerland) according to the manufacturer’s specifications. Briefly, DNA was purified using magnetic beads, denatured, and underwent bisulfite conversion followed by desulfonation and purification. The TrueMethyl converted DNA samples were then eluted in 10 µL and then processed through the Illumina Infinium MethylationEPIC BeadChip array (Illumina, San Diego, CA) protocol. In brief, 7 µl of converted DNA was denatured with 1 µL of 0.4N sodium hydroxide prior to whole genome amplification on the MSA4 plate. All other steps were followed as per manufacturer’s guidelines.

tag: disease state 1

value: Clonal hematopoiesis

tag: disease state 2


title: Ctl8F_Day0_repl2


title: Ctl7C_Day0_repl1


title: XZ60540 (PyMT-N tumor): CD45+CD11b- cells from the tumors of PyMT-N tumor-bearing mice

city: Houston

first: Xiaoxin

last: Hao

address: 1 Baylor Plaza-Alkek N1130

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

data_processing:
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Assembly: mm10
Supplementary files format and content: Compressed .gz files contain the filtered_feature_bc_matrix output folder from Cellranger. Files include a .mtx file, which is the count matrix, and two .tsv files that list the feature names and sample annotations.

source_name: PyMT-N

extract_protocol:
Tumors were resected, washed in PBS, cut into small pieces, and transferred into a digestion medium (DMEM) containing 1 mg/mL type-1 collagenase (Sigma, C0130), 1 mg/mL type-2 collagenase (Thermo Fisher, 17101015), 1 mg/mL Dispase II (Sigma-Aldrich, D4693), 1 mg/mL BSA, 0.1 mg/mL Dnase-1, HEPES, and EDTA (1 mM). Tumor tissues were dissociated at 37°C for 45 min, then cells were liberated by pipetting and filtered through a 70 μm cell strainer. Next, cells were lysed in red blood cell lysis buffer (Tonbo) for 10 min. To enrich tumor-infiltrating lymphocytes, CD11b+ cells were depleted through magnetic sorting, followed by FACS sorting of CD45+ cells for 3’ scRNA-seq.
The single-cell gene expression library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics).

value: PyMT-N

tag: cell type

value: PyMT-N tumor-infiltrating immune cells


title: Ctl7C_Day19_repl1


title: W17_D9_PBS_E1835_E

city: Aurora

first: Ben-Zheng

last: Li

state: CO

department: Department of Physiology and Biophysics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Quality control was conducted by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
The RNA-seq reads were processed with BBDuk (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/) and aligned to mouse genome GRCm38.p6 (release 96) with STAR.
The differential expression analysis was performed on TMM (trimmed-mean M values) normalized count data using negative binomial generalized linear model and likelihood ratio test implemented in the edgeR package (version 4.0.11, https://doi.org/10.5281/zenodo.3748085)
The Benjamini–Hochberg multiplicity correction was applied on p-values to calculate false discovery rates.
Assembly: mm10
Supplementary files format and content: csv file include raw  counts of sequencing reads

extract_protocol:
RNA extraction was performed using an RNA Plus mini-Kit from Qiagen (Qiagen, 74136).
NuQuant Universal Plus mRNA seq kit was used to prepare mRNA sequencing libraries.

value: Skin

tag: genotype

value: BKS.Cg-Dock7m+/+Leprdb/J (db/db)

tag: treatment

value: Vehicle

tag: time

value: Day 9


title: Ctl8F_Day0_repl1


title: Ctl7C_Day0_repl2


title: W17_D9_PBS_E1834_D


title: DD1C_Day35_repl1


title: Ctl1B_Day19_repl1


title: W17_D9_PBS_E1831_A


title: Methylation - Patient 48


title: Ctl1B_Day0_repl1


title: W17_D9_0628_point5_E1836_F


title: W17_D9_0628_point5_E1837_G


title: Ctl1B_Day0_repl2


title: Methylation - Patient 44


title: Methylation - Patient 41


title: Methylation - Patient 46


title: MCF7,IAA,rep1

city: Wuhan

first: Ziang

last: Lu

address: Wuhan University, No.299, Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
After trimming adapters, CUT&TAG raw reads were aligned to hg38 human genome using bowtie2 and duplicate reads were removed from unique mapping reads using Picard MarkDuplicates.
The clean reads were used to call peaks using MACS2. After removing peaks in blacklist, the high repeatability peaks between biological replicates were get using IDR.
After trimming adapters, AMUC-seq raw reads were alinged to human rRNA using bowtie2 to remove rRNA sequences.
Unmapped reads were mapped to hg38 human genome with STAR. Duplicate reads were removed from unique reads using Picard MarkDuplicates .
Mutation sites were collected and annotated with REDItools, and SNP sites were removed.
Assembly: Mutation rate calculation and s4U labeled reads extraction were performed with custom script. Raw counts of s4U labeled mRNA and all mRNA were obtained using htseq. TPM expression matrix and fold change were calculated with custom script.
Supplementary files format and content: hg38
Supplementary files format and content: bigwig, aligned reads or labeled reads in AMUC-seq
Supplementary files format and content: bed, IDR peak result
Library strategy: CUT&TAG

growth_protocol: All cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco) in the presence of 5% CO2 at 37°C incubators.

extract_protocol:
Genomic DNA was extracted by EasyPure Genomic DNA Kit (TransGen Biotech). Total RNA was extracted by Invitrogen TRIzol (Thermofisher) . PolyA RNA was extracted by NEBNext® High Input Poly(A) mRNA Isolation Module.
CUT&TAG libraries were constructed with CUT&TAG kit (Vazyme, #TD903). AMUC-seq libraries were constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 500μM s4U and 500μM IAA will be treated in corresponding samples.

tag: antibody

value: BG4 sigma MABE9917

value: IAA treated


title: Methylation - Patient 16


title: MCF7,noIAA,rep2

value: noIAA treated


title: I__W15_D11_0628_1_D049

value: Day 11


title: H__W15_D11_0628_1_D048


title: Methylation - Patient 8


title: Methylation - Patient 12


title: Methylation - Patient 6


title: Methylation - Patient 26


title: W17_D9_0628_point5_E1839_I


title: G__W15_D11_0628_1_D047


title: MCF7,noIAA,rep1


title: E__W15_D11_PBS_D035


title: D__W15_D11_PBS_D034


title: hBMSC-WNT1-B

city: Shenzhen

first: Peikai

address: 1 Haiyuan Rd

institute: The University of Hong Kong - Shenzhen Hospital

data_processing:
The fastq data files were aligned to human reference genome hg38, using hisat (v. 2-2.0.4) with default parameters.
The resulting bam files were processed with cufflinks (v2.2.1) for quantification of FKPM, with gene models provided by GENCODE  (v. 25).
The resulting bam files were also processed with HTSeq count (version 0.11.0) for quantification of gene counts, with gene models provided by GENCODE  (v. 25).
Assembly: GRCh38
Supplementary files format and content: tab delimited files gzipped

source_name: Bone marrow MSCs

extract_protocol:
The transfected bone marrow MSCs (pcDNA3.1 and pcDNA3.1-WNT1) were lysed with Trizol (Thermo Fisher) for RNA extraction. RNA concentration was measured by Qubit and RNA integrity was assessed using the Agilent 2100. A total amount of 2 µg RNA per sample was used for sequencing.
Libraries were generated using VAHTS mRNA-seq Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads in Berry Genomics Co. (Beijing).

treatment_protocol: Bone marrow MSCs were transfected with pcDNA3.1-WNT1 or empty vectors. After selection, cells were treated with osteoblastic and adipogenic differentiation media for 14~28 days followed by staining with Alizarin red (Sigma) or Oil red (Beyotime Biotechnology).

value: Bone marrow MSCs

value: transfected with pcDNA3.1-WNT1, duplicate 2


title: MCF7, DHX36, rep1

value: DHX36 Rabbit pAb (Abclonal,#A5191)


title: Ctl7C_Day19_repl2


title: A__W15_D11_PBS_D031


title: MCF7, DHX36, rep2


title: Methylation - Patient 36


title: Methylation - Patient 35


title: Methylation - Patient 1


title: OSKM iPSC,Tsc1 KO,Day10,anti-HDAC2

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end--very-sensitive--local--no-mixed--no-discordant--no-unal--phred33-I10-X700. Then, Sambamba was used to remove duplicate reads and samtools was used to sort the data. Peaks were called using MACS2 (v.2.2.7.1) with the following parameters: --SPMR--nomodel--extsize 200--keep-dup all--q 0.001. Reads that mapped to mitochondrial DNA or unassigned sequences were discarded. For paired-end sequencing data, only transformed into read coverage files (bigwig format) using deepTools with RPKM normalization. For the sample without repeats, differential binding region was analysis by manorm (v.1.3.0) with P-value <= 0.05.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: embryonic stem cells

extract_protocol:
Around 100000 living cells were collected for each sample CUT&Tag library construction.
For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein, N259-YH01) was used. Around 1×105 living cells were collected for each sample, and the CUT&Tag library was sequenced on a illumina nova6000, carried out by CNGB.

value: embryonic stem cells

value: Tsc1 KO

value: iPSC


title: Methylation - Patient 45

value: Clonal hematopoiesis


title: Methylation - Patient 17


title: hBMSC

value: transfected with empty vectors, duplicate 1


title: OSKM iPSC,Tsc1 KO,Day10,anti-TFE3


title: Methylation - Patient 33


title: Type XV OI sample

description: 10X Genomics

data_processing:
10X single-cell sequencing was performed using Illumina Novaseq 6000 platform at Berry Genomics Co. (Beijing), with 150GBp throughput per sample. The raw data were aligned to human genome (GRCh38/hg38). Cells with fewer than 1,600 genes or clusters expressing PTPRC (CD45) were excluded. Data was further processed with Seurat (v3.9.9) 35. In all, 3,570 (average 3,712 genes per cell) and 126 (average 1,103 genes per cell) cells were found in the LLD and OI type XV samples, respectively. Population signatures were identified by comparing every population against all other cells, using Seurat’s FindAllMarkers function, with an FDR cutoff of <0.05, log2(fold-change)>1, and expressed percentage point difference >25%. The osteogenic cells were integrated using the canonical correlation analysis (CCA) approach. Gene-ontology analyses were performed using GSEA (gsea-msigdb.org).
Assembly: GRCh38
Supplementary files format and content: h5 binary files

source_name: bone

extract_protocol:
Single-cell RNA sequencing was conducted as previously described (Chu, Chen et al. 2023). Soft tissues were carefully removed, and blood cells were fully washed away with brief TrypLE Express digestion (Gibco). Then bone was cut into fragments and digested with 0.25% Dispase, 0.25% type II collagenase in HBSS at 37ºC on a shaker for 1.5 hours. During the digestion, cells were collected every 30 minutes interval and filtered with a 40µm cell strainer. Red blood cells were removed using Red Blood Cell Lysis Solution (Miltenyi Biotec) and cleaned up with Dead Cell Removal Kit (Miltenyi Biotec). Single cells suspension was washed twice with DPBS (Gibco). Viabilities of 85% and 82% were recorded for the LLD and type XV OI samples, respectively. A raw total input of 10000 cells was estimated for each 10x sequencing.
Single-cell encapsulation and library preparation were prepared by Chromium single-cell platform (10X Inc.) in Berry Genomics Co. (Beijing). Cells were counted and loaded into individual well of 10X Chromium Single-Cell chip. Single cells were then encapsulated into GEMs by 10X Chromium Controller. Single Cell 3’ Reagent Kits v3 was used for library construction according to manufacturer’s protocol. The double-stranded cDNA went through enzymatic fragmentation, adapter ligation, index PCR and SPRIselect size selection. Library size and concentration were determined by Qubit and Bioanalyzer assays.

value: bone

value: bone cells

tag: gender

value: male


title: OSKM iPSC,wildtype,Day10,anti-TFE3

value: Tsc1 WT


title: DD1C_Day19_repl2

value: induced pluripotent stem cells (iPSCs)


title: Control sample

description: 10X Genomics

value: AKT1 (c.49G>A, p.E17K, sample frequency 13.3%)


title: OSKM iPSC,wildtype,Day10,anti-HDAC2