title: UM-SCC-11B WT 1


title: BMO5

status: Public on Dec 04 2023

type: SRA

city: Munich

first: Stephanie

last: Frenz-Wiessner

address: Lindwurmstr. 4

department: Department of Pediatrics, Dr. von Hauner Children’s Hospital

country: Germany

institute: Ludwig-Maximilians-University Munich

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Homo sapiens

source_name: bone marrow-like organoids (BMOs)

extract_protocol: Library prep was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics)

tag: tissue

value: bone marrow-like organoids (BMOs)


title: Stereo-seq of CBA/J mouse endometrium at E9.5, rep1

status: Public on Dec 18 2023

city: Beijing

first: Min

last: Yang

state: Beijing

address: No. 5, yiheyuan road, haidian district,

country: China

institute: Peking University

description: Fresh frozen spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
Paired-end raw sequencing fastq reads were generated by MGI DNBSEQ-TX sequencer. Read 1 contained the CID (coordinate identity) and the MID (molecular identiﬁer, UMI), and Read 2 contained the cDNA sequence. By mapping the CID with the chip, the coordinates were obtained. After preprocessing, retained reads were aligned to the reference genome (mm10) by STAR and then the mapped reads were ﬁltered with MAPQ >=10 using handleBam. MID with the same CID and the same gene locus were collapsed. Finally, the gene expression matrix was generated using the exonic reads with CID information. The gene expression matrix was divided into X * X DNB (bin X), with X ∈ (10, 20, 50, 100), and the reads of the same gene were aggregated within each bin. In our data, DSCs have a large cell size and therefore we used bin 50, whereas the immune cells have a smaller cell size and we thus used bin 20. Then the data were transferred to Seurat for the downstream analyses. Initially, we employed the SCTransform function to normalize and scale the raw matrix of scStereo-seq data. Next, we performed unsupervised cell clustering on each slide data using the FindCluster function, with a resolution parameter of 0.3 (res = 0.3), similar to the scRNA-seq method. Finally, uniform manifold approximation and projection (UMAP) dimension reduction analysis was used to display the clustering results.
Assembly: mm10
Supplementary files format and content: ssDNA image and spot-gene exrepssion matrix.
Supplementary files format and content: tar archives include the H&E image files, representing the adjacent slide to each Stereo-seq slide.
Library strategy: Spatial Transcriptome

molecule: total RNA

organism: Mus musculus

source_name: Endometrium

extract_protocol:
E6.5-E9.5 implantation sites of normal pregnant ICR mice and E8.5 and E9.5 implantation sites of DBA/2-mated CBA/J mice were embedded in Tissue-Tek O.C.T. Compound (Sakura, 4583) and snap-frozen on top of liquid nitrogen
BGI-Qingdao, Qingdao, China, performed sample library construction for scStereo-seq as described previously. 17 Cryosections of approximately 10 mm were cut and were attached to the scStereo-seq capture chip (1 cm x 1 cm), with spot size of 220 nm and center-to-center distance of 715 nm, and incubated at 37 _x0002_ C for 3 min. The tissue slides were ﬁxed and then stained a nucleic acid dye to assess the resolution of the data after sequencing. The tissue sections adjacent to the ones for scStereo-seq were used to examine the histology of the tissue structure through H&E stainings. The tissue sections attached to the chips were then permeabilized and the released RNA was then captured by the DNA nanoballs (DNB) on the chip. Then, the captured RNA was in situ reverse transcribed to generate cDNA. After tissue digestion and Exonuclease I treatment, the cDNA was ampliﬁed. For library construction, 20 mg of the cDNA was used for fragmentation and ampliﬁcation. Finally, the resulting PCR products were puriﬁed, and used for DNB generation. Then, the libraries were sequenced on a MGI DNBSEQ-Tx sequencer.

value: Endometrium


title: Stereo-seq of mouse endometrium at E9.5


title: Stereo-seq of CBA/J mouse endometrium at E8.5


title: BMO2

description: 10x Genomics


title: BMO3

description: 10x Genomics


title: Stereo-seq of mouse endometrium at E8.5, rep1


title: UPCI:SCC-154 WT 2

city: Liverpool

first: Lekh

last: Dahal

address: Sherrington Building, Ashton Street

country: United Kingdom

institute: University of Liverpool

data_processing:
FastQ Screen v0.13.0
Raw sequence reads were trimmed for contaminating sequence adapters and poor quality bases using the program FastP1. Bases with an average Phred score lower than 15 were trimmed. Reads that were trimmed to less than 54 bases were discarded.
The sequenced reads where checked for other species contamination using the Fastq-Screen program, which selects a sample of the reads and aligns them to a selection of reference genomes that are routinely sequenced at Glasgow Polyomics. The quality trimmed reads were aligned to the reference genome using the program Hisat2 and the transcript abundance estiamted using Stringtie.
Assembly: Ensembl
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

extract_protocol:
RNA was harvested using total RNA Miniprep kit (NEB) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using QuantSeq Library Prep Kit following the manufacturer's protocol.

tag: cell line

tag: cell type

value: HNSCC

tag: genotype

value: HPV+


title: Stereo-seq of mouse endometrium at E6.5, rep2 and E7.5, rep1


title: FaDu WT 2

source_name: FaDu

value: FaDu

value: HPV-


title: Stereo-seq of mouse endometrium at E6.5, rep1 and E7.5, rep2


title: Col1a1-GFP_Cxcl12-creER P25

status: Public on Dec 01 2023

city: Houston

first: Mizuki

last: NAGATA

state: TX

address: 7500 Cambridge St

department: Orthodontics

country: USA

institute: UTHealth

description: Postnatal day 25

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: barcodes.tsv, genes.tsv & matrix.mtx for Sample 1, barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz for Sample 2, barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz for Sample 3,

source_name: Mandibular molars

extract_protocol:
Mandibular molars were extracted, dental pulp and periodontium were enzymatically dissociated and GFP+, tdTomato+ or GFP+tdTomato+ cells were FACS-isolated. ~10,000 cells were loaded onto 10X Genomic Chromium platform
10X Genomic Chromium Single Cell 3' v3 Libraries

value: Mandibular molars

value: GFP+, tdTomato+ and GFP+tdTomato+ mesenchymal cells in murine molars


title: Stereo-seq of CBA/J mouse endometrium at E9.5, rep2


title: BMO1

description: 10x Genomics


title: Cxcl12-GFP P6

description: Postnatal day 6

value: CXCL12-GFP+ mesenchymal cells in tooth bud


title: 198-C1N1

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: digested cartilage tissue

data_processing:
The unstranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by featureCounts.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files including raw counts for genes.

source_name: Human articular cartilage

growth_protocol: Chondrocyte spheroid were generated and cultured with or without Pam3CSK4, L-NAME under hyperxia condition.

extract_protocol:
RNA was isolated using µMACS™ mRNA Isolation Kits (Miltenyi). RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions

value: Human articular cartilage

tag: donor

value: OA patient 198

tag: cells

value: chondrocytes

tag: condition


title: UM-SCC-1 WT 3


title: 197-C1

description: digested cartilage tissue

value: OA patient 197


title: 167-C1N1

description: digested cartilage tissue

value: OA patient 167


title: 167-C1

description: digested cartilage tissue


title: Cxcl12-creER P6

description: Postnatal day 6

value: tdTomato+ mesenchymal cells in tooth bud

value: Cxcl12-creER; R26R(tdTomato/+)


title: 199-C0

description: digested cartilage tissue

value: OA patient 199

value: Unstimulated


title: 199-C1N1

description: digested cartilage tissue


title: 198-C1

description: digested cartilage tissue


title: 197-C0

description: digested cartilage tissue


title: 167-C0

description: digested cartilage tissue


title: 199-C1

description: digested cartilage tissue


title: CK248

status: Public on Nov 01 2023

city: CLICHY

first: Camille

last: PIGNOLET

address: 100 Bd du Général Leclerc

department: CRI U1149

country: France

institute: INSERM

data_processing:
Reads were aligned using STAR and gene expression counts obtained with FeatureCount
The  normalized TPM matrix was generated from fastq  with kallisto tools and ensemble_v107_GRCh38b for reference human genome.
Assembly: hg38
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample, tab_delimited tsv file includes normalized TPMs for each Sample

source_name: Biopsy

extract_protocol:
Five µm-thick sections were cut from FFPE blocks. Total RNAs were further isolated using the Qiagen FFPE RNA extraction kit (RNeasy FFPE kit, Qiagen)
Gene expression was analysed using SMARTer Stranded Total RNA-Seq Kit.

tag: sample id

value: Biopsy

tag: gender

value: Male

tag: age at_the_time_of_sampling

tag: death

tag: os


title: CK246


title: 197-C1N1

description: digested cartilage tissue


title: BMO4

description: 10x Genomics

value: bone marrow-like organoids (BMOs)


title: 198-C0

description: digested cartilage tissue


title: CK244


title: CK247

value: Female


title: treatment1

status: Public on Nov 22 2023

city: Guangdong

first: Di

last: Can

address: Guangzhou

institute: Sun Yat-Sen university

description: 10x Genomics

data_processing:
1. sn-seq: Raw BCL files obtained from the 10x GENOMICS Single-nucleus RNA-seq platform were convert to FASTQ files. The resulting FASTQ files were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x GENOMICS). For quality control, nuclei were excluded from further analysis if they were outliers in terms of number of the genes, UMIs, and the percentage of mitochondrial genes using the R (v4.1.0) software package Seurat (v4.0.6) (http://satijalab.org/seurat). After filtering, a total of 20,198 nuclei (10,444 from normal, 9,754 from EO771-VM) remained for downstream analysis. 2. ST: Raw ST sequencing data were processed using the open source ST Pipeline v1.7.2 with the genome reference mm10 transcriptome. The ST pipeline was executed with two-pass mode enabled for alignment and discarding reads in which the UMI had at least 6 low quality bases. The count matrices (spots by genes) were filtered to keep only protein-coding, long non-coding, and antisense genes, and Ensembl IDs were replaced by gene names. The matrix of counts underwent another filtering step, where only spots inside the tissue were kept using the file generated in the previous step (image alignment).  3. RNA-seq: Raw sequencing reads were quality-filtered and adapter removal was performed by fastp (v.0.18.0). Paired-end clean reads were mapped to the human reference genome Ensembl_release106 using HISAT2 (v.2.4). Gene level quantification and normalization was using RSEM (v.1.3.3) software. Fragment per kilobase of transcript per million mapped reads (FPKM) was used as an index of gene quantification.
Assembly: mm10;human reference genome Ensembl_release106
Supplementary files format and content: 1.sn-seq: Tab-separated values files and matrix files. 2. ST: Tab-delimited text files containing genes by barcode counts matrices. Tissue_positions_list.csv includes cell barcode for X,Y coordinates. 3.RNA-seq: tab-delimited text files include RPKM values for each Sample

source_name: choroid plexus and ventricular wall

extract_protocol:
1. sn-seq: The lateral ventricles including the choroid plexus and an about 2 mm thin layer of tissue surrounding the ventricles were carefully micro-dissected and homogenized using scissors. The resulting homogenates were filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min to pellet nuclei. To purify nuclei, the pellet was resuspended and centrifuged at 25,000 rpm at 4 ℃ for 2 hr using an ultra-centrifuge equipped with swinging bucket rotor. The supernatant was carefully removed via aspiration. 1 ml of stain buffer was added to resuspend the nuclear pellet. The nuclei were pelleted at 500 g for 10 min at 4 ℃. Stain buffer with mouse anti-NeuN conjugated to Alexa-Fluor-488 was added. The samples were incubated for 30 min at 4 ℃ and then centrifuged for 5 min at 500 g to pellet nuclei. The pallets were resuspended in stain buffer that contained 0.1 µg/ml DAPI. Single nucleus sorting was carried out on FACSAria III. Nuclei were gated on their morphology and DAPI signal. Nuclei negative for NeuN were sorted. 2. ST: EO771-VM bearing mouse brains were embedded in Tissue-Tek O.C.T. Compound and frozen in isopentane on liquid nitrogen. The embedded mouse brains were cryosectioned coronally to a thickness of 10 mm (at -0.6 mm from the bregma) slice on a cryostat. Sections were placed respectively on Visium Spatial Tissue Optimization Slide and Visium Spatial slide within the capture area. 3. RNA-seq: The different mRNA profiles of HCPEpiC cells treated with or without 500 ng/mL recombinant human tryptase  were compared by RNA-seq. Total RNA was extractedusing the TRIzol  reagent according to the manufacturer’s instructions. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies).
1. sn-seq:Single nucleus was loaded on a 10x GENOMICS GemCode Single-nucleus instrument that generated single-nucleus Gel Bead-In-EMlusion (GEMs). Reverse transcription and libraries preparation were performed using the Chromium Next GEM Single nucleus 3’ Reagent Kits v3.1 (10x GENOMICS, CG000204) according to the manufacturer’s protocol. Libraries were sequenced on an lllumina NovaSeq 6000 system.  2.ST: After permeabilization, tissues were degraded and removed from the slides. Reverse transcription mix containing SuperScript III reverse transcriptase  was added to each section and incubated overnight at 42 ℃ to generated cDNA with spatial barcode information. The spatially barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. The libraries were sequenced on the lllumina NovaSeq 6000 system using paired-end sequencing. 28 bases were sequenced on read 1 to determine the spatial barcode and UMIs, and 120 bases were sequenced on read 2 to cover the genetic region. 3. RNA-seq: Libraries of RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina. RNA-seq was performed using the Novaseq6000  with paired-end reads.

value: choroid plexus and ventricular wall

tag: age

value: 9-12 weeks

value: non-neuronal nuclei

tag: strain

tag: treatment

value: mice injected EO771-VM cells


title: normal3

description: 10x Genomics


title: treatment3

description: 10x Genomics


title: treatment2

description: 10x Genomics


title: CK239


title: normal2

description: 10x Genomics


title: normal1

description: 10x Genomics


title: CK242


title: CK233


title: CK240


title: CK250


title: CK230


title: CK249


title: CK243


title: CK241


title: CK237


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title: CK112


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title: CK109

source_name: Surgical specimen

value: Surgical specimen


title: CK110


title: CK106


title: CK105


title: CK108


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title: CK102


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title: CK097


title: CK103


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title: CK001


title: Iz_B_Hash

status: Public on Oct 25 2023

city: Manhasset

first: Izumi

last: Kurata-Sato

address: 350 Community Drive

institute: the Feinstein Institutes for Medical Research

description: 4 VNS (E1, E2, E4, E6) and 4 sham (S1-S4) mice cells are processed in a single cell library. Each mice is able to be identified by hashing oligos (Hashing sequences used are listed in VNS_feature_ref.csv file.

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

source_name: spleen

extract_protocol:
Freshly isolated splenocytes are treated with RBC lysis buffer to remove red blood cells. Cells from each mouse are hashed with hashing antibodies and stained with anti-B220 and anti-GL7 antibodies and fluorochrome-labelled NP antigen. B220+GL7+NP+ cells were sorted with FACSAria cell sorter.
Library preparation was performed according to the manufacturer's instructions (Next GEM Single Cell 5'GEM v3.1 protocol).

value: spleen

value: primary

value: B cell

value: WT


title: RNA_HS18_to_20_del_rep3

status: Public on Oct 31 2023

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Assembly: M. musculus, UCSC mm10 or H.sapiens hg38
Supplementary files format and content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

source_name: cortex

extract_protocol:
1 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.

value: cortex

value: cortex-neuron

value: neuron


title: RNA_HS18_to_20_del_rep4


title: Iz_B_Gexp


title: 23

status: Public on Oct 11 2023

city: New York

first: Madeline

last: Kim

state: NY

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from skin biopsy

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genomic features with <10 counts in at least 7 (n of smallest group) samples were filtered out (filterByExpr [edgeR R package] default parameters)
Data was then transfomed to log2-counts per million by voom-transform
Fold changes (FCHs) vs. normals were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Assembly: GRCh37
Supplementary files format and content: expression matrix (csv file) of voom-transformed counts in log2 counts per million

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragmented mRNA by reverse transcription, second strand synthesis and ligation of specific adapters.

tag: patient id

tag: disease

value: Healthy Control

tag: tissue type

value: Normal


title: Head_E15.5_WT_rep1

status: Public on Oct 16 2023

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
The resolution of unique spatial barcoding in situ allows the matching of RNA abundance with the original spatial location in the tissue section, providing a whole-transcriptome RNA-sequencing with 2-dimensional spatial relation. All differential spatial sequencing analyses were conducted using the 10X Genomics Loupe Browser (Version 6) using the standard manufacturer recommendations and protocol.
Reads were aligned to the Spaceranger reference transcriptome gex-mm10-2020-A
Assembly: mm10-2020-A
Supplementary files format and content: matrix.mtx.gz: Tab-delimited text files containing genes by barcode counts CellRanger matrix
Supplementary files format and content: features.tsv.gz: CellRanger feature file containng list of transcripts used in matrix file
Supplementary files format and content: barcodes.tsv.gz: CellRanger barcode file containing list of cell barcodes used in matrix file
Supplementary files format and content: image.png: PNG of all replicate images
Supplementary files format and content: positions.csv: barcode files containing spot barcode position information
Supplementary files format and content: scalefactors_json.json: JSON files containing scale factor information for PNG images

source_name: Whole head

extract_protocol:
Tissues were prepared as formalin-fixed paraffin-embedded (FFPE) tissue sections, following the 10X Genomics Visium Manual Workflow for FFPE.
All steps from 10X Genomics’ FFPE Visium Spatial workflow were followed. In brief, spatial RNA sequencing (spRNA-seq) slides are coated with an array of poly-T primers, which encode unique spatial barcodes. These barcodes contain thousands of encoded oligonucleotides within a catchment frame of 6.5 × 6.5 mm. The oligonucleotides are selectively hybridized with the 3’ end of mRNA eluted upon tissue permeabilization, enabling scRNA-seq-like mRNA sequencing with the individual barcode spots replacing the individual suspended cells. Each barcoded spot on the slide is ~55 µm in diameter, which is predicted to capture ~10 cells per spot. FFPE tissue was sectioned directly onto the barcoded slide, H&E stained, and then underwent enzymatic permeabilization, which allowed for mRNA release and subsequent capture by primer-coated slides. These mRNA molecules are visualized through the incorporation of fluorescent nucleotides into the complementary DNA (cDNA) synthesis process.
Spatial Transcriptomics

tag: tissue

value: Whole head

value: Wild-type

tag: timepoint

value: 15.5 days


title: Head_E15.5_WT_rep2,3,4

tag: genotype


title: Head_E14.5_WT_rep2,3,4

value: 14.5 days


title: 25

description: Gene expression data from skin biopsy


title: 24

description: Gene expression data from skin biopsy


title: 21

description: Gene expression data from skin biopsy


title: 22

description: Gene expression data from skin biopsy


title: Head_E14.5_WT_rep1


title: 16

description: Gene expression data from skin biopsy

value: Lesional


title: 15

description: Gene expression data from skin biopsy


title: 20

description: Gene expression data from skin biopsy


title: 17

description: Gene expression data from skin biopsy


title: 14

description: Gene expression data from skin biopsy


title: CK004

value: Female


title: 18

description: Gene expression data from skin biopsy


title: 13

description: Gene expression data from skin biopsy


title: 10A

description: Gene expression data from skin biopsy

value: Atopic Dermatitis


title: 10B

description: Gene expression data from skin biopsy

value: Nonlesional


title: 12

description: Gene expression data from skin biopsy


title: 9A

description: Gene expression data from skin biopsy


title: 11

description: Gene expression data from skin biopsy


title: 8A

description: Gene expression data from skin biopsy


title: 8B

description: Gene expression data from skin biopsy


title: 7B

description: Gene expression data from skin biopsy


title: 6B

description: Gene expression data from skin biopsy


title: 6A

description: Gene expression data from skin biopsy


title: 4A

description: Gene expression data from skin biopsy


title: 5A

description: Gene expression data from skin biopsy


title: 4B

description: Gene expression data from skin biopsy


title: 5B

description: Gene expression data from skin biopsy


title: 7A

description: Gene expression data from skin biopsy


title: 19

description: Gene expression data from skin biopsy


title: 3

description: Gene expression data from skin biopsy


title: 2

description: Gene expression data from skin biopsy


title: PTC-028 treated ASCs rep1

status: Public on Oct 05 2023

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

description:
pooled from two mice
Lyn2117-plus-2135

data_processing:
Paired end fastq files were trimmed off adaptors with TrimGalore
Trimmed paires of files were aligned to mm39 genpme with Hisat2
Duplicates were marked with MarkDuplicates from picard tools and removed from further analysis.
Number of reads in genes where obtained using featureCounts function from Rsubread Bioconductor package (with inbuilt mm39 annotation)
Due to the very high expression of Ig genes, DE was done with them, without them and only for them. Results without Ig genes were used for further analysis.
Assembly: Differential Expression was done with edgeR Bioconductor package. Genes were deemed DE if adjusted p-value was < 0.05 and |logFC| > 1.
Supplementary files format and content: GO analysis was done using topGO Bioconductor package with classic algorithm and Fisher's Exact Test. For this analysis genes with FDR < 0.1 and |logFC| > log2(1.5) (FC > 1.5) were used. The analysis was done separately on all such genes, only up-regulated genes and only dpwn-regulated genes.
Supplementary files format and content: For the Cell Cycle analysis, We picked the list of genes associated with G1/S and G2/M stages. We computed Gene Set Enrichment score for theses genes (separately for G1/S and for G2/M) comparing their (signed) logFC to the logFC of all genes passing a threshold using our implementation of Subramanian et al original algorithm (PNAS 2005). Since we had only 4 samples, p-values were estimated by permuting the genes.

source_name: Spleen

extract_protocol:
RNA extraction was performed on cell pellets using the RNeasy Plus MicroKit (Qiagen #74034).
poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Spleen

tag: cell type

value: Antibody secreting cell

value: LynKO


title: PTC-028 treated ASCs rep2


title: 9B

description: Gene expression data from skin biopsy


title: Vehicle control treated ASCs rep1

value: Vehicle control


title: pfd6daf2_3

status: Public on Oct 04 2023

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
RNA-seq data analysis was performed as described previously (Pertea et al. 2016). Reads were aligned to theC. elegansgenome ce11 and analyzed by HISAT2 software (version 2.0.5) (Pertea et al. 2016) with default parameters. Transcript assembly and quantification were performed by using StringTie (version 1.3.3) (Pertea et al. 2015) and Ballgown (version 2.0.0) (Frazee et al. 2015).
Differentially expressed genes were analyzed by limma (version 3.24.15) (Phipson et al. 2016) with count values. Batch effects among biological repeats were removed with lmFit, contrasts.fit, and eBayes functions in limma (version 3.24.15) (Law et al. 2014).P-values were calculated by using limma (version 3.24.15) (Phipson et al. 2016) with R version 3.1.3 (http://www.r-project.org).
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: N2,pfd-6(gk493446),daf-2(e1370), andpfd-6(gk493446); daf-2(e1370)animals were grown on control RNAi-seeded plates until L4 stage and transferred to control RNAi-seeded orpfd-6RNAi-seeded plates containing FUdR. Synchronized day 1 adult worms were harvested using M9 buffer after two washes and frozen in liquid nitrogen.

extract_protocol:
Total RNAs were isolated from frozen worms using RNAiso plus (Takara) and ethanol precipitation.
The paired-end mRNA-seq library was prepared and sequenced by a HiSeq 2500 platform at Chunlab (Chunlab, Inc.). A total of three biological repeats of samples was analyzed for all conditions. RNA-seq experiments for two biological repeats were performed first, and the last set was added later to increase the robustness of the data.

tag: devlopment stage

value: Day 1 adult


title: pfd6daf2_2


title: pfd6_3


title: pfd6_1


title: pfd6_2


title: daf2_1


title: daf2_2


title: daf2_hsf1i_2

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 97) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
RNA-seq data analysis was performed as described previously (Pertea et al. 2016). Reads were aligned to theC. elegansgenome ce11 and analyzed by HISAT2 software (version 2.0.5) (Pertea et al. 2016) with default parameters. Transcript assembly and quantification were performed by using StringTie (version 1.3.3) (Pertea et al. 2015) and Ballgown (version 2.0.0) (Frazee et al. 2015). Differentially expressed genes were analyzed by limma (version 3.24.15) (Phipson et al. 2016) with count values. Batch effects among biological repeats were removed with lmFit, contrasts.fit, and eBayes functions in limma (version 3.24.15) (Law et al. 2014).P-values were calculated by using limma (version 3.24.15) (Phipson et al. 2016) with R version 3.1.3 (http://www.r-project.org).
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

growth_protocol: All strains were maintained as previously described (Stiernagle, 2006).

extract_protocol:
Total RNA in the animals was extracted using RNAiso plus (Takara), and cDNA was synthesized using the ImProm-II Reverse transcription kit (Promega).
TruSeq (unstranded) mRNA libraries (Illumina) were constructed and paired-end sequencing of Illumina HiSeq2500 was performed by Macrogen.

treatment_protocol: Worms that were grown on dsRNA-expressing bacteria-seeded NGM plates from eggs were transferred to 10 μM FUdR-containing plates to inhibit progeny hatching. To induce RNAi, 10 mM IPTG was treated on the bacteria seeded NGM plates.

tag: RNAi

value: hsf-1 RNAi


title: N2_1


title: N2_2


title: N2_3


title: daf2_hsf1i_1


title: 1

description: Gene expression data from skin biopsy


title: hel1daf2_1

data_processing:
The quality of generated sequencing reads was verified using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc). The adapter sequences (TruSeq Universal Adapter and indexed TruSeqTM Adapters, provided by Illumina) then were trimmed using the Cutadapt software. These adapter-trimmed reads were aligned to theC. elegansgenome (WS245) provided by WormBase using TopHat2 with default options. Two mismatches were allowed in the seed region defined by Bowtie. Alignment results were submitted to HTsEq to obtain the counts of the reads aligned onto each annotated gene. The locus information of all annotated genes was provided by WormBase (WS245). The obtained read counts then were normalized by the trimmed mean ofmvalues method implemented in edgeR (63). Normalized counts for all annotated genes were transformed to log2values after adding one to avoid negative infinity. Genes were considered expressed if the normalized counts of the genes were larger than a cutoff value in at least one condition, and the first quartile of the normalized count (in this study, 0.3271) was determined as the cutoff value. To identify DEGs, Student’sttest and the log2median ratio test were performed to computetvalues and median ratios for all the annotated genes (64–66). The adjustedPvalues from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjustedPvalues from the individual tests were combined to compute the overallPvalues using Stouffer's method (65,66), and genes with overallP< 0.05 and fold change >1.5 were selected as DEGs.
Assembly: WBcel235 (ce11)
Supplementary files format and content: txt files with read counts were generated by using RSEM (v.1.3.1)

growth_protocol: All strains were maintained at 20 °C. Some C. elegans strains used in this study were provided by Caenorhabditis Genetics Center, which is funded by the NIH National Center for Research Resources. Day 1 adult worms were obtained by culturing synchronized eggs from bleached gravid adults.

extract_protocol:
Total RNAs were extracted from the day 1 adult worms using RNA Isoplus (Takara) extraction methods. For each condition [wild-type, daf-2(e1370), hel-1(gk148684), or hel-1(gk148684); daf-2(e1370)], two independent biological repeats were used and processed as duplicates until final analysis.
mRNAs were extracted and converted to cDNAs by reverse transcription. The cDNAs were sequenced using a HiSEq 2500 platform (Chunlab Inc.).


title: daf2_ctrl_2

value: control RNAi


title: Vehicle control treated ASCs rep2

description:
pooled from two mice
Lyn2126-plus-2127


title: hel1_2


title: daf2_2


title: hel1daf2_2


title: pfd6daf2_1


title: daf2_1


title: hel1_1


title: N2_1


title: N2_2


title: daf2_3


title: Visium_Partial Responder sample of Tumor liver (Mouse 2)

status: Public on Sep 27 2023

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: 10x Visium

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software v1.2.2 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and spatial information (images and coordinates)
Library strategy: Spatial Transcriptomics

source_name: Liver containing metastases of CRC origin

extract_protocol:
Immediately after euthanizing the mice and perfusion of the liver with PBS containing 5 mM EDTA, small pieces of the liver containing metastasis from the mice were taken and shock-frozen in isopentane which was cooled down with liquid nitrogen. Afterwards, the samples were embedded in Killik, O.C.T. Compound embedding medium for cryostat (Bio-Optica/ 05-9801). The samples were stored at -80 °C.
Sections of previously prepared tissues were prepared using a cryostat (cooled to 16 °C) and placed on the visium slides. Methanol fixation and Hematoxilin & Eosin (H&E) staining was performed according to the manual provided by 10x Genomics under the name Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (10x Genomics/ CG000160 Rev A) using a Aperio ePathology digital scanner (Leica Biosystems) for image acquisition. Afterwards, the samples were processed for Visium analysis according to the manual: User Guide Visium Spatial Gene Expression Reagent Kits (10X Genomics/ CG000239 Rev F).

tag: condition

value: Partial Responder


title: Visium_Partial Responder sample of Tumor liver (Mouse 3)

description: 10x Visium

value: Liver containing metastases of CRC origin


title: Visium_Control sample of Tumor liver (Mouse 3)

description: 10x Visium

value: Control


title: Visium_Resistant sample of Tumor liver (Mouse 2)

description: 10x Visium

value: Resistant


title: Visium_Control sample of Tumor liver (Mouse 2)

description: 10x Visium


title: Visium_Partial Responder sample of Tumor liver (Mouse 1)

description: 10x Visium


title: Visium_Resistant sample of Tumor liver (Mouse 1)

description: 10x Visium


title: Visium_Control sample of Tumor liver (Mouse 1)

description: 10x Visium


title: Bulk RNA-seq Rapamycin Replicate 3

status: Public on Sep 21 2023

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

data_processing:
Demultiplexed with bcl2fastq
Transcript reads aligned and counted with kallisto (v0.46.1) & bustools (v0.39.3)
Sample barcodes identifying sample matched to metadata
Assembly: SacCer3 (modified to include UTR sequences)
Supplementary files format and content: 2021_RAPA_BULK_TIMECOURSE.tsv.gz is a 33 rows × 5847 columns tab-separated values file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Oligo', 'Time', 'Replicate', 'Sample_barcode') are sample-specific metadata

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures were subcultured into 25 mL of YPD and grown with shaking for 4 hours at 30C. At 4 hours, 1mL of culture was pelleted and snap-frozen as untreated (0 minute).

extract_protocol:
RNA extracted with TRIZOL
cDNA reverse transcribed with Maxima RT using sample barcode and UMI dT30VN priming and a template switch oligo. Whole transcriptomes amplified with Kapa HiFi. 3' end libraries created by tagmenting with Illumina Nextera XT and indexing PCR with a 3' end specific primer (i5) and a Nextera (i7) primer.

treatment_protocol: 200 ng/mL rapamycin was added to cultures and 1 mL of culture was pelleted and snap-frozen at 2.5, 5, 7.5, 10, 15, 30, 45, 60, 90, and 120 minutes

tag: cell line

value: WT

value: Rapamycin


title: Bulk RNA-seq Rapamycin Replicate 1


title: Bulk RNA-seq Rapamycin Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 6 (30 to 40) Replicate 2

data_processing:
Demultiplexed with bcl2fastq
Transcript reads aligned and counted with kallisto (v0.46.1) & bustools (v0.39.3)
Transcriptional barcodes identifying genotype matched to individual cells, and doublet cells removed with fastqTomat0 (https://github.com/flatironinstitute/fastqToMat0)
Assembly: SacCer3 (modified to include UTR sequences)
Supplementary files format and content: 2021_RAPA_TIMECOURSE.tsv.gz is a 173348 rows × 5847 columns tab-separated values file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Gene', 'Replicate', 'Pool', and 'Experiment') are cell-specific metadata.
Supplementary files format and content: 2021_RAPA_TIMECOURSE_EXTRA_METADATA.tsv.gz is a 173347 rows x 8 columns TSV file that contains additional row-specific metadata for 2021_RAPA_TIMECOURSE.tsv.gz.

growth_protocol: Overnight cultures were pooled from a 96-well plate into a single 50 mL conical, washed twice with 25 mL YPD, and resuspended in 10 mL of YPD. 10^9 cells were used to inoculate a 1L baffled flask containing 500 mL pre-warmed YPD which was grown with shaking for 4 hours at 30C. At 4 hours, a stir bar was added to the flask, and it was transferred onto a stir plate in a 30C environmental chamber.

extract_protocol:
Single-cell sample preparation with the 10x Genomics Chromium Single Cell 3' Kit (v3.1 Chemistry)
Library construction with the 10x Genomics Chromium Single Cell 3' Kit (v3.1 Chemistry)

treatment_protocol: Samples were collected continuously into 50 mL conicals containing 20 mL RNAlater and a stirring magnetic stir disc. Sample collection conicals were changed every 10 minutes and the collected samples were immediately placed on ice. After 20 minutes, 200 ng/mL rapamycin was added to the stirring culture. The collection tubing was disconnected from the sampling conical, 8 mL of volume was drawn through using a syringe (~2x the 4 mL dead volume of the sampling tubing), and the sampling tubing was immediately reconnected for continued collection. Sampling continued for 60 additional minutes, yielding 2 10-minute sample pools without rapamycin treatment and 6 10-minute sample pools with rapamycin treatment.

value: Pooled WT & fpr1 deletion

value: Rapamycin (30-40 minutes)


title: scRNA-seq Genotype PCR Rapamycin Time 7 (40 to 50) Replicate 2

value: Rapamycin (40-50 minutes)


title: scRNA-seq Genotype PCR Rapamycin Time 5 (20 to 30) Replicate 2

value: Rapamycin (20-30 minutes)


title: scRNA-seq Genotype PCR Rapamycin Time 3 (0 to 10) Replicate 2

value: Rapamycin (0-10 minutes)


title: scRNA-seq Genotype PCR Rapamycin Time 2 (-10 to 0) Replicate 2

value: Untreated


title: scRNA-seq Genotype PCR Rapamycin Time 1 (-20 to -10) Replicate 2


title: scRNA-seq Rapamycin Time 8 (50 to 60) Replicate 2

value: Rapamycin (50-60 minutes)


title: scRNA-seq Rapamycin Time 6 (30 to 40) Replicate 2


title: scRNA-seq Rapamycin Time 5 (20 to 30) Replicate 2


title: scRNA-seq Rapamycin Time 4 (10 to 20) Replicate 2

value: Rapamycin (10-20 minutes)


title: scRNA-seq Rapamycin Time 3 (0 to 10) Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 8 (50 to 60) Replicate 1


title: scRNA-seq Rapamycin Time 2 (-10 to 0) Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 7 (40 to 50) Replicate 1


title: scRNA-seq Genotype PCR Rapamycin Time 4 (10 to 20) Replicate 1


title: scRNA-seq Rapamycin Time 1 (-20 to -10) Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 8 (50 to 60) Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 1 (-20 to -10) Replicate 1


title: scRNA-seq Genotype PCR Rapamycin Time 3 (0 to 10) Replicate 1


title: scRNA-seq Genotype PCR Rapamycin Time 6 (30 to 40) Replicate 1


title: scRNA-seq Rapamycin Time 8 (50 to 60) Replicate 1


title: scRNA-seq Rapamycin Time 4 (10 to 20) Replicate 1


title: scRNA-seq Genotype PCR Rapamycin Time 5 (20 to 30) Replicate 1


title: scRNA-seq Rapamycin Time 5 (20 to 30) Replicate 1


title: scRNA-seq Rapamycin Time 7 (40 to 50) Replicate 1


title: scRNA-seq Rapamycin Time 3 (0 to 10) Replicate 1


title: scRNA-seq Genotype PCR Rapamycin Time 4 (10 to 20) Replicate 2


title: scRNA-seq Rapamycin Time 6 (30 to 40) Replicate 1


title: scRNA-seq Rapamycin Time 1 (-20 to -10) Replicate 1


title: scRNA-seq Rapamycin Time 7 (40 to 50) Replicate 2


title: scRNA-seq Genotype PCR Rapamycin Time 2 (-10 to 0) Replicate 1


title: S. pombe_total tRNA_Q_rep2

status: Public on Sep 19 2023

first: Yu

last: Sun

address: Philippstr. 13

department: Institut für Biologie

institute: Humboldt-Universität zu Berlin

library_source: other

data_processing:
Reference curation: The reference for S. pombe tRNAs contains sequences of all unique mature tRNA  from GtRNAdb and all unique mitochondrial tRNAs from Ensembl Fungi, and both 5’ and 3’ splint adaptor sequences were added. For E. coli, sequences of all unique mature tRNAs were from GtRNAdb, and splint adaptor sequences were added.
Base calling and alignment: Base calling was done with Guppy (version 6.3.8) in high-accuracy mode. The resulting fastq reads were processed to convert Us to Ts. Sequence alignment was performed on “passed” and “failed” fastq files separately using an optimal local sequence alignment approach (Smith-Waterman) as implemented in parasail. Bam files from “passed” and “failed” reads were then merged and employed for subsequent analysis.
Analysis of base miscalling: JACUSA2 was employed for determination of base miscalling.
Supplementary files format and content: The excel-files include tRNA, position, Kmer, coverage, mismatch rate (Mis_rate), insertion rate (Ins_rate), deletion rate (Del_rate), and mismatch rate of each nucleotides (A_mm, C_mm, G_mm, and T_mm).

molecule: other

organism: Schizosaccharomyces pombe

source_name: yeast cell

growth_protocol: The S. pombe strain AEP1 was grown in YES medium with or without 0.1 μM of queuine at 30°C and 140 rpm. The E. coli strains (including wt, queA∆, queF∆, and tgt∆) were grown in M9 medium at 37°C and 180 rpm. M9 medium for the deletion strains was supplemented with kanamycin (40 µg/ml). Cells were grown to an OD600 of 1.

extract_protocol:
In vitro synthesis of tRNAs: The plasmid containing tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis sequence, respectively, was linearized with NsiI, and 3 µg of the linear plasmid were used for in vitro transcription by T7 RNA polymerase (Thermo Fisher Scientific) according to the manufacturer’s instructions. After a 7 h incubation at 37°C and subsequent DNase I treatment, the transcription reaction was purified using phenol/ chloroform/ isoamylalcohol extraction followed by gel filtration on Sephadex G50 (GE Healthcare). Extraction of small RNAs from cells: Small RNAs were extracted according to the manufacturer’s protocol (PureLink™ miRNA Isolation Kit (Invitrogen)) with some adjustments. Briefly, cells were suspended in 1 ml Trizol (Ambion). The samples were vortexed for 2 min after adding 0.2 ml chloroform and glass beads, and then were centrifuged at 16 000 rcf, 4°C for 15 min. After adding 215 µl ethanol to the upper phase, the samples were transferred to a spin cartridge and centrifuged at 12 000 rcf for 1 min. 700 µl of ethanol was added to the flow-through, and the samples were transferred to a new spin cartridge followed by centrifugation at 12 000 rcf for 1 min. After washing the cartridge with wash buffer, small RNAs were eluted with 50 µl of DEPC-treated water.
For library preparation, 20 pmol of in vitro-transcribed tRNAAsp were used as input material. To promote ligation of sequencing adapters to tRNA, 16 pmol of custom double-stranded splint adapter (with CGGU overhang complimentary to 3’ termini of tRNAAsp GCCA) were used for the first ligation. The first ligation reaction was performed in a DNA LoBind tube at 25°C for 45 min. It also contained 1 x RNA ligase2 buffer (New England Biolabs), 5% PEG 8000, 2 mM ATP, 6.25 mM MgCl2, 6.25 mM DTT, and 0.5 units/µl T4 RNA ligase 2 (10 000 units/ml) in a total volume of 20 µl. For library preparation of mixtures of in vitro-transcribed tRNAs, 10 pmol of each of the four tRNAs (tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis) and 16 pmol of each of the two splint adapters (splint adapters with CGGU and UGGU overhang) were used in a reaction volume of 40 µl. Library preparation for tRNAs isolated from cells was performed using 40 pmol of deacylated small RNAs and 32 pmol of splint adapter (8 pmol of each of the four splint adapters). Ligation reaction samples were subsequently electrophoresed on a 7 M urea/TBE PAGE gel (8%), and ligation products were excised and purified from the gel. The concentration of gel-purified ligation products was measured with the Qubit RNA HS Assay Kit (Invitrogen). The second ligation of splint-ligated tRNAs to the RNA Adapter (RMX, included in the SQK-RNA002 kit, Oxford Nanopore Technologies) and subsequent library purification were performed following the Nanopore Sequence-Specific Direct RNA sequencing protocol, except that incubation time of the second ligation was increased from 10 min to 30 min to improve ligation efficiency.
Direct RNA nanopore sequencing

value: AEP1 (wild type)

value: yeast cell

value: grown in YES medium with 0.1 μM of queuine at 30°C


title: S. pombe_total tRNA_rep1

value: grown in YES medium  at 30°C


title: S. pombe_total tRNA_rep2


title: S. pombe_total tRNA_rep3


title: E. coli_total tRNA_queF_del

organism: Escherichia coli

source_name: bacterial cell

value: bacterial cell

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3), {lambda}-, {delta}queF721::kan, rph-1, {delta}(rhaD-rhaB)568, hsdR514

value: grown in M9 medium  at 37°C


title: S. pombe_total tRNA_Q_rep3


title: E. coli_total tRNA_tgt_del

value: tgt{delta}

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3), {delta}tgt::kan, {lambda}-, rph-1, {delta}(rhaD-rhaB)568, hsdR514


title: E. coli_total tRNA_wt

value: F- {delta}(araD-araB)567, {delta}lacZ4787 (::rrn B-3), {lambda}-, rph-1, {delta}(rhaD-rhaB)568, hsdR5154


title: daf2_ctrl_1

value: Day 1 adult

value: control RNAi


title: E. coli_total tRNA_queA_del

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3), {delta}queA769::kan, {lambda}-, rph-1, {delta}(rhaD-rhaB)568, hsdR514


title: scRNA-seq Rapamycin Time 2 (-10 to 0) Replicate 1

value: Pooled WT & fpr1 deletion


title: in vitro_tRNAAsp

organism: synthetic construct

source_name: in vitro-transcribed tRNA (tRNAAsp)

value: in vitro-transcribed tRNA (tRNAAsp)

value: without Q-modification


title: in vitro_tRNAAsn_tRNAAsp_tRNAHis_tRNATyr

source_name: in vitro-transcribed tRNA (tRNAAsn, tRNAAsp, tRNAHis, tRNATyr)


title: in vitro_tRNAAsp_Q

value: with Q-modification


title: in vitro_tRNAAsn_tRNAAsp_tRNAHis_tRNATyr_Q

value: in vitro-transcribed tRNA (tRNAAsn, tRNAAsp, tRNAHis, tRNATyr)


title: S. pombe_total tRNA_Q_rep1

value: AEP1 (wild type)

value: yeast cell


title: pituitary - Q97

status: Public on Sep 04 2023

city: Glasgow

first: Tyler

last: Stevenson

address: Jarrett building

institute: University of Glasgow

description: Photoperiod

data_processing:
fast5 files were demultiplex and basecalled by Guppy 4.2.1
Porechop v0.2.4 was conducted to remove adapters from reads
Filtlong v0.2.0 to filter long reads with minimum 25 bases and mean q weight of 9
Transcripts were aligned to the Japanese quail reference genome and transcriptome using Minimap2 v2.17
Transcript expression levels were determined using Salmon v0.14.2 and EdgeR v3.24.3 for normalisation and differential expression
Assembly: Minimap2 v2.17
Supplementary files format and content: tab-delimited text files and includes raw counts for each sample
Supplementary files format and content: tab-delmiinted text files and includes normalized values for each sample

organism: Coturnix japonica

source_name: Pituitary gland

extract_protocol:
RNA was extracted using QIAGEN RNEasy Plus Mini Kit
RNA was synthesized into cDNA using Oxford Nanopore Direct cDNA Native Barcoding (SQK-DCS109 and EXP-NBD104) and followed the manufacturers protocol.

value: Pituitary gland


title: pituitary - Q98

description: Photoperiod


title: pituitary - Q90

description: Photoperiod


title: pituitary - Q99

description: Photoperiod


title: pituitary - Q89

description: Photoperiod


title: pituitary - Q87

description: Photoperiod


title: pituitary - Q86

description: Photoperiod


title: N63.Dataset [204551090028_R04C01]

status: Public on Sep 08 2023

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: Illumina protocol

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

data_processing: Following data collection, the SeSaMe normalization method was used to define beta values for each probe (W. Zhou et al 2018. PMID: 30085201). If a CpG does not map to a given species, it takes a value of 0.5. The mammalian array design is similar to the Illumina Infinium 450K array but it contains fewer up to 37492 CpGs.  Additional material on the mappability of CpGs can be found on the Github page https://github.com/shorvath/MammalianMethylationConsortium/  A vignette on using the mammal methylation array with SeSAMe is available from https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/mammal.html.

molecule: genomic DNA

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

tag: confidenceinageestimate

value: Liver

tag: female

tag: specieslatinname

value: Mus musculus

tag: agedetailed

value: m

tag: tissuecolor

value: brown

tag: predictedfemale

tag: predictedtissue

tag: tissues

value: Adipose / Aorta / Astrocyte / Blood / BoneMarrow / Brain / BrainTumor / Cerebellum / Cortex / Crypts / DifferentiatedBloodCells / Ear / ES / Fibroblast / Gut / Heart / Heart.Atrium / Heart.Teratoma / Heart.Ventricle / HematopoieticStem.Progenitor.LSK / HematopoieticStemCells / Hippocampus / Hypothalamus / iPSC / Kidney / Liver / Lung / MacrophageBoneMarrow / MacrophagePeritoneal / Muscle / Pancreas / Pituitary / Placenta / Retina / Serum / Skin / Spleen / Striatum / SVZ / Tail / Villi / WholeBrain


title: N63.Dataset [204551090028_R05C02]

tag: age


title: pituitary - Q78

description: Photoperiod

tag: tissue

tag: treatment


title: N63.Dataset [204551090028_R06C02]


title: N63.Dataset [204551090032_R03C01]


title: N63.Dataset [204551090028_R03C02]


title: N63.Dataset [204551090032_R01C02]


title: N63.Dataset [204551090032_R02C02]


title: N63.Dataset [204551090032_R05C01]


title: pituitary - Q77

description: Photoperiod


title: N63.Dataset [204551090028_R02C01]


title: N63.Dataset [204551090028_R01C02]


title: N63.Dataset [204551090028_R04C02]


title: N63.Dataset [204551090028_R02C02]


title: N63.Dataset [204551090032_R01C01]


title: pituitary - Q88

description: Photoperiod


title: pituitary - Q85

description: Photoperiod


title: N63.Dataset [204551090028_R06C01]


title: pituitary - Q79

description: Photoperiod


title: N63.Dataset [204551090028_R01C01]


title: N63.Dataset [204551090032_R06C01]


title: pituitary - Q75

description: Photoperiod


title: pituitary - Q65

description: Photoperiod


title: pituitary - Q67

description: Photoperiod


title: pituitary - Q64

description: Photoperiod


title: pituitary - Q76

description: Photoperiod


title: pituitary - Q66

description: Photoperiod


title: pituitary - Q63

description: Photoperiod


title: pituitary - Q6

description: Photoperiod


title: pituitary - Q53

description: Photoperiod


title: N63.Dataset [204551090028_R05C01]


title: pituitary - Q54

description: Photoperiod


title: pituitary - Q50

description: Photoperiod


title: pituitary - Q51

description: Photoperiod


title: pituitary - Q5

description: Photoperiod


title: pituitary - Q62

description: Photoperiod


title: pituitary - Q52

description: Photoperiod


title: pituitary - Q49

description: Photoperiod


title: pituitary - Q42

description: Photoperiod


title: N63.Dataset [204551090028_R03C01]


title: pituitary - Q74

description: Photoperiod


title: pituitary - Q3

description: Photoperiod


title: pituitary - Q30

description: Photoperiod


title: pituitary - Q29

description: Photoperiod


title: pituitary - Q27

description: Photoperiod


title: pituitary - Q2

description: Photoperiod


title: pituitary - Q26

description: Photoperiod


title: pituitary - Q25

description: Photoperiod


title: pituitary - Q28

description: Photoperiod


title: pituitary - Q37

description: Photoperiod


title: pituitary - Q18

description: Photoperiod


title: pituitary - Q38

description: Photoperiod


title: pituitary - Q17

description: Photoperiod


title: pituitary - Q41

description: Photoperiod


title: pituitary - Q16

description: Photoperiod


title: pituitary - Q15

description: Photoperiod


title: pituitary - Q102

description: Photoperiod


title: pituitary - Q101

description: Photoperiod


title: pituitary - Q100

description: Photoperiod


title: pituitary - Q40

description: Photoperiod


title: pituitary - Q13

description: Photoperiod


title: pituitary - Q1

description: Photoperiod


title: pituitary - Q39

description: Photoperiod


title: Mediobasal hypothalamus - Q91

description: Photoperiod

source_name: Mediobasal hypothalamus

treatment_protocol: Tissue was dissected, frozen on powdered dry ice and stored at -80C

value: Mediobasal hypothalamus


title: Mediobasal hypothalamus - Q98

description: Photoperiod


title: Mediobasal hypothalamus - Q89

description: Photoperiod


title: Mediobasal hypothalamus - Q99

description: Photoperiod


title: Mediobasal hypothalamus - Q88

description: Photoperiod


title: Mediobasal hypothalamus - Q90

description: Photoperiod


title: pituitary - Q4

description: Photoperiod


title: Mediobasal hypothalamus - Q86

description: Photoperiod


title: pituitary - Q14

description: Photoperiod


title: Mediobasal hypothalamus - Q79

description: Photoperiod


title: Mediobasal hypothalamus - Q87

description: Photoperiod


title: Mediobasal hypothalamus - Q76

description: Photoperiod


title: Mediobasal hypothalamus - Q78

description: Photoperiod


title: Mediobasal hypothalamus - Q8

description: Photoperiod


title: Mediobasal hypothalamus - Q80

description: Photoperiod


title: Mediobasal hypothalamus - Q67

description: Photoperiod


title: Mediobasal hypothalamus - Q75

description: Photoperiod


title: Mediobasal hypothalamus - Q77

description: Photoperiod


title: Mediobasal hypothalamus - Q7

description: Photoperiod


title: Mediobasal hypothalamus - Q68

description: Photoperiod


title: Mediobasal hypothalamus - Q64

description: Photoperiod


title: Mediobasal hypothalamus - Q66

description: Photoperiod


title: Mediobasal hypothalamus - Q63

description: Photoperiod


title: Mediobasal hypothalamus - Q53

description: Photoperiod


title: Mediobasal hypothalamus - Q54

description: Photoperiod


title: Mediobasal hypothalamus - Q51

description: Photoperiod


title: Mediobasal hypothalamus - Q50

description: Photoperiod


title: Mediobasal hypothalamus - Q6

description: Photoperiod


title: Mediobasal hypothalamus - Q40

description: Photoperiod


title: Mediobasal hypothalamus - Q5

description: Photoperiod


title: Mediobasal hypothalamus - Q55

description: Photoperiod


title: Mediobasal hypothalamus - Q52

description: Photoperiod


title: Mediobasal hypothalamus - Q43

description: Photoperiod


title: Mediobasal hypothalamus - Q41

description: Photoperiod


title: Mediobasal hypothalamus - Q39

description: Photoperiod


title: Mediobasal hypothalamus - Q38

description: Photoperiod


title: Mediobasal hypothalamus - Q65

description: Photoperiod


title: Mediobasal hypothalamus - Q3

description: Photoperiod


title: Mediobasal hypothalamus - Q31

description: Photoperiod


title: Mediobasal hypothalamus - Q29

description: Photoperiod


title: Mediobasal hypothalamus - Q30

description: Photoperiod


title: Mediobasal hypothalamus - Q28

description: Photoperiod


title: Mediobasal hypothalamus - Q26

description: Photoperiod


title: Mediobasal hypothalamus - Q18

description: Photoperiod


title: Mediobasal hypothalamus - Q17

description: Photoperiod


title: Mediobasal hypothalamus - Q16

description: Photoperiod


title: Mediobasal hypothalamus - Q42

description: Photoperiod


title: Mediobasal hypothalamus - Q19

description: Photoperiod


title: Mediobasal hypothalamus - Q100

description: Photoperiod


title: Mediobasal hypothalamus - Q101

description: Photoperiod


title: Mediobasal hypothalamus - Q103

description: Photoperiod


title: Mediobasal hypothalamus - Q14

description: Photoperiod


title: Gut_CD4PosTimPosCD163Neg_1

status: Public on Aug 18 2023

city: Manchester

first: Ian

middle: Edward

last: Prise

state: Select state

address: Oxford Road

institute: University of Manchester

data_processing:
Raw files trimmed with Trimmomatic using defualt setting
Timmed Fastqs aligned with STAR (v2.5.3) using default settings
Aligned reads were sorted with Samtools
Counts were normalized and analysed with Cufflinks (v2.2.1)
Assembly: GRCm38.p5
Supplementary files format and content: Tab separated text file of Cuffnorm output

source_name: intestine

extract_protocol:
total RNA was extracted from samples stored in RLT at –80C using a Qiagen RNeasy micro kit as following the manufactures instructions, including an on column DNase digest
SMART-Seq® v4 PLUS RNA Kit (Takara Bio USA) with 9 cycles of amplification

value: intestine

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4+TIM4+CD163- Macrophage

tag: strain

tag: gender

value: male

value: naïve spf adult


title: Gut_CD4PosTimPosCD163Neg_2

tag: cell type


title: Mediobasal hypothalamus - Q4

description: Photoperiod


title: Mediobasal hypothalamus - Q102

description: Photoperiod


title: Gut_CD4PosTimPosCD163Neg_0


title: Mediobasal hypothalamus - Q15

description: Photoperiod


title: Sample2

status: Public on Aug 29 2023

city: London

first: Konstantinos

last: Theofilatos

address: 125 Coldharbour Lane

institute: King's CollegeLondon

description: Fresh frozen spatial RNA-sequencing

data_processing:
Raw sequencing data were processed with the 10X Genomics Space Ranger pipeline to generate fastq files.
The FASTQ files and the manually aligned histology images were analyzed with Space Ranger 1.3.1 and the human probeset provided by 10X genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A).
Visualization of spatial cluster output from Space Ranger as well as differential gene expression analysis to determine cluster-specific up- or downregulated genes was performed on Loupe Browser 6.0.0 (10X Genomics).
Assembly: mm10
Supplementary files format and content: barcodes.tsv list of spatial barcodes
Supplementary files format and content: features.tsv list of Gene IDs
Supplementary files format and content: matrix.mtx gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg aligned figucials of the tissue image
Supplementary files format and content: scalefactors_json.json scale factors in json format
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: tissue_hires_image.png high res image of tissue
Supplementary files format and content: tissue_low_image.png low res image of tissue
Supplementary files format and content: tissue_posotions_list.csv list of spatial barcodes and thecoordinates specifying spots

source_name: Carotid plaque tissue

extract_protocol:
A 5μm tissue section from each carotid plaque sample was placed onto one capture area of a Visium Spatial Gene Expression slide. Two samples were selected form Asymptomatic male patients for spatial RNA-seq.
Visium for formalin-fixed paraffin-embedded (FFPE) spatial gene expression slide and reagent kit was used according to manufacturer instructions (PN: 1000338; 10X Genomics).
OTHER: Spatial Transcriptomics

value: Carotid plaque tissue

value: Mixed

value: No treatment


title: Gut_CD4PosTimNegCD163Neg_2

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4+TIM4-CD163- Macrophage


title: Gut_CD4PosTimNegCD163Neg_0


title: Gut_CD4PosTim4PosCD163Pos_3

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4+TIM4+CD163+ Macrophage


title: Gut_CD4PosTimNegCD163Neg_1


title: Gut_CD4PosTim4PosCD163Pos_1


title: Gut_CD4PosTim4PosCD163Pos_0


title: Gut_CD4PosTim4NegCD163Pos_3

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4+TIM4-CD163+ Macrophage


title: Gut_CD4PosTim4NegCD163Pos_1


title: Gut_CD4PosTim4PosCD163Pos_2


title: Gut_CD4PosTim4NegCD163Pos_2


title: Mediobasal hypothalamus - Q27

description: Photoperiod


title: Gut_CD4NegTimNegCD163Neg_2

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4-TIM4-CD163- Macrophage


title: Gut_CD4PosTim4NegCD163Pos_0


title: Gut_CD4NegTim4NegCD163Pos_2

value: Live CD45+Lin-CD11b+MHC II+CD64+ CD4-TIM4-CD163+ Macrophage


title: Gut_CD4NegTimNegCD163Neg_0


title: Gut_CD4NegTimNegCD163Neg_1


title: Gut_CD4NegTim4NegCD163Pos_0


title: Sample1

description: Fresh frozen spatial RNA-sequencing


title: Gut_CD4NegTim4NegCD163Pos_1


title: CCR2KO_Small_Intestine_Macrophages

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
Individual intestines were stripped of mucus and epithelial cells and processed into single cell suspensions using Liberase TL enzymatic digestion and mechanical disruption, filtered through 70 and 40um strainers. 3-4 intestines were combined and stained for FACS to isolate Live CD45+Lin-(CD3,TCRb,B220,SiglecF,Ly6C,Ly6G)CD11b+MHCII+CD64+ Macrophages. Sorted cells were loaded onto the 10X Genomics platform and subsequent sequencing.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: small intestine

tag: genotype

value: JAX strain #:004999, bred in-house


title: WT_Small_Intestine_Macrophages

description:
10x Genomics
The WT sample was split between two lanes/runs, which accounts for the two labels of barcodes (barcode-1, barcode-2).

value: WT

value: C57BL/6J, male, Janvier


title: PID161, scRNA seq

status: Public on Jun 19 2023

city: San Francisco

first: Kailin

last: Yin

state: California

address: 1650 Owens street

institute: Gladstone Institutes

description:
10X Genomics
LC10xLibGEX18

data_processing:
The scRNA-seq samples included a total of 12 samples with four from each of the 3 groups (Group A (high expression of  ALAS2, PASC subjects), Group B (high expression of OR7D2, PASC subjects) and Group C (low expression of both ALAS2 and OR7D2 in non-PASC subjects )). The demultiplexed fastq files for these samples were aligned to the human reference genome (GRCh38) using the 10x Genomics Cell Ranger v7.1.0 count pipeline (Zheng et al. 2017), as described in the Cell Ranger documentation. The include-introns flag for the count pipeline was set to true to count the reads mapping to intronic regions.
The filtered count matrices generated by the Cell Ranger count pipeline for the 12 samples were processed using the R package for single-nucleus analysis Seurat (Hao et al. 2021). Each sample was pre-processed as a Seurat object and the top 1% of cells per sample with a high number of unique genes, cells with <=200 unique genes, and cells >=10% mitochondrial genes were filtered out for each sample. The 15 samples were merged into a single Seurat object and normalization and variance stabilization was performed using sctransform86 with the “glmGamPoi” method (Ahlmann-Eltze and Huber 2021) for initial parameter estimation.
Graph-based clustering was performed using the Seurat (Hao et al. 2021) functions FindNeighbors and FindClusters. First, the cells were embedded in a k-nearest neighbor (KNN) graph (with k=20) based on the Euclidean distance in the PCA space. The edge weights between two cells were further modified using Jaccard similarity. Next, clustering was performed using the Louvain algorithm (Blondel et al. 2008) implementation in the FindClusters Seurat function. Clustering with 15 Principal Components (PCs) (determined based on location of elbow in the plot of variance explained by each of the top 25 PCs) and 0.1 resolution (determined using the resolution optimization method described for the Cytof data) resulted in 11 distinct biologically relevant clusters, which was used for further analyses.
Cell type assignment. Data visualization using Seurat in the UMAP space for the 12 samples revealed no apparent batch effects due to age, sex, race or hospitalization status of the subjects. The marker genes for each cluster were identified using the FindAllMarkers Seurat function on the SCT assay data. This algorithm uses the Wilcoxon Rank Sum test to iteratively identify differentially expressed genes in a cluster against all the other clusters. Marker genes were filtered to keep only positively expressed genes, detected in at least 25% of the cells in either population and with at least 0.5 log2 fold change.
Assembly: GRCh38
Supplementary files format and content: xlsx file, named as DEG.xlsx which includes all differentially expressed genes' information among different clusters.

source_name: Peripherial blood

growth_protocol: At each visit, whole blood was collected in EDTA tubes followed by density gradient separation and isolation of PBMCs and plasma, as described previously 31. Serum was obtained concomitantly from serum-separator tubes. Serum and plasma were stored at -80C and PBMCs were cryopreserved and stored in liquid nitrogen.

extract_protocol:
Total RNA was extracted usjing the Chromium Next GEM Single cell 5's Reagent Kits V2 according to the manufacturer's instructions.
scRNA-seq library preparation was performed on total PBMCs from n=12 individuals (4 non-LCs and 8 LCs) in our cohort using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (10x Genomics) as per instructions, followed by sequencing on the Illumina NovaSeq 6000 S4 300 platform (UCSF).

treatment_protocol: No

value: Peripherial blood

value: PBMC

tag: status

value: LC

tag: Sex

value: Female

tag: hospitalized

value: No


title: PID804, scRNA seq

description:
10X Genomics
LC10xLibGEX19


title: PID546, scRNA seq

description:
10X Genomics
LC10xLibGEX17

value: Yes


title: PID147, scRNA seq

description:
10X Genomics
LC10xLibGEX16


title: PID927, scRNA seq

description:
10X Genomics
LC10xLibGEX20


title: Sham, scRNAseq

status: Public on Jul 18 2023

city: Hangzhou

first: Zhejun

last: Cai

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology, The Second Affiliated Hospital

institute: Zhejiang University School of Medicine

description: 10x Genomics

data_processing:
The 10X Genomics Cell Ranger workflow was used to demultiplex raw data and map them to the reference genome using default settings. Except as otherwise noted, all downstream single-cell analyses were carried out using CellRanger and Seurat(16, 17). In order to create digital expression matrices, specific molecular identifiers were counted for each gene and each cell barcode (filtered by CellRanger). Seurat used a secondary filtration method in which a gene had to be expressed in at least 200 cells and in more than 3 cells to be regarded to be expressed. Additionally, we removed some of the foreignDNA from mitochondria.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Infrarenal segment of the aorta

extract_protocol:
Before taking infrarenal abdominal aorta samples, animals were euthanized by cervical dislocation and injected with 5 ml PBS at the left ventricular apex to perfuse the blood vessels. The infrarenal aorta was removed and crushed. Aortic samples were incubated in hank solution (450 units/ml collagenase I, 125 units/ml XI, 60 units/ml hyaluronidase, and 60 units/ml DNase I dissolved in PBS) at 37 °C for 1 hour. The cell solution was filtered with 70 μm cell mesh and centrifuged to remove lumpy tissues. To isolate CD45-positive immune cells, the cell pellet was resuspended in buffer with CD45 and viability microbeads and magnetically separated. Each group (n=20 AAA, n=50 control) mixes all aortic sample cells.
A 10× Chromium Controller (10X Genomics) barcoded the cell solution in Chromium microfluidic chips with 3' chemistry. RNA from barcoded cells was reverse-transcribed and sequencing libraries were created using reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics). Illumina's instructions guided sequencing.

value: Infrarenal segment of the aorta

tag: cell line

value: CD45+ cells

value: Immune cells

value: Wild type

value: Induced with PBS


title: PID799, scRNA seq

description:
10X Genomics
LC10xLibGEX14


title: PID414, scRNA seq

description:
10X Genomics
LC10xLibGEX15


title: PID709, scRNA seq

description:
10X Genomics
LC10xLibGEX13


title: PID608, scRNA seq

description:
10X Genomics
LC10xLibGEX11


title: PID102, scRNA seq

description:
10X Genomics
LC10xLibGEX12


title: PID913, scRNA seq

description:
10X Genomics
LC10xLibGEX10


title: K562 RIMSseq TES Replicate 3

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

library_source: genomic

data_processing:
illumina adapter sequence was trimmed trim_galore
reads were mapped to human genome using bowtie2
C to T transition was extracted using samtools mpileup
regional methylation was calculated using custom scripts based on the C to T transition rate
SNP was identified using gatk
Assembly: hg38
Supplementary files format and content: custom format with regional methylation level
Library strategy: RIMS-seq

extract_protocol:
genomic DNA isolated from the GM12878 cell line by Coriell Institute
RIMSseq with or without exome Target enrichment

value: lymphoblast


title: Breast tissue RIMSseq TES Replicate 3

source_name: Breast

value: Breast


title: PID942, scRNA seq

description:
10X Genomics
LC10xLibGEX9


title: Breast tissue RIMSseq TES Replicate 1


title: K562 RIMSseq TES Replicate 1


title: K562 RIMSseq TES Replicate 2


title: Breast tissue RIMSseq TES Replicate 2


title: NA12878 RIMSseq TES Replicate 2

value: lymphoblastoid


title: CHP134-ChIPseq-C38b_WDR5-rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Differential binding peaks were identified using DiffBind.
Assembly: hg19
Supplementary files format and content: peaks for each sample

growth_protocol: CHP-134 and IMR-32 cell lines were maintained in RPMI 1640 with l-glutamine (Corning) with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin

extract_protocol:
For ChIP-seq, chromatin from 10 million IMR-32 cells or CHP-134 cells treated with 0.005% dimethyl sulfoxide were crosslinked in 1% formaldehyde for 10 min, followed by quenching in 0.125 M glycine. Nuclei were extracted and chromatin was generated from nuclei through lysis in FALB buffer (50 mM HEPES, pH 7.5, 1% Triton, 1 mM EDTA, 140 mM NaCl) containing 1% SDS, PMSF, and protease inhibitor cocktail (Roche) using a Diagenode Bioruptor Plus instrument.
Three ChIPs from identical samples were pooled together and purified using a Qiagen PCR purification kit. Eluted DNA was used to generate libraries  using the Ultra II DNA library Prep protocol (New England Biolabs).
Ultra II DNA library Prep protocol (New England Biolabs) with dual index primers.

treatment_protocol: IMR-32 cells were untreated prior to chromatin collection. CHP-134 cells were treated with either 0.0005% DMSO or C91 (419) for 4 hrs prior to chromatin collection.

tag: agent

tag: chip antibody

value: 5 microliter of anti-WDR5 (Cell Signaling, 13105)


title: CHP134-ChIPseq-C38b_WDR5-rep3


title: AAA_14, scRNAseq

description: 10x Genomics

value: Induced with elastase


title: CHP134-ChIPseq-C38b_WDR5-rep1


title: NA12878 RIMSseq TES Replicate 3


title: NA12878 RIMSseq TES Replicate 1


title: CHP134-ChIPseq-C38b_MYC-rep1

value: 5 microliter of custom serum to target N-MYC


title: CHP134-ChIPseq-C38b_MYC-rep2


title: RNA-seq_Day4_PpFm_3

status: Public on Jun 16 2023

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

data_processing:
Transcripts were aligned to the indexed reference for mm10 with default settings using TopHat2 v2.1.1 (Kim et al. 2013).
Reads were filtered using bamtools using the following settings: -isDuplicate false -mapQuality “>10” (Barnett et al. 2011).
Transcript reads were counted post-alignment using StringTie (Pertea et al. 2015).
Differential expression testing was performed using edgeR v3.16.5 (Robinson and Smyth 2007; Robinson and Smyth 2008; Robinson et al. 2010; McCarthy et al. 2012; Zhou et al. 2014) and limma v3.30.13 (Ritchie et al. 2015) packages in R v3.3.2.
Low level genes were removed within each condition using median log2-transformed counts per gene per million mapped reads (cpm) of 1 and a union generated from those lists.
Differential expression testing was performed using a general linear model (GLM) framework. For comparing FAB and FAB+V, a covariate for replicate was included to correct for batch effect.
Sequencing reads were aligned to the mm10 genome using Bowtie2 v2.3.0 (Langmead and Salzberg 2012) and SAMtools v0.1.19 (Li et al. 2009; Li 2011).
Peak calling was performed using MACS2 callpeak (Zhang et al. 2008; Feng et al. 2012) using the settings --nomodel --shift -100 --extsize 200 -q 0.1 after pooling biological replicates.
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser.
Following removal of ENCODE blacklist sites (Amemiya et al. 2019; ENCODE Project Consortium 2012), a union set of sites was generated by identifying summits that overlapped within 200bp and arbitrarily selecting the summit of highest positional value. Summits were then extended by 200bp in both directions to create the set of union sites.
Fold-enrichment scores were assigned to each site using the multiBigwigSummary function from deepTools (Ramírez et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_Compilation.txt contains all outputs related to the RNA-seq datasets, including TPM values for every biological replicate and differential expression testing. TSS_TAD.bed contains the TSS and TAD assignments. UnifiedATAC_Dataset.txt contains a list of the union sites, positional information, and fold-enrichment scores. edgeR_Results_FABVoverFAB.txt is the differential accessibility testing comparing the FAB+V and FAB conditions. All files "_summits_noBlacklist.bed" contain the summit calls from MACS2 following removal of ENCODE blacklist sites. All "_FE.bw" are bigWig files containing the MACS2 fold-enrichment scores.

source_name: mouse embryonic stem cells

growth_protocol: Bry-GFP and ZX1 ES cell lines were maintained in a serum- and feeder-free culture system (Ying et al. 2003; Gadue et al. 2006; Ying et al. 2008; Kattman et al. 2011). Neurobasal medium and DMEM/F12 (50%/50%; Thermo Fisher Scientific) were supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), 0.05% BSA (MilliporeSigma), 150mM mono-thioglycerol (MilliporeSigma), 1000unit Mouse LIF (MilliporeSigma), 1μM PD0325901 (Stemgent), 3μM CHIR99021 (Stemgent), L-glutamine (Life Technologies), penicillin-streptomycin (Thermo Fisher Scientific). PD0325901 and CHIR99021 were not added at 2 days prior to start differentiation. For differentiation start, ES cells were dissociated with trypLE express (Thermo Fisher Scientific) and cultured, at 1.0x105 cells/ml for 48hrs (Gadue et al. 2006; Kattman et al. 2011). In brief, IMDM and Ham’s F12 medium (75%/25%) were supplemented with N2, B27, BSA, L-glutamine, 0.5mM ascorbic acid (MilliporeSigma), 450mM mono-thioglycerol (MilliporeSigma), penicillin-streptomycin. The cells were differentiated in 10 cm petri-dishes (Becton Dickenson). The 48hr-old embryoid bodies (EBs) were dissociated with trypLE express and the cells were re-aggregated in StemPro-34 SFM medium (Thermo Fisher Scientific) in the present of L-glutamine, 200μg/ml human transferrin, 500μM ascorbic acid, 450μM mono-thioglycerol, 6ng/ml bFGF, 8ng/ml Activin A and 1ng/ml BMP4 for Bry+, PDGFRα+ and Flk1+ mesoderm induction. 5ng/ml VEGF was treated at D2 for bipotential mesoderm induction. Human Activin A, human BMP4, mouse VEGF, human bFGF were purchased from R&D systems. For hematopoietic lineage and cardiac lineage induction, sorted cells were cultured in StemPro-34 SF medium, supplemented with 2 mM L-glutamine, 1 mM ascorbic acid (MilliporeSigma), and 10 ng/ml bFGF (Kattman et al. 2006; Kattman et al. 2011). 2×105/ml sorted cells were seeded into individual wells of a 48-well flat bottom plate (Becton Dickenson) coated with gelatin after sorting.

extract_protocol:
Total RNA was extracted using NucleoSpin RNAII kit (Clonetech). ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed as previously described (Buenrostro et al. 2015).
For RNA-seq, library preparation was performed by the University of Chicago Genomics Facility using the Illumina TruSeq RNA Sample prep kit v2 (Part #RS-122-2001). Library fragments were approximately 275bps in length and were quantitated using the Agilent Bio-analyzer 2100 and pooled in equimolar amounts. Single-ended, 51bp sequencing was performed on the Illumina HiSeq2500 in Rapid Run Mode by the University of Chicago Facility. For ATAC-seq, libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer's protocols. Libraries were quantitated using the Agilent Bioanalyzer, pooled in equimolar amounts, and sequenced with 50-bp single-end reads on the Illumina HiSeq following the manufacturer's protocols through the Genomics Core Facility at the University of Chicago.

value: mouse embryonic stem cells

tag: day

value: Day 4

value: FAB+V

tag: sort

value: P+F-


title: CHP134-ChIPseq-C38b_MYC-rep3


title: RNA-seq_Day4_PmFp_3

value: P-F+


title: RNA-seq_Day4_PpFm_2


title: RNA-seq_Day4_PmFp_2


title: RNA-seq_Day4_PpFm_1


title: RNA-seq_Day4_PmFp_1


title: RNA-seq_Day4_PpFp_2

value: P+F+


title: RNA-seq_Day4_PpFp_1


title: H3K27ac-T-E145-Col2a1GFP-GFPp-R1

status: Public on May 11 2023

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing:
A similar number of reads (39x106) were randomly sampled from each ChIP-seq dataset to correct for sequencing depth variation using Seqtk v1.3 (-s 100). TruSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). Reads were then mapped to GRCm39/mm39 using Bowtie2 v2.3.5.1 with default parameters. Reads were then filtered for a MAPQ≥30 using Samtools view v1.10 and the coverage was obtained after extension of the reads by 200 bp using MACS2 v2.2.7.1 (callpeak --nomodel --call-summits --extsize 200). Coverage was normalized by the number of million tags used by MACS2.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Embryonic Trunk

growth_protocol: Limbs and trunks from E14.5 mouse embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted according to GFP status.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
Following FACS sorting, cells were centrifuged for 5′ at 400 × g at 4 °C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% formaldehyde. The fixation was blocked by the addition of 1.25 M glycine, cells were isolated by centrifugation (1000 × g, at 4 °C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000 × g, at 4 °C for 3′), washed in cold 1× PBS, and stored frozen at −80 °C. 5 × 105 fixed nuclei were sonicated to a 200–500 bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP (Diagenode, C15410174) was performed as previously described (68), using 1/500 dilution of the antibody, with the addition of 5 mM of Na-Butyrate to all buffers.
Libraries were prepared with <10 ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were sequenced on an Illumina HiSeq 4000 with single-end reads of 50 or 100 bases.

tag: background

value: Embryonic Trunk

tag: embryonic stage

tag: gfp status

value: GFP+

tag: biological replicate


title: H3K27ac-L-E145-Col2a1GFP-GFPn-R1

source_name: Embryonic Limb Bud

tag: tissue

value: Embryonic Limb Bud

value: GFP-


title: H3K27ac-T-E145-Col2a1GFP-GFPn-R1


title: H3K27ac-L-E145-Col2a1GFP-GFPp-R1


title: unkIs7_cobS_VB12_1

status: Public on Apr 28 2023

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

data_processing:
The trimmed sequencing reads were mapped to C. elegans reference genome (WB235) using STAR (2.7.10) with the option --quantMode geneCounts. The counts were then normalized and the differentially expressed genes were then identified using the standard pipeline of DESeq2 in R.
Assembly: WB235
Supplementary files format and content: tab-delimited text files contain the read count generated by STAR

source_name: whole worm

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with K12 cobS(-); cobA(-) bacteria and 64nM vitamin B12 and grown until L4 stage before being harvested.

extract_protocol:
The L4 animals were washed with water and the worm pellet was extracted using TRIzol reagent (Invitrogen). The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).
The library was constructed by BGI using the standard DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing service (P_Stranded Library & PE100 Seq).

value: whole worm

tag: treatment

value: Fed with K12 cobS(-); cobA(-) bacteria and treated with VB12


title: unkIs7_cobS_PA_1

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with K12 cobS(-); cobA(-) bacteria and 10mM PA and grown until L4 stage before being harvested.

value: Fed with K12 cobS(-); cobA(-) bacteria and treated with propionic acid


title: unkIs7_cobS_PA_2


title: unkIs7_K12wt_PA_2

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with K12 WT bacteria and grown until L4 stage before being harvested.

value: Fed with K12 WT bacteria and treated with propionic acid


title: unkIs7_K12wt_PA_1


title: unkIs7_cobS_1

growth_protocol: The animals were bleached to obtain eggs, which were hatched in M9 overnight. The next day, L1s were seeded onto NGM plates with K12 cobS(-); cobA(-) bacteria and grown until L4 stage before being harvested.

value: Fed with K12 cobS(-); cobA(-) bacteria


title: unkIs7_cobS_2


title: CD14+CD16+ monocyte

status: Public on Mar 13 2023

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

data_processing:
Sequencing reads were aligned to a human reference genome in the Bowtie software (version 1.1.2).
Duplicate reads were removed using Picard tools.
Expression was quantitated using Cufflinks software.
Assembly: hg38/GRCh38
Supplementary files format and content: EXCEL file includes FPKM values for all samples.

source_name: PB leukocytes

extract_protocol:
Total RNA from sorted cells was extracted with the TRIzol LS reagent.
RNA-seq libraries were prepared using the Nextera XT Kit (Illumina) according to the manufacturer's protocol.

value: PB leukocytes

tag: cell subtype

value: CD14+CD16+ monocyte


title: Neutrophil

tag: cell type

value: Neutrophil


title: CXCR1+CD14+ monocyte

value: CXCR1+CD14+ monocyte


title: 147_PASC_WT

status: Public on Feb 09 2023

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh37 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: hg19
Supplementary files format and content: DEGs file includes normalized counts for each individual sample

source_name: Total PBMC

growth_protocol: PBMCs were cultered in RPMI 1640 medium containing 10% FBS, 1% penicillin-streptomycin, 1% L-Glu at 37 degree incubator with 5% carbon dioxide supplied.

extract_protocol:
Following incubation, total RNAs were extracted from PBMCs using the AllPrep kit as per manufacturer's instructions (Qiagen).
Briefly, following oligo dT enrichment, fragmentation and random priming, cDNA syntheses was completed. End repair, 5’ phosphorylation and dA-tailing were performed, followed by adaptor ligation, PCR enrichment, and sequencing.

treatment_protocol: No treatments were performed in this project.

tag: pid

tag: lc status

value: LC

value: Female

value: Total PBMC

value: PBMC

tag: genotype

value: WT

tag: time (collection_point)

value: 8 months


title: 447_PASC_WT

tag: Sex


title: 923_PASC_WT

value: Male


title: 203755070086_R07C01

status: Public on Feb 21 2023

city: Berlin

first: David

last: Kaul

address: Augustenburger Platz 1

department: Department of Radiation Oncology

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion using the Zymo EZ Methylation Kit (Zymo Research Irvine, USA), the Infinium HD FFPE DNA Restore Kit was used for DNA restoration. DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450k BeadChip and Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
The calculations were carried out in R, version 4.2.0 "Virgorous Calesthenics"
Average beta-Values after normalization using detection p values

label: cy3, cy5

source_name: Tumor

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted form FFPE tumor samples using the Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) , according to the manufacturer’s instructions

tag: age

tag: incoming diagnosis

value: Ependymoma (WHO grade II)

tag: tumor location

value: supratentorial

tag: progression-free survival (months)

tag: progression (0=no, 1=yes)

tag: overall survival (months)

tag: death (0=no, 1=yes)

tag: material type

value: FFPE


title: CXCR1-CD14+ monocyte

value: CXCR1-CD14+ monocyte


title: 927_PASC_WT

tag: tissue


title: 621_PASC_WT


title: 896_Non-PASC_WT

value: Non-LC


title: 102_Non-PASC_WT


title: 804_PASC_WT


title: 717_PASC_WT


title: 414_PASC_WT


title: 213_PASC_WT


title: 476_PASC_WT


title: unkIs7_cobS_VB12_2

value: whole worm

tag: treatment

value: Fed with K12 cobS(-); cobA(-) bacteria and treated with VB12


title: 831_PASC_WT


title: 245_PASC_WT


title: 799_PASC_WT


title: 203774250049_R04C01


title: 546_PASC_WT


title: 560_PASC_WT


title: 439_Non-PASC_WT


title: 670_PASC_WT


title: CD14-CD16+ monocyte

value: PB leukocytes

tag: cell subtype

value: CD14-CD16+ monocyte


title: 709_PASC_WT

tag: cell type


title: 741_Non-PASC_WT

tag: pid


title: 233_PASC_WT

tag: lc status


title: 230_Non-PASC_WT

tag: genotype


title: 204_PASC_WT

tag: time (collection_point)


title: 564_Non-PASC_WT

tag: Sex


title: 900_PASC_WT


title: 313_Non-PASC_WT


title: 283_PASC_WT


title: 161_PASC_WT


title: 914_Non-PASC_WT


title: 608_Non-PASC_WT


title: 913_Non-PASC_WT


title: 942_Non-PASC_WT


title: 871_PASC_WT