title: Sorted WT-emiRFP (W) cells from WT+WT mosaic gastruloids 48h rep2

description: Library name: WW0483


title: CITE-seq CD64+ Synovial Macrophages from Old Female Mice, ADT

status: Public on Feb 12 2026

type: SRA

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

country: USA

institute: Northwestern University

description:
Library name: Joint_Mac_Old_Female_ADT
Antibody Derived Tag
Joint_Mac_Old_Female_raw_matrix.h5
Joint_Mac_Old_Female_filtered_matrix.h5

library_source: other

data_processing:
The cellranger v.7.1.0 pipeline was run with the mm10-2020-A reference transcriptome.
AgingJoint_feature_reference.csv was used to assign ADT
Assembly: mm10
Supplementary files format and content: Matrix files with UMI and feature counts for all data (raw)
Supplementary files format and content: Matrix files  with UMI and feature counts after filtering for cells (filtered)
Library strategy: CITE-seq

molecule: protein

organism: Mus musculus

source_name: Ankle Joint Synovium

growth_protocol: Male and female C56BL/6 mice were euthanized at approximately 8 (young) or 22 months (old) for this study.

extract_protocol:
Synovial tissue was processed into a single-cell suspension and live CD45+CD11b+Ly6g-SiglecF-Cd64+ cells were sorted
Cellular Indexing of Transcriptome and Epitopes by sequencing (CITE-seq) was performed using the 10x Genomics 3’ GEX v3 and Feature Barcoding kits
Libraries were sequenced on an Illumina NextSeq 2000 targeting 40,000 reads per cell.

tag: tissue

value: Ankle Joint Synovium

tag: cell type

value: CD64+ Synovial Macrophages

tag: genotype

tag: age

value: old (22 months)

tag: Sex

value: female

tag: samples pooled

tag: library type

value: ADT


title: WT_CT_P6NGO_H3K27ac_rep2

city: Davis

first: Satoshi

last: Namekawa

state: CA

address: One Shields Avenue

institute: UC Davis

library_source: genomic

data_processing:
For CUT&Tag data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html).
Raw paired-end reads were trimmed by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.10)
Trimmed reads were aligned with the mouse genome (GRCm38/mm10) using Bowtie2 83 (version 2.4.5) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA for CUT&Tag. For mapping D. melanogaster spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates from all mapped bam files were removed using the ‘MarkDuplicates’ command in Picard tools (version 3.0.0) (https://broadinstitute.github.io/picard/ ).
To compare replicates, Pearson correlation coefficients were calculated and plotted by ‘multiBamSummary bins’ and ‘plot correlation’ commands from deepTools 84 (version 3.5.5). Biological replicates were pooled using the ‘merge’ command in samtools for visualization and other analyses after confirming reproducibility (Pearson correlation coefficient > 0.85). Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10,000 / aligned spike-in reads).
Spike-in normalized genome coverage tracks with 1 bp resolution in BigWig format were generated using ‘bamCoverage’ from deepTools with the parameters ‘--binSize 1 --extendReads --samFlagInclude 64 --normalizeUsing RPKM --scaleFactor $scale_factor’. Track views were visualized and exported from Integrative Genomics Viewer 85 (version 2.14.1).
Assembly: mm10
Supplementary files format and content: bigWig, spike-in normalized tracks
Supplementary files format and content: bed, peaks
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: ovary

extract_protocol:
CUT&Tag libraries of oocytes were prepared as previously described32,33 with some modifications (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). To perform quantitative spike-in CUT&Tag, Drosophila S2 cells were added to mouse oocytes at a fixed ratio (e.g. 2000 S2 cells to 1000 mouse oocytes) at the beginning of each reaction.
CUT&Tag libraries were prepared using NEBNext HiFi 2x PCR Master mix (NEB, M0541L) according to the protocol (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3 ).

value: ovary

tag: cell line

value: primary cells

value: P6 non-growing oocytes

value: WT

tag: antibody

tag: reads length


title: CITE-seq CD64+ Synovial Macrophages from Young Male Mice, GEX

description:
Library name: Joint_Mac_Young_Male_GEX
Gene Expression

library_source: transcriptomic

molecule: polyA RNA

value: young (8 months)

value: male

value: GEX


title: WT_CT_E18O_H3K27ac_rep2

value: E18.5 oocytes


title: CITE-seq CD64+ Synovial Macrophages from Young Female Mice, GEX

description:
Library name: Joint_Mac_Young_Female_GEX
Gene Expression


title: WT_CT_E18O_H3K27ac_rep1


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 144h rep3

city: Barcelona

first: Joshua

middle: D

last: Frenster

address: Carrer del Doctor Aiguader, 88

country: Spain

institute: Universitat Pompeu Fabra

description: Library name: WF1444

data_processing:
Adapter trimming and low-quality filtering were conducted with TrimGalore (version 0.6.7), removing reads with a Phred score below 20.
The processed sequencing data were aligned to the mouse genome (GRCm38.p6) using Gencode annotation (version 25) and the STAR aligner (version 2.7.11b). Alignments were performed with default settings and uniquely mapped read counts were generated using the --quantMode option in STAR
The final count matrix was created by concatenating the assembled reads in a Python 3 environment.
Assembly: mouse genome (GRCm38.p6) using Gencode annotation (version 25)
Supplementary files format and content: normalized reads, csv file containing all samples

extract_protocol:
Cells were FACS isolated from mosaic gastruloids and RNA was isolated using the Qiagen RNeasy Micro Kit according to the manufacturor protocol.
stranded library preparation with poly A enrichment

tag: sample group


title: bovine embryo, CUT&Tag, siSP1, 16C, rep1

city: hangzhou

first: Hao

last: Jin

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

country: China

institute: Zhejiang University

description: Library name: b_CUT_Tag_siSP1_16C_rep1

data_processing:
Bulk RNA-Seq data were trimmed and then aligned to the bovine (ARS-UCD1.2) or human (hg19) reference genome by HISAT2 (Version 2.2.1). For scRNA-Seq data, bases 1 - 8 of read 2 were extracted as cell barcodes by UMI-tools (version 1.1.2). Read 1 was trimmed to remove adapter and template switching oligo (TSO) sequences at the 5′ end and poly(A) tails at the 3′ end. Then, aligned reads were split based on their corresponding cell barcodes using Picard (version 2.26.3). The read counts and FPKM values of each gene were calculated by FeatureCounts (version 2.0.1) and StringTie (version 2.1.2).
For CUT&Tag, ChIP-seq, and ATAC-seq data,  Paired end CUT&Tag, ChIP-seq, and ATAC-seq reads were trimmed and then aligned to bovine (ARS-UCD1.2) or human (hg19) genome with Bowtie (version 2.2.5). Low quality reads (MAPQ <20) and PCR duplicated were removed by samtools (version 1.10) and sambamba (version 0.6.6). For downstream analysis, read counts were normalized to RPKM in a 50bp bin by bamCoverage from deepTools (version 3.5.3).
Assembly: bovine (ARS-UCD1.2) or human (hg19)
Supplementary files format and content: excel files include raw counts for scRNA-Seq and FPKM values for bulk RNA-Seq
Supplementary files format and content: bigwig for CUT-Tag, ChIP-Seq and ATAC-Seq signals

organism: Bos taurus

source_name: bovine embryo

extract_protocol:
The zona pellucidae of embryos were removed using 0.5% pronase E (Sigma- Aldrich, 107433). Then the embryos were washed in 0.5% BSA (Sigma- Aldrich, SRE0098) and manually transfer into PCR tubes
For RNA-Seq, library construction were performed according to the protocol described previously (Hu et al., 2024). For ChIP-Seq, library construction were performed according to the protocol described previously (Brind’Amour et.al 2015). For ATAC-Seq, library construction were performed according to the protocol described previously (Wu et al., 2018). For CUT-Tag, library construction were performed according to the protocol of Vazyme TD904 kit.

value: 16-cell bovine embryos

value: wild type

tag: treatment


title: WT_CT_P7GO_H3K4me3_rep1

value: P7 growing oocytes

value: H3K4me3(Active Motif; #39159)


title: bovine embryo, CUT&Tag, WT, 16C, rep3

description: Library name: b_CUT_Tag_WT_16C_rep3


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 144h rep2

description: Library name: WF1443


title: CITE-seq CD64+ Synovial Macrophages from Old Male Mice, GEX

description:
Library name: Joint_Mac_Old_Male_GEX
Gene Expression

value: Ankle Joint Synovium


title: bovine embryo, CUT&Tag, WT, 16C, rep2

description: Library name: b_CUT_Tag_WT_16C_rep2


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 144h rep1

description: Library name: WF1442


title: CITE-seq CD64+ Synovial Macrophages from Old Female Mice, GEX

description:
Library name: Joint_Mac_Old_Female_GEX
Gene Expression

value: CD64+ Synovial Macrophages


title: WT_CT_P7GO_H3K4me3_rep2


title: bovine embryo, CUT&Tag, WT, 16C, rep1

description: Library name: b_CUT_Tag_WT_16C_rep1


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 120h rep3

description: Library name: WF1204


title: WT_CT_P6NGO_H3K4me3_rep1


title: BLKS92, SCAFs

city: Illkirch

first: Matej

last: Durik

state: Alsace

address: 1 rue Laurent Fries

department: Development and stem cells

country: France

institute: IGBMC

description:
Library name: SCAFs 3
RNA prepared from THP-1 derived M0 macrophages, in culture

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bclconvert 3.8.4.
Alignment: Reads were mapped onto GRCh38 assembly of human genome using STAR 2.7.10b.
Quantification: Gene expression was also quantified using STAR and Ensembl release 111 annotations.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file containing raw read counts in each sample.

organism: Homo sapiens

growth_protocol: To differentiate THP-1 into M0 macrophages, they were treated with 200 nM of PMA for 24 hours, washed and cultured another 24 hours in normal media.

extract_protocol:
P3245
Cells were washed 1x with PBS and lysed in 350 µl of Guanidine thiocyanate-based lysis buffer.
P3218, P3245 : RNA-Seq libraries were generated from 300 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).

treatment_protocol: M0 macrophages were treated with 300 000 SCAFs or inert beads for 20 hours under normal culture conditions.

value: Differentiated to M0

value: SCAFs 300 000 pcs

tag: batch


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 120h rep2

description: Library name: WF1203


title: BLKS90, SCAFs

description:
Library name: SCAFs 1
RNA prepared from THP-1 derived M0 macrophages, in culture

extract_protocol:
P3218
Cells were washed 1x with PBS and lysed in 350 µl of Guanidine thiocyanate-based lysis buffer.
P3218, P3245 : RNA-Seq libraries were generated from 300 ng of total RNA using Illumina Stranded mRNA Prep, Ligation kit and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA) according to manufacturer's instructions. Following polyA selection, mRNAs were fragmented at 94oC for 8 minutes. DNA library were amplified using 12 cycles of PCR. Surplus PCR primers were further removed by two successive purifications using SPRIselect beads (Beckman-Coulter, Villepinte, France).  The final libraries were checked for quality and quantified using Bioanalyzer 2100 system (Agilent technologies, Les Ulis, France).


title: BLKS91, SCAFs

description:
Library name: SCAFs 2
RNA prepared from THP-1 derived M0 macrophages, in culture


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 120h rep1

description: Library name: WF1202


title: WT_CT_P1O_H3K4me3_rep1

value: P1 oocytes


title: bovine embryo, CUT&Tag, WT, 8C, rep1

description: Library name: b_CUT_Tag_WT_8C_rep1

value: 8-cell bovine embryos


title: WT_CT_P6NGO_H3K4me3_rep2

value: ovary

value: primary cells


title: WT_CT_E18O_H3K4me3_rep2

value: WT


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 96h rep2

description: Library name: WF0963


title: BLKS87, Inert beads

description:
Library name: Beads 2
RNA prepared from THP-1 derived M0 macrophages, in culture

value: Inert beads 300 000 pcs


title: BLKS89, Inert beads

description:
Library name: Beads 3
RNA prepared from THP-1 derived M0 macrophages, in culture


title: WT_CT_P1O_H3K4me3_rep2


title: bovine embryo, CUT&Tag, WT, 8C, rep3

description: Library name: b_CUT_Tag_WT_8C_rep3


title: bovine embryo, CUT&Tag, WT, 8C, rep2

description: Library name: b_CUT_Tag_WT_8C_rep2


title: BLKS86, Inert beads

description:
Library name: Beads 1
RNA prepared from THP-1 derived M0 macrophages, in culture


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 96h rep3

description: Library name: WF0964


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 96h rep1

description: Library name: WF0962


title: WT_CT_E18O_H3K4me3_rep1


title: bovine embryo, RNA-Seq, SP1KOCtrl, 16C, 4

description: Library name: b_RNA_SP1KOCtrl_16C_4

value: SP1 KO Ctrl


title: bovine embryo, RNA-Seq, SP1KOCtrl, 16C, 2

description: Library name: b_RNA_SP1KOCtrl_16C_2


title: DDX53 IP, rep2

city: Poznan

first: IHG PAS

last: Bioinfo Team

state: Greater Poland

address: Strzeszynska 32

department: Bioinformatics Team

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description: Library name: IP_D2

data_processing:
The eCLIP experiment was performed by Eclipse BioInnovations’ standard RBP-eCLIP pipeline as previously described. Raw sequencing reads were trimmed of UMIs and adapters, filtered out of reads that mapped to repeat elements, aligned to the reference genome (hg38) with STAR, and filtered of PCR duplicates.
Clusters (regions within the IP sample that contain a pileup of reads) were identified using CLIPper (https://github.com/YeoLab/clipper). Each cluster was normalized against the paired input sample. Final peaks for each sample were filtered for enrichment over the input (|log2FC| ≥ 3) and statistical significance (adjusted p-value ≤ 0.001). Replicated peaks were then identified by positionally intersecting peaks of each replicate of the same condition with the intersect command of bedtools, with the -s option.
Assembly: GRCh38/hg38, Gencode v44
Supplementary files format and content: bigWigs with identified peaks

molecule: total RNA

growth_protocol: TCam-2 cells were cultured at 37 °C and 5% CO2 in Roswell Park Memorial Institute 1640 Medium (RPMI 1640 Medium, GlutaMAX™ Supplement Thermo Fisher Scientific, 61870044) supplemented with 10% heat-inactivated Fetal Bovine Serum (Cytiva, HYCLSV30160.03) and 1% Antibiotic-Antimycotic solution (100X) (Thermo Fisher Scientific, 15240062).

extract_protocol:
Two biological replicates of 20 million cells (TCam-2 transfected with DDX53-FLAG) were used in eCLIP-seq. Briefly, 48 hours after transfection, TCam-2 cells grown on culture dishes were crosslinked at 254 nm UV with an energy setting of 400 mJ/cm² (Analytik Jena, CL-3000). The cells were then harvested in ice-cold DPBS, and the pellets were flash-frozen in liquid nitrogen and stored at -80°C before the IP reaction with an anti-FLAG antibody, performed by Eclipse BioInnovations (USA).
Libraries were constructed using the eCLIP protocol as previously described (van Nostrand et al, 2016).

value: human testicular cancer cell line

value: DDX53 overexpression


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 72h rep3

description: Library name: WF0724


title: ATAC DW EP300i

city: Stanford

first: Michael

last: Januszyk

address: 257 Campus Dr

institute: Stanford University

library_source: genomic single cell

data_processing:
Base calls were converted to reads using the Cell Ranger (10X Genomics; version 3.1) implementation mkfastq and then aligned against  the Cell Ranger GRCh38 v3.0.0 human reference genome, available at: http://cf.10xgenomics.com/supp/cell-exp/, or using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample.
Base calls were converted to reads using the Cell Ranger (10X Genomics, Pleasanton, CA, USA; version 3.1) implementation mkfastq and then aligned against the GRCh38 v3.0.0 (human) genome using Cell Ranger’s count function with SC3Pv3 chemistry and 5,000 expected cells per sample. Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 300 unique transcripts profiled, less than 100,000 total transcripts, and less than 10% of their transcriptome of mitochondrial origin. Unique molecular identifiers (UMIs) from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1)
Aggregated data were then evaluated using uniform manifold approximation and projection (UMAP) analysis over the first 15 principal components [21]. Cell annotations were ascribed using SingleR (version 3.11) against the Human Primary Cell Atlas (HPCA) reference dataset.
Assembly: GRCh38

source_name: dorsal wounded EP300i-treated (DW EP300i)

extract_protocol:
Full-thickness skin from the face, scalp, ventrum and dorsum of unwounded animals and of excisional wounds at POD 7 and 14 were harvested and mechanically digested with sharp dissecting scissors (n = 6 per condition). Tissue was added to an enzymatic digestion consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were added to an orbital shaker at 150 rpm for 90 minutes at 37ºC. FACS buffer was added to quench the digest and samples were filtered through 70 µm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C, resuspended in FACS buffer, filtered for a second time using 40 µm cell strainers, and cell numbers were quantified on a hemocytometer. Cells from each sample were tagged with hashtag oligos (HTOs) per the manufacturer’s protocol and then pooled. scATAC-seq was performed following 10x Genomics protocols. In brief, nuclei were isolated as described above from dermal mouse wounds. For snRNA-seq, mouse wounds from n = 6 mice were pooled for each condition (unwounded facial dermis, unwounded dorsal dermis, d14 facial scars, d14 facial scars treated with EP300 inhibitor, d14 dorsal scars, and d14 dorsal scars treated with EP300 inhibitor). Nuclei then underwent transposition, GEM generation and barcoding, post GEM incubation cleanup, library consutrction, and qualitative control on an Agilent Bioanalyzer High Sensitivity DNA chip (10x genomics protocol CG000496 Rev B). Libraries were pooled and cDNA libraries sequenced on the Illumina platform.
Single-cell RNA-seq (scRNA-seq) and Singel cell ATAC seq (snRNA-seq) was performed at the Stanford Functional Genomics Facility (SFGF) for droplet-based microfluidic single cell RNA sequencing (scRNA-seq) using the 10x Chromium Single Cell platform (Single Cell 3′ v3, 10X Genomics, Pleasanton, CA, USA). A droplet of the cell suspensions, reverse transcription master mix, and partitioning oil was loaded onto a single cell chip and processed on the Chromium Controller. Reverse Transcription was performed at 53 °C for 45 min. cDNA was amplified for 12 cycles total (BioRad C1000 Touch thermocycler) with cDNA size selected using SpriSelect beads (Beckman Coulter, Indianapolis, IN, USA) and a ratio of SpriSelect reagent volume to sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32 °C, followed by end repair and A-tailing at 65 °C for 30 min. cDNA were double-sided size selected using SpriSelect beats. Sequencing adaptors were ligated to the cDNA at 20 °C for 15 min. cDNA was amplified using a sample-specific index oligo as primer, followed by another round of double-sided size selection using SpriSelect beads.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: skin (dorsum)

value: all cells (unsorted)

value: EP300 treatment


title: bovine embryo, RNA-Seq, SP1KOCtrl, 16C, 1

description: Library name: b_RNA_SP1KOCtrl_16C_1

value: 16-cell bovine embryos

value: wild type


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 72h rep2

description: Library name: WF0723


title: DDX53 INPUT, rep2

description: Library name: INPUT_D2


title: DDX53 IP, rep1

description: Library name: IP_D1


title: ATAC DUW

source_name: dorsal unwounded (DUW)


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 72h rep1

description: Library name: WF0722


title: ATAC FW EP300i

source_name: facial wounded EP300i-treated (FW EP300i)

value: skin (face)


title: bovine embryo, RNA-Seq, SP1KO, 16C, 3

description: Library name: b_RNA_SP1KO_16C_3

value: SP1 KO

value: Sp1 KO


title: bovine embryo, RNA-Seq, SP1KO, 16C, 2

description: Library name: b_RNA_SP1KO_16C_2


title: DDX53 INPUT, rep1

description: Library name: INPUT_D1


title: 2D

city: Huelve

first: Ana

last: Molina Márquez

state: Huelve

address: Avd. Fuerzas Armadas, S/N

department: Chemistry

institute: University of Huelva

description: Library name: PDSKO6

data_processing:
The first read was used to identify the Illumina library index and CEL-Seq sample barcode. The second read was aligned to the Chlamydomonas reinhardtii 281_v5.6 reference transcriptome using BWA-MEM (Li & Durbin, 2010).
Reads mapping to multiple genomic locations were discarded.
Read mapping and countings were performed using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
Differential expression analysis was performed using the DEA-Transcriptomic module of OmicsBox software (Biobam Bioinformatic solutions), using the weighted trimmed mean of M-values (TMM) method to normalise library sizes and the EdgeR quasi-likelihood F-test of EdgeR package with robust settings for statistics analysis (Robinson et al., 2009).
Assembly: C. reinhardtii 281_v5.6
Supplementary files format and content: TSV files include raw gene-level read counts for each sample

organism: Chlamydomonas reinhardtii

source_name: cell

growth_protocol: Wild-type (WT) cells were cultured in TAP medium supplemented with 10 µg mL-1  of arginine (TAP-Arg) and PDS Knockout (PDSKO) cells were grown in unsupplemented TAP medium. Both cell types were mantained under dark conditions at 25ºC for four weeks and hasvested by centrifugation.

extract_protocol:
Total RNA from six independent samples from parental line and six samples from selected PDSKO transformants (E10, A2 y D2) was extracted using the standard TRIzol protocol.
For the library preparation, mRNA was processed as previously described, following an adapted version of the single-cell mRNA-seq protocol of CEL-Seq (Hashimshony et al., 2012; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second-strand synthesis. The resulting cDNA was amplified by an overnight in vitro transcription reaction. Sequencing libraries were prepared with Illumina Truseq small RNA primers. The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles). The first read was used to identify the Illumina library index and CEL-Seq sample barcode. The second read was aligned to the C. reinhardtii 281_v5.6 reference transcriptome using BWA MEM (H. Li & Durbin, 2010). Reads that mapped to multiple locations were discarded. Mapping and counting of reads were performed using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).

treatment_protocol: Collected PDSKO cells were sorted by fluorescence-activated cell sorting (FACS) to exclude transformants that had acquired the plasmid without undergoing knockout, as well as, potential revertants.

value: cell

value: vegetative cells (liquid culture)

value: PDS kock out (PDSKO)


title: ATAC FW PBS

source_name: facial wounded PBS (FW PBS)

value: PBS


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 48h rep2

description: Library name: WF0483

value: WT


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 48h rep3

description: Library name: WF0484


title: ATAC DW PBS

source_name: dorsal wounded PBS (DW PBS)


title: bovine embryo, RNA-Seq, SP1KO, 16C, 4

description: Library name: b_RNA_SP1KO_16C_4


title: bovine embryo, RNA-Seq, SP1KO, 16C, 1

description: Library name: b_RNA_SP1KO_16C_1


title: ATAC FUW

source_name: facial unwounded (FUW)


title: Sorted WT-mCh (F) cells from WT+WT mosaic gastruloids 48h rep1

description: Library name: WF0482


title: p53KO-H2B-emiRFP670("K") mESC 0h rep3

description: Library name: K0004

value: p53KO-H2B-emiRFP670("K") mESC 0h


title: 2A

description: Library name: PDSKO5


title: bovine embryo, RNA-Seq, SP1KOCtrl, 8C, 4

description: Library name: b_RNA_SP1KOCtrl_8C_4

value: 8-cell bovine embryos

value: SP1 KO Ctrl


title: RNA DW EP300i

library_source: transcriptomic single cell


title: RNA DW PBS


title: E10BL_2

description: Library name: PDSKO3


title: bovine embryo, RNA-Seq, SP1KOCtrl, 8C, 3

description: Library name: b_RNA_SP1KOCtrl_8C_3


title: p53KO-H2B-emiRFP670("K") mESC 0h rep2

description: Library name: K0003


title: E10BL_3

description: Library name: PDSKO4


title: RNA DUW


title: bovine embryo, RNA-Seq, SP1KOCtrl, 8C, 2

description: Library name: b_RNA_SP1KOCtrl_8C_2


title: E10BL_1

description: Library name: PDSKO2


title: bovine embryo, RNA-Seq, SP1KOCtrl, 8C, 1

description: Library name: b_RNA_SP1KOCtrl_8C_1


title: E10BL

description: Library name: PDSKO1


title: RNA FW PBS


title: RNA FW EP300i


title: WT-H2B-emiRFP670("W") mESC 0h rep2

description: Library name: WT0003

value: WT-H2B-emiRFP670("W") mESC 0h


title: WT3

description: Library name: WT6

value: Wild Type (WT)


title: bovine embryo, RNA-Seq, SP1KO, 8C, 4

description: Library name: b_RNA_SP1KO_8C_4


title: WT-H2B-emiRFP670("W") mESC 0h rep3

description: Library name: WT0004


title: RNA FUW

value: all cells (unsorted)


title: WT2

description: Library name: WT5


title: p53KO-H2B-emiRFP670("K") mESC 0h rep1

description: Library name: K0002


title: bovine embryo, RNA-Seq, SP1KO, 8C, 3

description: Library name: b_RNA_SP1KO_8C_3


title: bovine embryo, RNA-Seq, SP1KO, 8C, 2

description: Library name: b_RNA_SP1KO_8C_2


title: WT1

description: Library name: WT4


title: WT-H2B-mCherry("F") mESC 0h rep3

description: Library name: F0004

value: WT-H2B-mCherry("F") mESC 0h


title: P3-60810, 13119b, tbi38, TBI, Veh

city: Bethesda

first: Regina

middle: C

last: Armstrong

state: MD

address: 4301 Jones Bridge Rd

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University of the Health Sciences

description:
Library name: P3-60810
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

data_processing:
Visium Spatial RNA-seq and H&E images were processed using 10x Genomics Space Ranger analysis pipeline (v2.1.1) to align raw reads to the mouse reference genome and generate gene count by spot matrices aligned to corresponding tissue images. Based on the detected UMIs and genes in each spot, quality controls were applied. Five neuroanatomical regions of interest were manually defined for each sample using the Loupe browser. Downstream analysis and visualization used the R package Seurat (v5.2.0).  Clusters of spots were detected using Seurat unsupervised shared-nearest-neighbor (SNN) clustering on a cell state gene set (gene n = 264).
The spot level spatial transcriptomics data were collapsed to 5 pseudo-bulk profiles per sample by taking the sum of expression per manually defined neuroanatomical region of interest (ROI).  The pseudo-bulk dataset was then analyzed using DESeq2 (v1.48.2), which normalized the raw gene counts and corrects for laboratory sample batch prior to testing for differentially expressed genes.
To spatially map mouse brain cell types defined by single-cell transcriptomics, we used cell2location (v0.1.3) with Visium data. Briefly, we first estimated reference expression signatures for major cell types in healthy adult mouse brain using regularized negative binomial regressions and 2.3 million single-cell transcriptomes from The Allen Brain Cell Atlas.  We then calculated cell-type proportions using the cell-type-specific abundance estimations for each spot in the Visium sections with the inferred reference cell state signatures.
GSEA was conducted using the R package fGSEA (v1.34.2) to identify enriched gene sets. The analysis includes both customized, published, and publicly available MSigDB (https://www.gsea-msigdb.org/gsea/msigdb) gene sets for cell phenotypes and molecular pathways. The fGSEA method utilizes a ranked list derived from DESeq2 outputs for differentially expressed genes (DEGs), with the ranking determined by the 'stat' column from the DESeq2 results.
Assembly: mm10
Supplementary files format and content: Processed data files include tissue section images and spaceranger output.
Library strategy: Spatial Transcriptomics

source_name: brain

growth_protocol: Mice were housed in a 12h light/dark cycle with ad libitum access to food and water.

extract_protocol:
After the last injection 7 days post-injury, mice were perfused with 10% formalin fixative, and extracted whole brains stored in fixative for no longer than 3 days. Dissected 3 mm tissue blocks centered with bregma (0 mm A-P) were embedded in paraffin. Coronal FFPE brain tissue sections (7 µm) with RNA quality DV200 value greater than 50% were prepared for Visium CytAssist spatial transcriptomics that generated cDNA libraries for sequencing.
Generation of spatial transcriptomic libraries was performed following the FFPE Visium CytAssist Spatial Gene Expression User Guide (Document number CG000495, 10X Genomics)

treatment_protocol: At 8 weeks of age, mice received sham or TBI surgeries, followed by either 4-AP or vehicle starting the day after surgery b.i.d. over 7 days.

value: brain

tag: sample id_#

value: C57BL/6J wild-type

tag: timepoint post-injury

tag: disease state

value: TBI

value: Vehicle


title: WT-H2B-emiRFP670("W") mESC 0h rep1

description: Library name: WT0002


title: bovine embryo, RNA-Seq, SP1KO, 8C, 1

description: Library name: b_RNA_SP1KO_8C_1

value: SP1 KO


title: bovine embryo, RNA-Seq, SP1KOCtrl, 16C, 3

description: Library name: b_RNA_SP1KOCtrl_16C_3

value: 16-cell bovine embryos

value: wild type


title: WT-H2B-mCherry("F") mESC 0h rep2

description: Library name: F0003


title: X3404VE_2

description: Library name: WT3

value: cell

value: vegetative cells (liquid culture)


title: P3-60808, 13116b, tbi36, Sham, Veh

description:
Library name: P3-60808
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Sham


title: bovine embryo, RNA-Seq, siCtrl, MO, rep3

description: Library name: b_RNA_siCtrl_MO_rep3

value: morula bovine embryos

value: siCtrl


title: P3-60809, 13103b, tbi37, Sham, Veh

description:
Library name: P3-60809
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: WT-H2B-mCherry("F") mESC 0h rep1

description: Library name: F0002

value: WT


title: X3404VE_1

description: Library name: WT2


title: X3404VE

description: Library name: WT1


title: bovine embryo, RNA-Seq, siCtrl, MO, rep2

description: Library name: b_RNA_siCtrl_MO_rep2


title: bovine embryo, RNA-Seq, WT, L8C_16C

description: Library name: b_scRNA_WT_L8C_16C

value: late 8-cell and 16-cell bovine emrbyos


title: P3-60806, 12867b, tbi34, TBI, Veh

description:
Library name: P3-60806
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: bovine embryo, RNA-Seq, siCtrl, MO, rep1

description: Library name: b_RNA_siCtrl_MO_rep1


title: WT02

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description:
Library name: WT02
WT02

data_processing:
The Illumina bcl2fastq2 Conversion Software v2.20 was used to demultiplex sequencing data and convert base call files into fastq files.
The Cell Ranger v.6.1.2 count function was used with default parameters.
The count matrix of the cells of each library were imported into R, and combined into a single dataset for further downstream analysis using the Seurat package.
Assembly: mm10 (v. refdata-gex-mm10-2020-A downloaded from the 10x Genomics website)
Supplementary files format and content: For each library of single cells, we provide the 3 files generated by the Cell Ranger count pipeline within the filtered_feature_bc_matrix folder (i.e the cells called by Cell Ranger): barcodes.tsv.gz (tab-separated file, contains the cell barcodes), features.tsv.gz (tab-separated file, contains the genes included in the mm10 transcriptome) and matrix.mtx.gz (sparse matrix format, contains the raw counts per gene (in the rows), per cell (in the columns)). The prefix of the three files per library corresponds to the sample name.
Supplementary files format and content: We provide a csv file with meta data per cell for the cells retained after QC filtering (csv file labeled with retained_cells_metadata.csv). The meta data file contains cluster ID, annotated cell type, QC metrics and UMAP coordinates, generated using the Seurat package.
Supplementary files format and content: We provide the raw counts of the cells retained after QC filtering (mtx file labeled with UMI_counts_retained_cells.mtx), the first column contains gene symbols of genes.

source_name: mesenteric adipose tissue

extract_protocol:
Mesenteric adipose tissue was collected and enzymatically digested at 37°C for 30 minutes in Hank’s Balanced Salt Solution (HBSS) containing Liberase TL and DNase I. Tissues were pipetted up and down to promote dissociation, then filtered and subjected to red blood cell lysis. Single cell suspension was stained using CD45-PE and CD31-BV421.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) from 10x Genomics

value: mesenteric adipose tissue

value: endothelial cells

value: Myct1 (fl/fl)

value: male

value: 14 weeks


title: WT01

description:
Library name: WT01
WT01


title: bovine embryo, RNA-Seq, siSP1, MO, rep2

description: Library name: b_RNA_siSP1_MO_rep2


title: bovine embryo, RNA-Seq, siSP1, MO, rep3

description: Library name: b_RNA_siSP1_MO_rep3


title: P3-60804, 12863, tbi32, TBI, Veh

description:
Library name: P3-60804
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: brain

value: C57BL/6J wild-type

value: TBI


title: bovine embryo, RNA-Seq, WT, 4C_E8C

description: Library name: b_scRNA_WT_4C_E8C

value: 4-cell and early 8-cell bovine embryos


title: P3-60805, 12866b, tbi33, Sham, Veh

description:
Library name: P3-60805
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Vehicle


title: KO01

description:
Library name: KO01
KO01

value: Myct1 (fl/fl); Pdgfb-CreERT2


title: bovine embryo, RNA-Seq, WT, GV_MII

description: Library name: b_scRNA_WT_GV_MII

value: GV and MII bovine oocytes

value: wild type


title: bovine embryo, RNA-Seq, siSP1, MO, rep1

description: Library name: b_RNA_siSP1_MO_rep1

value: morula bovine embryos


title: bovine embryo, RNA-Seq, siCtrl, 16C, rep3

description: Library name: b_RNA_siCtrl_16C_rep3

value: 16-cell bovine embryos

value: siCtrl


title: P3-58699, 13107, tbi30, Sham, 4-AP

description:
Library name: P3-58699
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Sham


title: KO02

description:
Library name: KO02
KO02

value: mesenteric adipose tissue


title: First tarsal segment, male, 36h APF, scRNA-seq

first: Ben

last: Hopkins

department: Evolution & Ecology

description:
Library name: DMEL36HM
Chromium Next GEM Single Cell 3’ kit v3.1

data_processing:
The reference index was built using the ‘mkref’ function in CellRanger (v7.0.0) and the Ensembl BDGP6.32 Drosophila melanogaster genome into which we introduced sequences for GAL4, GFP, and mCherry. The GTF was filtered to include features of gene_biotype ‘ncRNA’ and ‘protein_coding’.  Alignment, barcode assignment, and UMI counting were performed on each single-cell dataset using the ‘count’ function in CellRanger. For each dataset, we ran ‘count’ with default settings (including counting regions that mapped to intronic regions), other than using the ‘force-cells’ option to limit the number of cells detected to 12,000 (except in the case of the 24h female dataset where we used 14,000).
Assembly: Ensembl BDGP6.32 Drosophila melanogaster genome
Supplementary files format and content: All processed datasets uploaded are the components of the filtered feature barcode matrix output from cell ranger.

organism: Drosophila melanogaster

source_name: First tarsal segment

extract_protocol:
We prepared our single-cell suspensions from dissected first tarsal segment tissue following the protocol we previously developed as part of our cell atlas (Hopkins et al., 2023 PLOS Biology) and which is available on protocols.io (dx.doi.org/10.17504/protocols.io.x54v9dzbmg3e/v2). Briefly, white prepupae were collected, sexed, and transferred to folded kimwipe wet with water (300μl for 12h, 450μl for 20h, and 750μl for 36h) held inside a petri dish. The dish was moved to an incubator at 25°C on a 12:12 cycle and the pupae left to age. Pupae were removed from puparia using forceps and placed on top of a water-soaked kimwipe 1 h before the desired age was reached (e.g., 23 h after collection for the 24 h sample). Pupae were then placed ventral side up on tape, the base of the abdomen pierced to release fluid pressure, and the foreleg removed at the tibia/tarsal joint. The dissected leg was moved to a piece of tape, covered in a drop of 1X Dulbecco’s PBS (DPBS, Sigma, D8537), and a Micro Knife (Fine Science Tools, 10318–14) used to sever at the midpoint of the second tarsal segment. The first tarsal segment was then eased out of the pupal cuticle and transferred to a glass well on ice containing 100μl of 1X DPBS using a BSA-coated 10μl tip. Once 65-70 segments were collected, the DPBS was removed from the well and replaced with 100μl of dissociation buffer, which consisted of 10X TrypLE (Thermo Fisher Scientific, A12177-01) with a final concentration of 2 mg/mL of collagenase (Sigma, C0130). The well was sealed and submerged in a metal bead bath in an incubator at 37°C for 35 minutes. For the 36h APF sample, we incubated for 45 minutes to overcome the greater resistance to dissociation at this point. The dissociation buffer was then removed from the well and replaced with 50μl of room temperature DPBS before the suspension was pipetted up and down 20-40x using a 200μl, widebore, low bind, freshly BSA coated tip (Thermo Fisher Scientific, 2069G) on a 50μl pipette set to 40μl. The solution was then pipetted up and down a further 20-40x using a flame-rounded, BSA-coated 200μl tip, again on a 50μl pipette set to 40μl. Next, the solution was transferred to a 2mL, low-bind, wide-bottomed tube on ice. Cell concentration and viability was assayed using an acridine orange/propidium iodide stain and measured using a LUNA-FL Fluorescent Cell Counter averaged across 2 × 5μl aliquots.
Barcoded 3’ single cell libraries were prepared from single cell suspensions using the Chromium Next GEM Single Cell 3’ kit v3.1(10X Genomics, Pleasanton, California) for sequencing according to the manufacturer’s instructions.  The cDNA and library fragment size distribution were verified on a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. Libraries from the 16h, 20h, 24h, 30h, and 36h APF samples were sequenced on a NovaSeq 6000 sequencer (Illumina, San Diego, CA) with paired-end 150 bp reads. The 12h APF libraries were sequenced in a 28 x 10 x 10 x 90 bp configuration on an AVITI sequencer (Element Biosciences, San Diego, CA).  In each case, the sequencing generated approximately 50,000 reads per cell and 500 million reads per library .

value: First tarsal segment

value: Male

value: 36h APF

value: dsx-GAL4 > UAS-mCherry


title: P3-58697, 13105, tbi28, TBI, 4-AP

description:
Library name: P3-58697
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: brain


title: bovine embryo, RNA-Seq, WT, 1C_2C

description: Library name: b_scRNA_WT_1C_2C

value: zygote and 2-cell bovine embryos


title: bovine embryo, RNA-Seq, siCtrl, 16C, rep2

description: Library name: b_RNA_siCtrl_16C_rep2


title: P3-60803, 12860, tbi31, Sham, Veh

description:
Library name: P3-60803
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: C57BL/6J wild-type


title: Female Per2 knockout biol rep 1

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

description:
Library name: Per2_cKO_F1
biol rep 1

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC contents in the clean data were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count read numbers mapped to each gene and calculate FPKM based on the length of the gene and read counts mapped to the gene.
Assembly: mm10
Supplementary files format and content: A composite Excel file "gene_fpkm_Per2x12" contains fpkm values of all samples.

source_name: Osteoclasts

growth_protocol: Monocytes were harvested from the bone marrow of 8-12 weeks old mice and induced to differentiate into osteoclasts with M-CSF and RANKL for 4 days.

extract_protocol:
Total RNA wad prepared with a Quick RNA Microprep (Zymo Research, R1051).
NEB Next Ultra II RNA Library Prep by Illumina following manufacturer's protocols.

value: female

value: Osteoclasts

value: Per2 knockout

value: Differentiation day 4

value: batch 1


title: Female Per2 knockout biol rep 3

description:
Library name: Per2_cKO_F3
biol rep 3

value: batch 3


title: P3-58695, 13101, tbi26, TBI, Veh

description:
Library name: P3-58695
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: TBI

value: Vehicle


title: Female Per2 knockout biol rep 2

description:
Library name: Per2_cKO_F2
biol rep 2

value: batch 2


title: First tarsal segment, male, 20h APF, scRNA-seq

description:
Library name: DMEL20HM
Chromium Next GEM Single Cell 3’ kit v3.1

value: 20h APF


title: Female Per2 Control biol rep 3

description:
Library name: Per2_Cont_F3
biol rep 3

value: Control


title: bovine embryo, RNA-Seq, siCtrl, 16C, rep1

description: Library name: b_RNA_siCtrl_16C_rep1

value: 16-cell bovine embryos

value: wild type

value: siCtrl


title: First tarsal segment, female, 24h APF, scRNA-seq

description:
Library name: DMEL24HF
Chromium Next GEM Single Cell 3’ kit v3.1

value: First tarsal segment

value: Female

value: 24h APF


title: P3-58694, 12874, tbi25, TBI, 4-AP

description:
Library name: P3-58694
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: brain

value: C57BL/6J wild-type


title: First tarsal segment, male, 16h APF, scRNA-seq

description:
Library name: DMEL16HM
Chromium Next GEM Single Cell 3’ kit v3.1

value: Male

value: 16h APF

value: dsx-GAL4 > UAS-GFP


title: P3-58696, 13104, tbi27, TBI, Veh

description:
Library name: P3-58696
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: P3-58693, 12875, tbi24, Sham, Veh

description:
Library name: P3-58693
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Sham


title: bovine embryo, RNA-Seq, siSP1, 16C, rep2

description: Library name: b_RNA_siSP1_16C_rep2


title: ΔArp9_2, RPMI-1640, Day2

city: 福建省

first: mei

middle: dong

last: Ma

address: Shangxiadian Road, Jianxin Town, Cangshan District, Fuzhou City

institute: Fujian Agriculture and Forestry University

data_processing:
JCVI-afl1-v3.0_genomic
Assembly: Sequence reads were trimmed for adaptor SedUece/OW seduence using JCVI-afl1-v3.0_genomic (oarameter Quality limit: 0.05)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Aspergillus flavus

source_name: mycelium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 3 ug of total RNA was used for the construction of sequencing ibraries
RNA libraries for RNA-sea were prepared using SMARTER mRNA-Sea Library Prep Kit fo owina manufacturer's protocols

value: mycelium

value: Aspergillus

value: RPMI-1640 culture


title: Female Per2 Control biol rep 1

description:
Library name: Per2_Cont_F1
biol rep 1

value: female

value: Osteoclasts

value: Differentiation day 4

value: batch 1


title: bovine embryo, RNA-Seq, siSP1, 16C, rep3

description: Library name: b_RNA_siSP1_16C_rep3

value: 16-cell bovine embryos

value: wild type


title: bovine embryo, RNA-Seq, siSP1, 16C, rep1

description: Library name: b_RNA_siSP1_16C_rep1


title: ΔArp9_1, RPMI-1640, Day2


title: Male Per2 knockout biol rep 3

description:
Library name: Per2_cKO_M3
biol rep 3

value: male

value: Per2 knockout

value: batch 3


title: P3-58692, 12873, tbi23, Sham, 4-AP

description:
Library name: P3-58692
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: brain

value: C57BL/6J wild-type


title: bovine embryo, RNA-Seq, siCtrl, 8C, rep3

description: Library name: b_RNA_siCtrl_8C_rep3

value: 8-cell bovine embryos

value: siCtrl


title: Male Per2 knockout biol rep 2

description:
Library name: Per2_cKO_M2
biol rep 2

value: batch 2


title: P3-57302, 12861, tbi14, Sham, 4-AP

description:
Library name: P3-57302
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Sham


title: WT_2, RPMI-1640, Day2

value: mycelium

value: Aspergillus

value: WT


title: P3-57301, 13123, tbi22, TBI, Veh

description:
Library name: P3-57301
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: TBI

value: Vehicle


title: bovine embryo, RNA-Seq, siCtrl, 8C, rep2

description: Library name: b_RNA_siCtrl_8C_rep2


title: WT_1, RPMI-1640, Day2

value: RPMI-1640 culture


title: bovine embryo, RNA-Seq, siCtrl, 8C, rep1

description: Library name: b_RNA_siCtrl_8C_rep1


title: Male Per2 knockout biol rep 1

description:
Library name: Per2_cKO_M1
biol rep 1

value: Osteoclasts

value: Differentiation day 4

value: batch 1


title: SMO-1, Multiome, Spleen, ATAC

first: Nathan

last: Schoettler

address: 5841 S Maryland Ave

institute: the University of Chicago

description:
Library name: Spleen SMO-1_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz

data_processing:
Multiome files were checked for quality using FastQC and processed using the cellranger-arc pipeline. Data from multiple libraries of lung and spleen were separately combined using cellranger-arc aggr, with read depth normalized. The snRNA-seq libraries were processed using Seurat pipelines, while snATAC-seq libraries were processed with ArchR pipeline.
Assembly: hg38/GRCh38
Supplementary files format and content: Filtered feature matrix output from cellranger-arc:  fragments.tsv.gz, matrix.mtx.gz, barcodes.tsv.gz
Supplementary files format and content: cluster labels and UMAP coordinates for snRNA processed with Seurat: snRNA_cluster_labels.csv.gz
Supplementary files format and content: cluster labels and UMAP coordinates for snATAC processed with ArchR: snATAC_cluster_labels.gz
Supplementary files format and content: Union set of peaks for all cells: snATAC_all_cluster_peaks.bed.gz
Supplementary files format and content: Input files for cellranger aggr function on lung and spleen librarires: Lung_aggregation.csv, Spleen_aggregation.csv
Supplementary files format and content: Outputs for cellranger aggr function: Lung_aggr_filtered_feature_bc_matrix.h5
Supplementary files format and content: Outputs for cellranger aggr function: Spleen_aggr_filtered_feature_bc_matrix.h6
Supplementary files format and content: Outputs for cellranger aggr function: Spleen_aggr_atac_fragments.tsv.gz
Supplementary files format and content: Outputs for cellranger aggr function: Lung_aggr_atac_fragments.tsv.gz
GEX library: read1 file, read2 file and index read file.
ATAC library: read1 file, read2 file, and dual index read files.
Aggregated matrices for lung and spleen: multiple samples in lung and spleen were aggregated according to aggregation.csv in supplementary files. The generated outputs include aggregated ATAC fragments and HDF5 files.

source_name: Spleen

extract_protocol:
Lung tissue was perfused with sterile fetal bovine serum and phosphate-buffered saline instilled in the pulmonary arteries. The right lower lobe was minced and digested into a single cell suspension. Mononuclear cells were isolated and cryopreserved. To obtain leukocytes from the spleen, tissue was minced into small pieces, filtered, and then broken up to release the cells from the outer layer of connective tissue. Mononuclear cells were enriched for leukocytes. They were isolated and incubated with DNase for 10 minutes followed by processes that removed dead cells and debris. Processed leukocytes were further sorted to enrich for lymphocytic cells.
Lymphocytic cells were processed for single cell Multiome sequencing on a Chromium X system with a Chromium Next GEM Chip from 10XGenomics. Gene expression and ATAC libraries were constructed with Chromium Next GEM Single Cell Multiome ATAC and Gene Expression Reagent from 10XGenomics.

value: Spleen

value: ATAC


title: Male Per2 Control biol rep 3

description:
Library name: Per2_Cont_M3
biol rep 3

value: male

value: Control

value: batch 3


title: bovine embryo, RNA-Seq, siSP1, 8C, rep3

description: Library name: b_RNA_siSP1_8C_rep3

value: 8-cell bovine embryos

value: wild type


title: P3-57300, 13122, tbi21, TBI, 4-AP

description:
Library name: P3-57300
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: brain

value: C57BL/6J wild-type


title: Male Per2 Control biol rep 2

description:
Library name: Per2_Cont_M2
biol rep 2

value: batch 2


title: bovine embryo, RNA-Seq, siSP1, 8C, rep2

description: Library name: b_RNA_siSP1_8C_rep2


title: SMO-10, Multiome, Spleen, ATAC

description:
Library name: Spleen SMO-10_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz


title: P3-57299, 13121, tbi20, Sham, 4-AP

description:
Library name: P3-57299
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

value: Sham


title: P3-57298, 13118, tbi19, Sham, Veh

description:
Library name: P3-57298
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: Male Per2 Control biol rep 1

description:
Library name: Per2_Cont_M1
biol rep 1


title: SMO-4, Multiome, Spleen, ATAC

description:
Library name: Spleen SMO-4_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz


title: bovine embryo, RNA-Seq, siSP1, 8C, rep1

description: Library name: b_RNA_siSP1_8C_rep1


title: Female Per1 knockout biol rep 3

description: Library name: Per1_cKO_F3

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC contents in the clean data were calculated. All the downstream analyses were based on the clean data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count read numbers mapped to each gene and calculate FPKM based on the length of the gene and read counts mapped to the gene.
Assembly: mm10
Supplementary files format and content: A composite Excel file "gene_fpkm_Per1x12" contains fpkm values of all samples.

value: Per1 knockout

tag: replicate

value: biol rep 3


title: COB-9, Multiome, Spleen, ATAC

description:
Library name: Spleen COB-9_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz

tag: tissue


title: K562_ActD_lib2_t_8h

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

description: Library name: K562_ActD_lib2_t_8h

data_processing:
The UMI was extracted and added to the read name using custom python scripts. Libraries were aligned to the reference sequences using BWA-MEM. Alignments were filtered using a custom python script. UMIs were deduplicated using a custom script with unique matching. Alignments for each reference were counted using a custom python script. Further downstream processing was performed using custom python scripts.
Supplementary files format and content: Processed data is provided as .csv files. They contain: Raw counts, log2FC, and normalized stability data for plasmid stability assays. Raw counts and calculated half-life values for Actinomycin D data. Raw counts, calculated relative distribution across polysome peaks and mean ribosome load for polysome profiling data. Metadata necessary for the analysis of the actionmycin D and polysome profiling data.

molecule: other

extract_protocol:
Protocol 1 and 2: If cells were adherent, they were detached cells with TrypLE. Cells were spun down for 5 min at 210 g. We resuspended the cells in 1 ml of cold PBS and placed them on ice. We took 25 µl of each sample, added 175 µl of PBS, and measured the GFP fluorescence on the Attune NxT flow cytometer to determine cell numbers and transfection efficiencies. We used the Monarch Total RNA Miniprep Kit (NEB, T2010S) to purify total RNA. We eluted in 100 µl of nuclease-free water and determined concentrations using a NanoDrop 2000c (Thermo Fisher). mRNA was purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L). We eluted in 18 µl of nuclease-free water. mRNA was reverse transcribed and amplified using custom primers. Protocol 3: Cells were pelleted (100 g RT, then 1000 g 4°C after PBS wash) and frozen at −80°C. The appropriate spike-in amount was calibrated using a t=0 sample by testing serial spike-in dilutions and estimating relative spike-in vs. cellular RNA abundance via qPCR. The selected spike-in amount (targeting the highest spike-in species at ~2x the most abundant cellular mRNA at t=0) was added to all samples during lysis (NEB RNA miniprep kit), followed by library preparation and sequencing as described above. Protocol 4: Cells were treated with cycloheximide and lysed. Media was replaced with 5 mL RT DPBS + CHX, incubated 5 min at 37°C, replaced with ice-cold DPBS + CHX, and cells were lysed in 300 µL cold lysis buffer. Lysates were incubated on ice (10 min), homogenized (25G needle), centrifuged (16,000 g, 5 min, 4°C), treated with DNase I (0.005 U/µL, 30 min, ice), and stored at -80°C. Polysome profiling was performed using 20–55% sucrose gradients (100 mM KCl, 20 mM HEPES pH 7.2, 10 mM MgCl₂) prepared by overnight diffusion at 4°C. Lysates were layered onto gradients and ultracentrifuged (151,000 g, 3 h, SW-41 Ti rotor). ~25 fractions were collected; free RNA and visible polysome peak fractions were retained for downstream analysis. Spike-in calibration was performed on total lysate by testing serial spike-in dilutions followed by Trizol extraction and RNA purification (Zymo RNA C&C-5 kit). qPCR curves were used to determine the spike-in amount targeting the most abundant spike-in species at ~2x the most abundant endogenous mRNA in the average fraction. All fractions were then processed with spike-in addition, Trizol extraction (scaled volumes), column purification, and standard library preparation. Fractions corresponding to the same polysome peak were combined during purification. mRNA isolation (magnetic beads) was performed for total lysate and free ribosome fractions only; ribosome-bound fractions were assumed to be mRNA-enriched.
Custom workflow


title: Female Per1 knockout biol rep 1

description: Library name: Per1_cKO_F1

tag: cell type

value: biol rep 1


title: P3-57295, 13117, tbi16, TBI, 4-AP

description:
Library name: P3-57295
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing

tag: genotype

value: TBI


title: P3-57297, 13124, tbi18, Sham, 4-AP

description:
Library name: P3-57297
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: K562_ActD_lib2_t_4h

description: Library name: K562_ActD_lib2_t_4h


title: COB-7, Multiome, Spleen, ATAC

description:
Library name: Spleen COB-7_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz


title: P3-55971, 12864, tbi13, TBI, 4-AP

description:
Library name: P3-55971
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: Female Control biol rep 3

description: Library name: Per1_Cont_F3

value: Osteoclasts

value: Differentiation day 4


title: Female Per1 knockout biol rep 2

description: Library name: Per1_cKO_F2

value: biol rep 2


title: COB-8, Multiome, Spleen, ATAC

description:
Library name: Spleen COB-8_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz

value: Spleen

value: ATAC


title: K562_ActD_lib2_t_2h

description: Library name: K562_ActD_lib2_t_2h


title: K562_ActD_lib2_t_24h

description: Library name: K562_ActD_lib2_t_24h


title: Female Control biol rep 2

description: Library name: Per1_Cont_F2

value: Control


title: COB-10, Multiome, Spleen, ATAC

description:
Library name: Spleen COB-10_ATAC
Spleen_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Spleen_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Spleen_aggr_atac_fragments.tsv.gz


title: K562_ActD_lib2_t_1h

description: Library name: K562_ActD_lib2_t_1h


title: SMO-1, Multiome, Spleen, GEX

description:
Library name: Spleen SMO-1_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5

molecule: nuclear RNA

value: mRNA


title: P3-55970, 12862, tbi12, TBI, 4-AP

description:
Library name: P3-55970
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: Female Control biol rep 1

description: Library name: Per1_Cont_F1

value: batch 1


title: P3-55969, 12865, tbi11, Sham, 4-AP

description:
Library name: P3-55969
FFPE Coronal Whole Section Visium CytAssist Spatial Transcriptomic Sequencing


title: K562_ActD_lib2_t_12h

description: Library name: K562_ActD_lib2_t_12h


title: SMO-10, Multiome, Spleen, GEX

description:
Library name: Spleen SMO-10_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5


title: NG2-4

city: Madrid

first: Ana Cristina

last: Ojalvo Sanz

state: Madrid

address: Avenida Doctor Arce 37, Laboratorio MB02

institute: Cajal Neuroscience Centre

description: Library name: Sample 9

data_processing:
The RNA sequencing data were processed and analyzed using a standardized pipeline. First, raw sequence reads in fastq format underwent initial quality control through in-house Perl scripts. Clean reads were obtained by removing reads containing adapters, poly-N sequences, and low-quality. To ensure data quality Q20, Q30, and GC content were calculated by Novogene. All downstream analyses were based on high-quality clean reads. Cleaned reads were aligned to the reference genome (Mus musculus, GRCm38.p6) using HISAT2 (version v2.0.5). Aligned reads were quantified at the gene level using featureCounts (version 1.5.0-p3). Expression levels were calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads), considering both sequencing depth and gene length.
aligment with reference genome
Assembly: Mus musculus, GRCm38.p6
Supplementary files format and content: .bam and .bam.bai

source_name: dorsal brain

growth_protocol: After targeting, NG2+ and GFAP+ cells were isolated by FACs sorting, after cell disotiation using mechanical dissociated, followed by enzymatic digestion with TrypLE Express

extract_protocol:
RNA isolation was performed using the RNAqueous™ Micro Total RNA Isolation Kit (Invitrogen™, #AM1931).
RNA samples were amplified using SMARTer amplification (Novogene, UK). After quality assessment, mRNA libraries were prepared with Poly A enrichment and sequenced on the NovaSeq™ System PE150 (Novogene, UK), yielding 6 GB of raw data per sample.

value: dorsal brain

value: Neural Stem Cells

value: WT

value: IUE with StarTrack


title: SMO-4, Multiome, Spleen, GEX

description:
Library name: Spleen SMO-4_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5


title: Female Per2 Control biol rep 2

description:
Library name: Per2_Cont_F2
biol rep 2

value: female

value: batch 2


title: NG2-5

description: Library name: Sample 10


title: Male Per1 knockout biol rep 3

description: Library name: Per1_cKO_M3

value: Per1 knockout

value: batch 3

value: biol rep 3


title: Male Per1 knockout biol rep 2

description: Library name: Per1_cKO_M2

value: Osteoclasts


title: NG2-2

description: Library name: Sample 7


title: NG2-3

description: Library name: Sample 8


title: K562_ActD_lib2_t_05h

description: Library name: K562_ActD_lib2_t_05h


title: SMO-9, Multiome, Spleen, GEX

description:
Library name: Spleen SMO-9_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5


title: Male Per1 knockout biol rep 1

description: Library name: Per1_cKO_M1

value: Differentiation day 4

value: biol rep 1


title: COB-8, Multiome, Spleen, GEX

description:
Library name: Spleen COB-8_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5

value: Spleen


title: NG2-1

description: Library name: Sample 6


title: HeLa_polysome_lib2_S9

description: Library name: HeLa_polysome_lib2_S9

source_name: HeLa

value: HeLa


title: COB-7, Multiome, Spleen, GEX

description:
Library name: Spleen COB-7_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5


title: Male Control biol rep 3

description: Library name: Per1_Cont_M3

value: Control


title: Male Control biol rep 2

description: Library name: Per1_Cont_M2

value: biol rep 2


title: K562_ActD_lib2_t_0h

description: Library name: K562_ActD_lib2_t_0h


title: HeLa_polysome_lib2_S8

description: Library name: HeLa_polysome_lib2_S8


title: GFAP-4

description: Library name: Sample 4

value: GFAP


title: Male Control biol rep 1

description: Library name: Per1_Cont_M1

value: batch 1


title: GFAP-3

description: Library name: Sample 3

value: dorsal brain

value: Neural Stem Cells


title: HeLa_polysome_lib2_S6

description: Library name: HeLa_polysome_lib2_S6


title: HeLa_polysome_lib2_S7

description: Library name: HeLa_polysome_lib2_S7


title: GFAP-5

description: Library name: Sample 5

value: WT

value: IUE with StarTrack


title: GFAP-2

description: Library name: Sample 2


title: female, 5xFAD-iβARK, replicate 4

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

description: Library name: Z

data_processing:
Low quality reads were filtered from the raw data in FASTQ format using fastp (version 0.23.2, accessible at https://github.com/OpenGene/fastp) with default parameters. The generated clean data were aligned to the NCBI ribosomal database employing Bowtie2 (version 2.4.5, available at https://github.com/BenLangmead/bowtie2) to eliminate rRNA sequences.
The rRNA-depleted sequences were aligned to the reference genome GRCm38 using Hisat2 (v2.2.1, https://github.com/infphilo/hisat2). Rsem (version 1.3.3, https://github.com/ deweylab/RSEM) was used for quantifying transcript abundances.
Genes with low expression (count < 6 in over 70% of the samples) were excluded from further analysis. To normalize the raw counts and conduct differential expression analysis, DESeq2 (version 1.32.0) was utilized.
Differentially expressed genes (DEGs) were designated as those with FDR adjusted p-value < 0.1.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include feature counts for each Sample

source_name: mPFC

growth_protocol: Both female and male 5xFAD mice, along with their wild-type age-matched littermates, were housed in a controlled environment, including a 12-hour light/dark cycle, consistent humidity and temperature, and ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from mPFC tissues using the RNeasy Mini Kit (74106, QIAGEN, Germany). RNA concentration was quantified using the Qubit 3.0 and Nanodrop One (Thermo Fisher Scientific, MA, USA), while RNA integrity (RIN) was assessed using the Agilent 4200 TapeStation (Agilent Technologies, Waldbronn, Germany).
The mRNA was isolated from total RNA samples meeting the integrity criteria (RIN > 7) with polyT oligo-attached magnetic beads and then processed using the ALFA-SEQ Directional RNA Library Prep Kit (Findrop, China) following the manufacturer's protocol. The library preparation and subsequent RNA sequencing were performed by Illumina Novaseq 6000 (MAGIGENE, Guangzhou, China).

treatment_protocol: Mice were injected with AAV2/5 carrying iβARK-mCherry or mCherry at 3-4 months of age, with evaluations of transcriptional profile conducted 45 days after intervention.

value: mPFC

value: Whole tissue

value: iβARK-mCherry


title: female, 5xFAD-iβARK, replicate 3

description: Library name: Y


title: SMO-9, Multiome, Lung, ATAC

description:
Library name: Lung SMO-9_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz

source_name: Lung

value: Lung

value: ATAC


title: SMO-2, Multiome, Lung, ATAC

description:
Library name: Lung SMO-2_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: COB-10, Multiome, Spleen, GEX

description:
Library name: Spleen COB-10_mRNA
Spleen_aggregation.csv
snRNA_cluster_labels.csv.gz
Spleen_aggr_filtered_feature_bc_matrix.h5

value: mRNA


title: HeLa_polysome_lib2_S5

description: Library name: HeLa_polysome_lib2_S5


title: SMO-3, Multiome, Lung, ATAC

description:
Library name: Lung SMO-3_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: GFAP-1

description: Library name: Sample 1


title: HeLa_polysome_lib2_S4

description: Library name: HeLa_polysome_lib2_S4


title: SMO-8, Multiome, Lung, ATAC

description:
Library name: Lung SMO-8_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: female, 5xFAD-iβARK, replicate 2

description: Library name: X


title: SMO-7, Multiome, Lung, ATAC

description:
Library name: Lung SMO-7_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: HeLa_polysome_lib2_S3

description: Library name: HeLa_polysome_lib2_S3


title: HeLa_polysome_lib2_S2

description: Library name: HeLa_polysome_lib2_S2


title: SMO-5, Multiome, Lung, ATAC

description:
Library name: Lung SMO-5_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: GBM post-oHSV Patient 46 region 1

type: RNA

city: Boston

first: Maxime

last: Meylan

state: MA

address: 450 Brookline Avenue

department: Cancer Immunology Virology

institute: Dana-Farber Cancer Institute

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P46_POST

hyb_protocol: FFPE tissue blocks were sectioned at 5μm thickness onto SuperFrost Plus slides. Tissue sections were deparaffinized using xylene and rehydrated through an ethanol series. Tissue permeabilization, target retrieval, and probe hybridization were performed according to the 10X Genomics Xenium FFPE preparation protocol

data_processing:
Raw imaging data was processed using Xenium Analyzer software (v1.0.1) for transcript detection, background correction, and cell segmentation.
GRCh38
cell_feature_matrix.h5: Cell-by-gene expression matrix
transcripts.parquet: Spatial coordinates of detected transcripts
morphology.ome.tif: High-resolution tissue image
cells.parquet: Cell-level metadata
gene_panel.json: Targeted gene list
analysis_summary.html: QC and preliminary data analysis.
surface_area.csv: Xenium explorer export containing annotation polygons and surface area

source_name: FFPE tissue section

extract_protocol: Pre-treatment tumor biopsies were collected prior to oncolytic virus administration. Post-treatment tumor specimens were collected at time of tumor progression or recurrence following a single intratumoral injection of rQNestin34.5v.2 (CAN-3110) oncolytic virus as part of a phase I clinical trial (NCT03152318) conducted at Dana-Farber Cancer Institute and Brigham and Women's Hospital. Collected tissues were fixed in 10% neutral buffered formalin and embedded in paraffin following standard pathology procedures. All tissue collection was performed with informed consent under IRB-approved protocol (Dana Farber Harvard Comprehensive Cancer Center IRB no. 16-557).

value: brain tumor

tag: tissue type

value: Post-Treatment resection


title: GBM pre-oHSV Patient 51 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P51_PRE

value: Pre-treatment biopsy

value: pre-treatment


title: female, 5xFAD-mCherry, replicate 5

description: Library name: V

value: mCherry


title: HeLa_polysome_lib2_S1

description: Library name: HeLa_polysome_lib2_S1

value: HeLa


title: GBM pre-oHSV Patient 46 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P46_PRE


title: female, 5xFAD-mCherry, replicate 4

description: Library name: U


title: COB-6, Multiome, Lung, ATAC

description:
Library name: Lung COB-6_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: female, 5xFAD-iβARK, replicate 1

description: Library name: W


title: HeLa_polysome_lib2_S13

description: Library name: HeLa_polysome_lib2_S13


title: female, 5xFAD-mCherry, replicate 2

description: Library name: S


title: HeLa_polysome_lib2_S12

description: Library name: HeLa_polysome_lib2_S12


title: GBM pre-oHSV Patient 45 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P45_PRE


title: COB-11, Multiome, Lung, ATAC

description:
Library name: Lung COB-11_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: HeLa_polysome_lib2_S11

description: Library name: HeLa_polysome_lib2_S11


title: COB-5, Multiome, Lung, ATAC

description:
Library name: Lung COB-5_ATAC
Lung_aggr_atac_fragments.tsv.gz.tbi
snATAC_cluster_labels.csv.gz
Lung_aggregation.csv
snATAC_all_cluster_peaks.bed.gz
Lung_aggr_atac_fragments.tsv.gz


title: GBM post-oHSV Patient 45 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P45_POST


title: female, 5xFAD-mCherry, replicate 1

description: Library name: R


title: GBM post-oHSV Patient 34 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P34_POST

value: recurrent glioblastoma


title: HeLa_polysome_lib2_S10

description: Library name: HeLa_polysome_lib2_S10


title: SMO-3, Multiome, Lung, GEX

description:
Library name: Lung SMO-3_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: female, 5xFAD-mCherry, replicate 3

description: Library name: T


title: SMO-2, Multiome, Lung, GEX

description:
Library name: Lung SMO-2_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: H293T_polysome_lib2_S9

description: Library name: H293T_polysome_lib2_S9


title: female, WT-mCherry, replicate 5

description: Library name: Q


title: GBM pre-oHSV Patient 34 region 2

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P34_PRE_2


title: GBM pre-oHSV Patient 34 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P34_PRE_1


title: SMO-9, Multiome, Lung, GEX

description:
Library name: Lung SMO-9_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: H293T_polysome_lib2_S8

description: Library name: H293T_polysome_lib2_S8


title: SMO-8, Multiome, Lung, GEX

description:
Library name: Lung SMO-8_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: GBM post-oHSV Patient 32 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P32_POST


title: H293T_polysome_lib2_S6

description: Library name: H293T_polysome_lib2_S6


title: GBM post-oHSV Patient 28 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P28_POST


title: female, WT-mCherry, replicate 2

description: Library name: N


title: GBM pre-oHSV Patient 32 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P32_PRE


title: female, WT-mCherry, replicate 4

description: Library name: P


title: H293T_polysome_lib2_S7

description: Library name: H293T_polysome_lib2_S7


title: SMO-7, Multiome, Lung, GEX

description:
Library name: Lung SMO-7_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: SMO-5, Multiome, Lung, GEX

description:
Library name: Lung SMO-5_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: female, WT-mCherry, replicate 1

description: Library name: M


title: H293T_polysome_lib2_S5

description: Library name: H293T_polysome_lib2_S5


title: female, WT-mCherry, replicate 3

description: Library name: O


title: male, 5xFAD-iβARK, replicate 3

description: Library name: K


title: COB-6, Multiome, Lung, GEX

description:
Library name: Lung COB-6_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: H293T_polysome_lib2_S4

description: Library name: H293T_polysome_lib2_S4


title: COB-5, Multiome, Lung, GEX

description:
Library name: Lung COB-5_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: GBM post-oHSV Patient 21 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P21_POST


title: male, 5xFAD-iβARK, replicate 2

description: Library name: J


title: COB-11, Multiome, Lung, GEX

description:
Library name: Lung COB-11_mRNA
Lung_aggregation.csv
snRNA_cluster_labels.csv.gz
Lung_aggr_filtered_feature_bc_matrix.h5


title: GBM pre-oHSV Patient 28 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P28_PRE


title: GBM pre-oHSV Patient 21 region 3

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P21_PRE_3


title: H293T_polysome_lib2_S2

description: Library name: H293T_polysome_lib2_S2


title: male, 5xFAD-mCherry, replicate 4

description: Library name: H


title: H293T_polysome_lib2_S1

description: Library name: H293T_polysome_lib2_S1


title: GBM pre-oHSV Patient 21 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P21_PRE_1


title: male, 5xFAD-iβARK, replicate 1

description: Library name: I


title: male, 5xFAD-mCherry, replicate 3

description: Library name: G


title: 7FAUS_16h_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA97544

data_processing:
Sequencing was performed on NovaSeq X Plus platform in a 101-base single-read mode.
Illumina Real Time Analysis v4 (RTA4) software was used for base calling.
Generated reads were mapped to the human (GRCh38) reference genome using HISAT 2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: RD-S

extract_protocol:
Total RNA was collected using ISOGEN II (Nippon Gene) according to the manufacturer’s protocol.
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: RD-S

value: human embryo rhabdomyosarcoma cell line stably expressing human SCARB2

tag: agent

value: infected with the chimeric EV-A71 strains carrying the 3C protease from a 7F-AUS-6-99 (7FAUS) strain


title: H293T_polysome_lib2_S13

description: Library name: H293T_polysome_lib2_S13


title: GBM post-oHSV Patient 51 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P51_POST


title: male, 5xFAD-mCherry, replicate 2

description: Library name: F


title: H293T_polysome_lib2_S12

description: Library name: H293T_polysome_lib2_S12


title: GBM pre-oHSV Patient 21 region 2

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P21_PRE_2


title: GBM pre-oHSV Patient 05 region 2

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P05_PRE_2


title: 7FAUS_16h_2

description: Library name: GA97543


title: 1095_16h_3

description: Library name: GA97541

value: infected with the chimeric EV-A71 strains carrying the 3C protease from a 1095/Japan 97 (1095) strain


title: H293T_polysome_lib2_S11

description: Library name: H293T_polysome_lib2_S11


title: H293T_polysome_lib2_S3

description: Library name: H293T_polysome_lib2_S3


title: 1095_16h_2

description: Library name: GA97540


title: 7FAUS_16h_1

description: Library name: GA97542


title: GBM pre-oHSV Patient 05 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P05_PRE_1


title: male, WT-mCherry, replicate 4

description: Library name: D

value: mPFC

value: WT


title: H293T_polysome_lib2_S10

description: Library name: H293T_polysome_lib2_S10


title: GBM post-oHSV Patient 05 region 1

description:
FFPE image based spatial transcriptomics with 10X genomics Xenium
P05_POST


title: 1095_16h_1

description: Library name: GA97539


title: male, 5xFAD-mCherry, replicate 1

description: Library name: E

value: Whole tissue


title: Patient 1023, baseline and end-of-treatment (filtered matrices)

city: New York

first: Juan-Jose

last: Garces

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: SD-2752_1023_BL_ES-GEX

data_processing:
Matrices with filtered unique molecular identifier (UMI) counts and peaks from cellranger ARC outputs were used as input for Seurat. Furthermore, these were filtered out according to the following criteria: (i) more than 5,000 or less than 500 expressed genes, (ii) more than 20,000 or less than 500 peak counts, (iii) a TSS (transcription start site) enrichment >1, (iv) a nucleosome signal <2, and (v) a percentage of mitochondrial genes ≥25%. Antibody-hashed cells were then demultiplexed taking the union of both Seurat’s HTODemux and the R package scDemultiplex. For more stringent criteria, expression-based doublets were additionally removed using the package R scds. All samples were merged into the same object in the final step.
Assembly: GRCh38
Supplementary files format and content: Filtered count and barcode matrices as Cellranger outputs
Supplementary files format and content: HTO information for sample demultiplexing

source_name: Bone marrow

extract_protocol:
Viably frozen paired bone marrow mononuclear cells from baseline and W52 from 13 participants (1001, 1003, 1004, 1006, 1009, 1011, 1012, 1013, 1014, 1015, 1017, 1022 and 1023) were sorted by fluorescence-activated cell sorting (FACS) for live CD45+ single cells (CD45: BD Bioscience, catalog# 563204; DAPI: Millipore Sigma, catalog# 508741) and submitted for single-cell sequencing in 0.04% bovine serum albumin in PBS.
They were processed using the Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog no. 1000282) and ATAC Kit A (catalog no. 1000280). We followed the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide with the difference that single-cell suspension was prepared as described (DOGMA-seq protocol with Digitonin buffer). Briefly, cells were treated with a digitonin lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.01% digitonin and 2 U/µl of RNase inhibitor) for 5 min on ice, followed by adding 1 mL of chilled wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, and 1 U/µl of RNAse inhibitor) and inversion before centrifugation at 500g for 5 min at 4 °C. The supernatant was discarded, and cells were resuspended in digitonin wash buffer, followed by counting using trypan blue and DAPI on a Countess II FL Automated Cell Counter. In addition, samples for each patient were pooled together on one lane of 10X Chromium (using Hash Tag Oligonucleotides - HTO). Final libraries were sequenced on an Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

treatment_protocol: High-fiber plan-based diet

value: Bone marrow

value: Immune microenvironment

value: CD45+ sorted cells


title: X5_b

city: Kifissia

first: Theoni

last: Margaritopoulou

state: Attiki

address: Stefanou Delta 8

department: Phytopathology

country: Greece

institute: Benaki Phytopathological Institute

description: Library name: X5_b

data_processing:
Bismark Methyl Extractor
Assembly: Arabidopsis thaliana genome GCF_000001735.4
Supplementary files format and content: bam files with percentage for each cytosine

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Per sample, frozen plant tissue was grounded with liquid nitrogen and genomic DNA was isolated using the SDS procedure of the NucleoSpin Plant II DNA isolation kit (MachereyNagel, Germany). A NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and agarose gel electrophoresis were used to determine DNA concentration and integrity after the genomic DNA extraction.
DNA libraries were prepared for bisulfite sequencing using the NEBNext® Enzymatic Methyl-seq kit (NEB, Ipswich, MA, USA).

value: leaf

tag: ecotype

value: Col-O

value: pathogen


title: WTSK_16h_3

description: Library name: GA97538

value: infected with the wild-type EV-A71 (WTSK)


title: male, WT-mCherry, replicate 3

description: Library name: C

value: mCherry


title: X5_a

description: Library name: X5_a


title: male, WT-mCherry, replicate 2

description: Library name: B


title: X2_b

description: Library name: X2_b


title: male, WT-mCherry, replicate 1

description: Library name: A


title: Patient 1023, baseline and end-of-treatment (HTO data)

description: Library name: SD-2752_1023_BL_ES-HTO

data_processing:
Matrices with filtered unique molecular identifier (UMI) counts and peaks from cellranger ARC outputs were used as input for Seurat. Furthermore, these were filtered out according to the following criteria: (i) more than 5,000 or less than 500 expressed genes, (ii) more than 20,000 or less than 500 peak counts, (iii) a TSS (transcription start site) enrichment >1, (iv) a nucleosome signal <2, and (v) a percentage of mitochondrial genes ≥25%. Antibody-hashed cells were then demultiplexed taking the union of both Seurat’s HTODemux and the R package scDemultiplex. For more stringent criteria, expression-based doublets were additionally removed using the package R scds. All samples were merged into the same object in the final step.
Assembly: GRCh38
Supplementary files format and content: Filtered count and barcode matrices as Cellranger outputs
Supplementary files format and content: HTO information for sample demultiplexing
Library strategy: CITE-seq


title: Patient 1022, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2752_1022_BL_ES-GEX


title: WTSK_16h_2

description: Library name: GA97537


title: X2_a

description: Library name: X2_a


title: WTSK_16h_1

description: Library name: GA97536


title: EA4

city: JiNan

first: Hui

last: Dong

address: Jiefang Street 105

institute: Shandong University

data_processing:
Total RNA was extracted and sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.
Samples are sequenced on the platform to get image files, which are transformed by the   software of the sequencing platform, and the original data in FASTQ format (Raw Data) is   generated.
Sequencing data contains a number of connectors, low-quality Reads, so we use   Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean   Data）for further analysis .
The reference genome and gene annotation files were downloaded from genome website.  The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: read count and fpkm

source_name: EA Group

extract_protocol:
Total RNA was extracted using Trizol (Accurate Biology AG) following the manufacturer 's instructions.
Sequencing libraries were generated according to the following steps. Firstly, mRNA   was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was   carried out using divalent cations under elevated temperature in an Illumina proprietary   fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and   Super Script II. Second strand cDNA synthesis was subsequently performed using DNA   Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via   exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′   ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for   hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library   fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).   DNA fragments with ligated adaptor molecules on both ends were selectively enriched using  Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP   system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100   system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform   (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

treatment_protocol: EA group received 10 μM Ellagic Acidtreatment and control group received the same dose of DMSO treatment.Total RNA was extracted after 48 hours of treatment.

value: Femur

value: mouse bone marrow mesenchymal stem cells

value: 10 uM EA treat 48hours


title: mock_16h_3

description: Library name: GA97535

value: RD-S

value: human embryo rhabdomyosarcoma cell line stably expressing human SCARB2


title: Patient 1009, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2752_1009_BL_ES-GEX


title: MS8_b

description: Library name: MS8_b

value: Control


title: EA3


title: EA2


title: Patient 1009, baseline and end-of-treatment (HTO data)

description: Library name: SD-2752_1009_BL_ES-HTO


title: MS8_a

description: Library name: MS8_a


title: mock_16h_2

description: Library name: GA97534


title: Patient 1022, baseline and end-of-treatment (HTO data)

description: Library name: SD-2752_1022_BL_ES-HTO


title: EA1


title: mock_16h_1

description: Library name: GA97533


title: MS7_b

description: Library name: MS7_b


title: MS7_a

description: Library name: MS7_a


title: 2C10_b

description: Library name: 2C10_b

value: SA-CNPs


title: Patient 17, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2589_17-GEX


title: Control3

source_name: Control Group

value: same dose of DMSO treat 48hous


title: Severe_MalariaSample_HepaticDysfunction_9

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression Profiling

hyb_protocol: Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium vivax Gene Expression Microarray 8X60K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

organism: Plasmodium vivax

source_name: Total RNA, Test Group 1, Sample 9

label_protocol: Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

extract_protocol:
Clinical samples collected from malaria patients
RNA from enriched blood was isolated using TRIzol as per manufacture's protocols.

treatment_protocol: Total RNA was extracted from venous blood samples collected from malaria patients. The patients exhibited symptoms categorized as un-complicated (n =5), hepatic dysfunction (n=9).

value: Enriched blood sample

tag: clinical complication

value: Severe malaria - Hepatic Dysfunction


title: Control2


title: Control4


title: Patient 17, baseline and end-of-treatment (HTO data)

description: Library name: SD-2589_17-HTO

value: Bone marrow

tag: cell line

value: Immune microenvironment


title: Patient 1006, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2752_1006_BL_ES-GEX

value: CD45+ sorted cells


title: 2C10_a

description: Library name: 2C10_a

value: leaf

value: Col-O


title: Severe_MalariaSample_HepaticDysfunction_8

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 8


title: Patient 14, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2589_14-GEX


title: Control1


title: Patient 1006, baseline and end-of-treatment (HTO data)

description: Library name: SD-2752_1006_BL_ES-HTO


title: 2C3_a

description: Library name: 2C3_a


title: 2C3_b

description: Library name: 2C3_b


title: Patient 14, baseline and end-of-treatment (HTO data)

description: Library name: SD-2589_14-HTO


title: Bcl6_KO2

city: Beijing

first: Qi

last: Xing

address: 30 Shuangqing Road

institute: Tsinghua University

description: Library name: Sample 12

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
Clean reads were aligned to Mus musculus genome (mm10) by Bowtie2 with default parameter. Uniquely mapped reads were counted by featureCounts (from Subread package).
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes (DEGs) were identified by DESeq2 with cut-off thresholds of 1.5-fold change and FDR adjusted p-value<0.05 (for Bcl6RFP and BLIMP1-WT/cKO comparisons) or 1.25-fold change and p-value<0.05 (for BCL6-WT/cKO and TCF1-WT/cKO comparisons).
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each sample

source_name: small intestine

extract_protocol:
Total RNA was extracted from sorted cells using MagZol  (Magen, cat#R4801-02) according to the manufacturer’s protocol.
RNA-seq library was constructed for deep sequencing by BGI Genomics or Novogene.

value: small intestine

value: Bcl6fl/fl Cd8cre


title: HIFRAP_21_4

city: Oxford

first: Vinay

last: Shukla

state: United Kingdom

address: South Parks Road Oxford

department: Department of Biology

institute: University of Oxford

description: Library name: Sample 9

data_processing:
Kallisto read allignment, edgeR differenital expression
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: gene_fpkm.txt

source_name: Whole seedling

extract_protocol:
RNA was isolated using GeneJET RNA Purification Kit (Thermo Scientific™) as per manufacturer’s instruction.
cDNA library preparation were carried out as described in Dalle Carbonare L., 2025

value: Whole seedling

value: Hypoxia


title: Bcl6_KO1

description: Library name: Sample 11


title: Severe_MalariaSample_HepaticDysfunction_7

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 7


title: Patient 13, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2589_13-GEX


title: HIFRAP_21_3

description: Library name: Sample 8


title: Bcl6_WT2

description: Library name: Sample 10


title: Severe_MalariaSample_HepaticDysfunction_6

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 6


title: Bcl6_WT1

description: Library name: Sample 9


title: HIFRAP_21_1

description: Library name: Sample 7


title: Severe_MalariaSample_HepaticDysfunction_5

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 5


title: Severe_MalariaSample_HepaticDysfunction_3

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 3


title: Severe_MalariaSample_HepaticDysfunction_4

description: Gene expression Profiling

source_name: Total RNA, Test Group 1, Sample 4


title: Patient 11, baseline and end-of-treatment (HTO data)

description: Library name: SD-2589_11-HTO


title: Patient 11, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2589_11-GEX


title: HIFRAP_1_3

description: Library name: Sample 5


title: 16S amplicon sequencing of sample GHIA_Faeces_8

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
Library name: GHIA_Faeces_8
16S V3-V4 amplicon sequencing

data_processing:
from raw to demultiplexed fastq files please contact BMR Sequencing Services (Padova, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNBGCWSCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores $threads --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 249 --p-trunc-len-r 150 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads $silva_ref --i-reference-taxonomy $silva_tax --p-perc-identity 0.99 --p-threads $threads --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose 2> ASV_matched_in_SILVA.txt
qiime metadata tabulate --m-input-file taxonomy_SILVA.qza --o-visualization confidence_taxonomy_SILVA.qzv
Assembly: SILVA 138
Supplementary files format and content: dna-sequences.fasta: sequences of representative ASVs
Supplementary files format and content: feature_table.tsv: ASV abundance table
Library strategy: 16S rRNA-seq

organism: Rattus norvegicus

source_name: Faeces

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Faeces

value: Bacteria consortium


title: Patient 1, baseline and end-of-treatment (filtered matrices)

description: Library name: SD-2589_1-GEX


title: HIFRAP_1_4

description: Library name: Sample 6