title: S72_HiGated_Ruc_24h

value: Hi


title: D4 ATAC 15h

status: Public on Jan 05 2026

type: SRA

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

country: USA

institute: Cincinnati Children's Hospital

description:
includes D0 spike-in resting control
act_15_set_4_atac

library_source: genomic single cell

data_processing:
Raw single-cell multiome (RNA+ATAC) sequencing data from 4 time points (0h, 2.5h, 5h, and 15h), each with 4 replicates (a.k.a. donors D1-D4), were first independently preprocessed in Scientific Data Analysis Platform (https://scidap.com) using the “Cell Ranger Count (RNA+ATAC)” pipeline, and then aggregated with the “Cell Ranger Aggregate (RNA+ATAC)” pipeline with library depth normalization disabled.
Alignment, filtering, and UMI counting using cellranger-arc-2.0.2  Quality filtering using Seurat V5.1.0 (genes > 400, UMI > 750, fragments > 2000, mito < 20%, fragments in blacklist < 5%, nucleosome signal < 2.5, TSS enrichment > 2)  Initial clustering and removal of non-CD4+ T cell populations (CD3E-, CD45-) using Seurat V5.1.0  RNA doublet detection with scDoubletFinder v1.15.2 with individual clustered Seurat objects converted to single cell experiments (sce).  ATAC doublet detection with ArchR v1.0.2 with individual sample fragment files as inputs. Doublets agreed upon across both RNA and ATAC doublet detection were filtered out.  Further doublet filtering using Seurat V5.1.0 (> 10k UMI or 50k ATAC fragments)  Cell ranger fragment file modification to include both transposase cut sites.  Peak calling on each filtered and initial clustered Seurat object with MACS2 (MACS2 parameters: --shift -25 --extsize 50 --tsize 50 --pvalue 1E-8 --keep-dup all).  Create reference peak set by taking the union of all peak calls and merging overlapping peaks.  Create peaks x cells matrix using FeatureMatrix function from Signac v1.13.0.  Log-normalize raw RNA counts data with Seurat’s NormalizeData followed by centering and scaling by z-scoring using Seurat’s ScaleData function.  Perform principal component analysis on the RNA data using Seurat’s RunPCA with the first 30 dimensions.  Term frequency inverse document frequency (TF-IDF) normalization of the raw ATAC data using Signac’s RunTFIDF function.  Latent semantic indexing (LSI) was run on the normalized ATAC data using Signac’s RunSVD function. Only features with >=1 cut site in 20 or more cells was included in the dimension reduction.  RNA integration using Harmony V3.8 (parms: assay = “RNA”, group.by.vars = “dataset”, reduction.use = “pca”, reduction.save = “harmony_rna”, max.iter = 25)  ATAC integration using Harmony V3.8 (parms: assay = “ATAC”, group.by.vars = “dataset”, reduction.use = “lsi”, reduction.save = “harmony_atac”, max.iter = 25, project.dim = F)  Construct weighted nearest neighbor graph using Seurat’s FindMultiModalNeighbors (params: reduction.list = list("harmony_rna", "harmony_atac"), dims.list = list(1:30, 2:30)  Cluster nearest neighbor graph using mart local moving (SLM) algorithm.  Repeat peak calling with MACS2 using the same parameters listed previously but grouped by each cluster-timepoint.  Create new reference peak set and counts matrix using same method as above.  Perform TFIDF normalization, LSI, and harmony integration on the new ATAC counts matrix using the same method as above.  Repeat weighted nearest neighbor graph and clustering using the new harmony_atac reduction as input using the same method as above.
Assembly: GRCh38/hg38
Supplementary files format and content: Gzip-compressed TAB-delimited file with the cell barcodes represented in the mtx file.
Supplementary files format and content: Gzip-compressed TAB-delimited file with the feature names represented in the mtx file.
Supplementary files format and content: Gzip-compressed sparse matrix file with the RNA read and ATAC fragment counts per feature and cell barcode combination.
Supplementary files format and content: Analysis results saved in RDS (R Data Serialization) format. The origin of cells can be tracked through the "dataset" metadata column.

molecule: genomic DNA

organism: Homo sapiens

source_name: human lymphocytes

growth_protocol: Blood leukocyte depletion filters containing cells collected from from de-identified donors were obtained from University of Cincinnati Hoxworth Blood Center. Filters were back-flushed with PBS and PBMCs were prepared by Ficoll centrifugation. Human CD4 T cell were negatively isolated from PBMC using CD4 isolation magnetic beads (STEM CELL #19052). To increase the fraction of TEM cells, naive and TCM cells were partially depleted using anti-CD27-biotin coated streptavidin magnetic beads (Invitrogen Dynabeads Biotin Binder 11047; CD27 antibody Biolegend 302804). Cell were cryopreserved in 50% CTS OpTmizer medium (A1048501), 40% human serum (Sigma H4522), 10% DMSO (ThermoFisher) and stored in liquid nitrogen.

extract_protocol:
Nuclei were prepared according to the modified 10XGenomics  protocol: 100ul of cold lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 1% BSA, 0.025% Tween-20,  0.025% Nonidet P40,  0.00125% Digitonin, 1mM DTT, 1 U/µl RNase inhibitor (Roche)) were added to cell pellets. Samples were incubated for 40s on ice, washed with 1ml of cold wash buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 1% BSA, 0.025% Tween-20, 1mM DTT, 1 U/µl RNase inhibitor (Roche)) and filtered with Flowmi cell strainer (Bel-Art H13680-0040).
The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression assay was performed according to the manufacturer’s instructions (10x Genomics) with the kit Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000283). Briefly, nuclei suspended in the multiome buffer were combined with a transposition mix and incubated for one hour. The transposition reaction was combined with the kit’s master mix and loaded together with partitioning oil and gel beads into the Chromium Next GEM Chip J Single Cell Kit (PN-1000234) to generate a gel bead-in-emulsion (GEM). The GEMs were then incubated producing 10x barcoded DNA from the transposed fragments (for ATAC) and 10x barcoded, full-length cDNA from poly-adenylated mRNA (for GEX). Next the GEMs were broken, the barcoded DNA and cDNA were purified, and the purified products were subjected to a pre-amplification PCR step . The pre-amplified material was then used as starting material for ATAC and RNA library construction per 10x protocol. ATAC libraries and GEX libraries were pooled separately. and sequenced at CCHMC DNA core.

treatment_protocol: Thawed purified cells were plated in CTS OpTmizer with 1% Penicillin-Streptomycin (Gibco 15140122) and incubated at 37oC for the duration activation: 15h/5h/2.5h. Activation was performed in a staggered manner so that cells were lysed at the same time. Activation was performed using Dynabeads Human T-Activator CD3/CD28 (Gibco 11131D). To prevent sample contamination with cell-free DNA released from dead cells DNase I (1:100) was added directly into the medium (NEB M0303S) during last 30min of incubation. After incubation cells were washed with PBS+0.1% BSA 2 times. For each multiome experiment, cells from the spike-in control donor and experiment donor were mixed at a ratio of 8% to 92% immediately prior to the nuclei prep.

tag: tissue

value: human lymphocytes

tag: cell line

value: primary

tag: cell type

value: effector enriched CD4 T

tag: timepoint

tag: treatment

value: aCD3/CD28 activated


title: D4 ATAC 5h

description:
includes D0 spike-in resting control
act_5_set_4_atac


title: S69_LoGated_Ruc_24h

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: transcriptomic

data_processing:
Reads were processed using cutadapt v4.7 (Martin 2011) to remove Illumina adapters, trim, and filter on quality with the settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, -n 1, -m 31, --nextseq-trim 20, --max-n 0
Processed reads were quantified against the GRCh38 transcriptome (Ensembl 107 annotations) by Salmon (Patro et al. 2017) with the following settings: -l A, --softclip, --softclipOverhangs, --allowDovetail, --seqBias, --gcBias.
Within DESeq2 v1.44.0 (Love, Huber, and Anders 2014), independent hypothesis weighting was conducted to optimise the power of p value filtering using IHW v1.32.0 (Ignatiadis et al. 2016) and log2 fold-change shrinkage was performed using ashr v2.2-63 (Stephens 2017). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: Transcript-level expression estimates

molecule: polyA RNA

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 2 mM Glutamine, 100 U/mL penicillin, 100 µg/mL streptomycin, 10% FCS at 37°C, 5% CO2 and passaged three times per week using TrypLE express.

extract_protocol:
After treatment, with or without FACS-sorting to separate rucaparib-high and low (top and bottom 20% of population), cells were washed in ice-cold PBS before extraction RNA using the RNeasy purification kit (Qiagen, 74106) according to manufacturer’s instructions. Unsorted controls cells were scraped directly into lysis buffer (RLT) using a cell scraper.
The NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module was used to generate RNA-Seq libraries according to the manufacturer’s protocol. Library quality was checked using the Agilent 2100 High-Sensitivity DNA assay, before checking concentrations with the Qubit dsDNA HS Assay Kit. Libraries were sequenced on a NextSeq 2000 after pooling in equimolar quantities.

treatment_protocol: PEO1 cells were treated for 2 or 24h with DMSO (vehicle) or the fluorescent compound Rucaparib at 8.5 µM. After incubation, the different conditions were harvested to FACS-sort the bottom and top 20% of the Rucaparib treated population when ranked according to the drug fluorescence intensity.

tag: facs gate

value: Lo

value: Ruc

tag: replicate


title: HDT546_kidney_1_tumor

type: RNA

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

country: Canada

institute: BC Cancer Research Centre

hyb_protocol: On day two, slides were subjected to a post-hybridization wash (37°C for 2 h), ligation (37°C for 2 h), amplification (30°C for 2 h), autofluorescence quenching and nuclei staining steps. Slides were then stored in PBS-T, overnight, at 4°C, in the dark.

scan_protocol: The following day, slides and consumables were loaded onto the Xenium Analyzer instrument according to the Xenium Analyzer (10X Genomics, CG000584, version Rev B) protocol. The whole slide area was selected for probe decoding and image acquisition, and the run was initiated.

data_processing:
The Xenium bundles were segmented with Xenium Ranger 1.7.1.1, with the expansion distance around nuclei set to 5 µm.
Raw data resulting from Xenium run, segmented with 5 micrometer expansion distance, without re-segmentation or processing by Proseg. Seurat object contains results after first re-segmenting with Proseg.

label: Xenium Mouse Probe Set

molecule: total RNA

organism: Mus musculus

source_name: Renal tumor

label_protocol: The slides were processed, over a two-day span, as per the Xenium In Situ for FFPE – Deparaffinization and Decrosslinking (10X Genomics, CG000580 version Rev C) and Xenium In Situ Gene Expression (10X Genomics, CG000582 version Rev C) protocols. On day one, slides were incubated at 60°C for 2 h on a Xenium thermocycler adaptor plate (BioRad, C1000 Touch Thermocycler), followed by deparaffinized through a series of immersions in xylene, 100%, 96% and 70% ethanol, and rehydration with nuclease-free water. Slides were assembled into Xenium cassettes for all downstream steps, starting with decrosslinking and permeabilization.

extract_protocol: Tissue sections were prepared as per the Xenium In Situ for FFPE – Tissue Preparation Guide (10X Genomics, CG000578 version Rev C) protocol. 5 μm sections were cut and mounted onto the Sample Area of a Xenium slide. The slides were air dried, followed by 3 h incubation at 42°C.

treatment_protocol: Mice were injected intraperitoneally with tamoxifen (dose: 1 mg/kg, 5 consecutive days for mice > 3 weeks old; 2 mg/kg, 3 consecutive days for mice <2 weeks old). The cohort received a tamoxifen injection within first 2 months of birth (<=61 days).

value: Renal tumor

tag: histology

value: Sarcoma

tag: genotype

tag: group

value: HDT tumor

tag: Sex

value: M

tag: days after tamoxifen injection

tag: tma core id

tag: tma core map


title: S68_HiGated_Ruc_24h


title: IMAS_2

city: Miami

first: Matthew

last: Tolerico

state: FL

address: 1580 NW 10th Ave

institute: University of Miami

description:
Library name: IMAS 2
IMWT_vs_IMAS_results.xlsx

data_processing:
Total RNA was quantified and qualified using the Nugen Universal Plus mRNA-Seq (M01442 v2) to have an RNA integrity score (RIN) above 7.
The quality of the reads was determined with FASTQC software for per base sequence quality, duplication rates, and overrepresented k-mers
Illumina adapters were trimmed from the ends of the reads using Trim Galore! package.
Gene count quantification for total RNA was performed using the GeneCounts function within STAR against the GENCODE vM35 transcript file.Gene count data were input into edgeR software for differential expression analysis, and gene counts were normalized against total aligned reads for each sample to generate counts per million (cpm) expression value for each gene in each sample.
Assembly: mm39
Supplementary files format and content: xlxs format with fold change and p values and raw counts

source_name: Col4a3-/- podocytes

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 1.5ug of total RNA was used to construct the sequencing libraries.
Total RNA was prepared with the Nugen Universal Plus mRNA-Seq (M01442 v2) using 100ng via Qubit and 15 cycles PCR.

value: Col4a3-/- podocytes

value: Vehicle


title: D4 ATAC 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_4_atac


title: S67_LoGated_Ruc_24h


title: D4 RNA 15h

description:
includes D0 spike-in resting control
act_15_set_4_rna

library_source: transcriptomic single cell

molecule: nuclear RNA


title: D4 RNA 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_4_rna


title: HDT340_kidney_1_tumor_b


title: D4 RNA 5h

description:
includes D0 spike-in resting control
act_5_set_4_rna


title: IMAS_3

description:
Library name: IMAS 3
IMWT_vs_IMAS_results.xlsx


title: HDT366_kidney_2_tumor

value: F


title: S66_UnGated_Ruc_24h

value: Un


title: D4 ATAC 0h

description:
includes D0 spike-in resting control
rest_set_4_atac

value: resting


title: S65_UnGated_Ruc_24h


title: IMWT_3

description:
Library name: IMWT 3
IMWT_vs_IMAS_results.xlsx

source_name: Col4a3+/+ podocytes

value: Col4a3+/+ podocytes


title: S70_HiGated_Ruc_24h

value: Hi


title: HDT365_kidney_1_tumor


title: S63_UnGated_Veh_24h

value: Veh


title: D3 ATAC 15h

description:
includes D0 spike-in resting control
act_15_set_3_atac

value: human lymphocytes

value: primary


title: HDT375_kidney_2_tumor_a


title: D4 RNA 0h

description:
includes D0 spike-in resting control
rest_set_4_rna

value: effector enriched CD4 T


title: IMWT_1

description:
Library name: IMWT 1
IMWT_vs_IMAS_results.xlsx


title: D3 RNA 15h

description:
includes D0 spike-in resting control
act_15_set_3_rna

value: aCD3/CD28 activated


title: S62_UnGated_Veh_24h


title: P10_GF, HTO

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: F10738_FB

library_source: other

data_processing:
Sequencing was performed on NovaSeq X Plus platform in 151+151 base paired-end mode.
Illumina Real Time Analysis RTA4 v4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-9.0.1, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: GRCm39-2024-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Library strategy: CITE-seq

molecule: protein

source_name: small intestine epithelium

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides (HTO) or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v3 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: small intestine epithelium

value: tissue

value: wildtype

tag: developmental stage

value: postnatal day 10

tag: microbiota status

value: Germ-Free

tag: library type

value: HTO

tag: hto

value: TotalSeq-C0304 anti-mouse Hashtag 4 (Sample No.7); TotalSeq-C0302 anti-mouse Hashtag 2 (Sample No.5); TotalSeq-C0303 anti-mouse Hashtag 3 (Sample No.6);


title: S61_UnGated_Veh_24h

tag: cell line


title: IMWT_2

description:
Library name: IMWT 2
IMWT_vs_IMAS_results.xlsx

value: Vehicle


title: IMAS_1

description:
Library name: IMAS 1
IMWT_vs_IMAS_results.xlsx

value: Col4a3-/- podocytes


title: S64_UnGated_Ruc_24h

value: Un

value: Ruc


title: P10_GF, GEX

description: Library name: F10738_GEX

tag: tissue

tag: cell type

value: mRNA


title: HDT340_kidney_1_tumor_a

value: Renal tumor

value: Sarcoma

value: HDT tumor

value: M


title: HDT361_kidney_1_tumor_a


title: D3 ATAC 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_3_atac

value: human lymphocytes

value: primary

value: effector enriched CD4 T

tag: timepoint

tag: treatment

value: aCD3/CD28 activated


title: D3 ATAC 5h

description:
includes D0 spike-in resting control
act_5_set_3_atac


title: P10_SPF, HTO

description: Library name: F10699_FB

value: small intestine epithelium

value: tissue

value: wildtype

value: postnatal day 10

value: Specific-Pathogen-Free

value: TotalSeq-C0301 anti-mouse Hashtag 1 (Sample No.1); TotalSeq-C0302 anti-mouse Hashtag 2 (Sample No.2); TotalSeq-C0303 anti-mouse Hashtag 3 (Sample No.3)


title: D3 RNA 5h

description:
includes D0 spike-in resting control
act_5_set_3_rna


title: HDT563_kidney_1_tumor


title: HDT375_kidney_1_tumor

value: F


title: P10_SPF, GEX

description: Library name: F10699_GEX


title: S59_LoGated_Ruc_2h

tag: facs gate

value: Lo

value: Ruc

tag: replicate


title: S60_HiGated_Ruc_2h

value: Hi


title: S58_HiGated_Ruc_2h


title: HDT339_kidney_1_tumor

value: Renal tumor

tag: histology

value: Low-grade mesenchymal neoplasm

tag: genotype


title: P24_GF, HTO

description: Library name: F10674_FB

value: postnatal day 24

value: Germ-Free

value: HTO

value: TotalSeq-C0301 anti-mouse Hashtag 1 (Sample No.13); TotalSeq-C0302 anti-mouse Hashtag 2 (Sample No.14); TotalSeq-C0303 anti-mouse Hashtag 3 (Sample No.15)


title: D3 ATAC 0h

description:
includes D0 spike-in resting control
rest_set_3_atac

value: human lymphocytes

value: primary

value: effector enriched CD4 T

value: resting


title: D3 RNA 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_3_rna

value: aCD3/CD28 activated


title: HDT300_kidney_2_tumor

value: Sarcoma

tag: group

value: HDT tumor

tag: Sex

value: M


title: S56_HiGated_Ruc_2h


title: S57_LoGated_Ruc_2h

value: Lo


title: D3 RNA 0h

description:
includes D0 spike-in resting control
rest_set_3_rna


title: HDT491_kidney_1

source_name: Kidney

value: Kidney

value: Non-neoplastic kidney

tag: days after tamoxifen injection

tag: tma core id


title: HDT366_kidney_1_tumor

value: Renal tumor

value: F

tag: tma core map


title: D2 ATAC 15h

description:
includes D0 spike-in resting control
act_15_set_2_atac


title: P24_SPF, GEX

description: Library name: F10628_GEX

value: small intestine epithelium

value: tissue

value: wildtype

tag: developmental stage

value: postnatal day 24

tag: microbiota status

value: Specific-Pathogen-Free

value: mRNA


title: P24_GF, GEX

description: Library name: F10674_GEX

value: Germ-Free

tag: library type


title: S54_UnGated_Ruc_2h

tag: cell line

value: Un

value: Ruc


title: S55_LoGated_Ruc_2h


title: P24_SPF, HTO

description: Library name: F10628_FB

tag: tissue

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 (Sample No.9); TotalSeq-C0302 anti-mouse Hashtag 2 (Sample No.10); TotalSeq-C0303 anti-mouse Hashtag 3 (Sample No.11)


title: D2 RNA 15h

description:
includes D0 spike-in resting control
act_15_set_2_rna

value: human lymphocytes

value: primary

tag: cell type

value: effector enriched CD4 T

tag: timepoint

value: aCD3/CD28 activated


title: HDT569_kidney_1

value: Kidney

value: Non-neoplastic kidney

value: HDT tumor

value: M


title: HDT298_kidney_1_tumor

value: Renal tumor

value: Low-grade mesenchymal neoplasm

value: F


title: D2 ATAC 5h

description:
includes D0 spike-in resting control
act_5_set_2_atac

tag: treatment


title: S53_UnGated_Ruc_2h

tag: facs gate

tag: replicate


title: female liver, LKO, 20-22month, biorep4

city: Birmingham

first: Alexander

middle: Tate

last: Lasher

state: AL

address: 902 14th St S

department: Biology

institute: University of Alabama at Birmingham

description:
Library name: D5
colname: ../starAligned/D5/Aligned.sortedByCoord.out.bam

data_processing:
Raw reads were aligned to the mouse genome using this index with STAR (v 2.7.1a) and the following options: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Gene level read counting was carried out using subread (v2.0.6) featureCounts with the following options: -p -s 2
Assembly: GRCm39
Supplementary files format and content: tab delimeted file containing gene level counts for all samples calculated using subread featureCounts.

source_name: female liver

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy Plus Mini Kit following the manufacturer protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: female liver

tag: genotype

value: LKO


title: HDT558_kidney_2

tag: histology

tag: group


title: female liver, LKO, 20-22month, biorep2

description:
Library name: D2
colname: ../starAligned/D2/Aligned.sortedByCoord.out.bam


title: S52_UnGated_Ruc_2h

value: Un


title: female liver, LKO, 20-22month, biorep1

description:
Library name: D1
colname: ../starAligned/D1/Aligned.sortedByCoord.out.bam


title: HDT361_kidney_2

tag: Sex

tag: days after tamoxifen injection


title: female liver, LKO, 20-22month, biorep3

description:
Library name: D4
colname: ../starAligned/D4/Aligned.sortedByCoord.out.bam


title: female liver, CRE-, 20-22month, biorep4

description:
Library name: C4
colname: ../starAligned/C4/Aligned.sortedByCoord.out.bam

value: CRE-


title: D2 ATAC 0h

description:
includes D0 spike-in resting control
rest_set_2_atac

value: resting


title: female liver, CRE-, 20-22month, biorep3

description:
Library name: C3
colname: ../starAligned/C3/Aligned.sortedByCoord.out.bam


title: D2 RNA 5h

description:
includes D0 spike-in resting control
act_5_set_2_rna


title: D2 RNA 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_2_rna


title: S49_UnGated_Veh_2h

value: Veh


title: D2 RNA 0h

description:
includes D0 spike-in resting control
rest_set_2_rna

value: human lymphocytes


title: S51_UnGated_Veh_2h


title: female liver, CRE-, 20-22month, biorep2

description:
Library name: C2
colname: ../starAligned/C2/Aligned.sortedByCoord.out.bam


title: S50_UnGated_Veh_2h


title: D2.ATAC 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_2_atac

value: primary


title: D1 ATAC 15h

description:
includes D0 spike-in resting control
act_15_set_1_atac

value: effector enriched CD4 T


title: HDT321_kidney_2

tag: tma core id

tag: tma core map


title: HDT348_kidney_1_tumor


title: HDT291_kidney_2


title: HDT546_kindey_2


title: HDT360_kidney_2


title: HDT340_kidney_2


title: male liver, LKO, 20-22month, biorep2

description:
Library name: B2
colname: ../starAligned/B2/Aligned.sortedByCoord.out.bam

source_name: male liver

value: male liver


title: S46_HiGated_Ruc_24h

value: Hi

value: Ruc


title: female liver, CRE-, 20-22month, biorep1

description:
Library name: C1
colname: ../starAligned/C1/Aligned.sortedByCoord.out.bam


title: D1 ATAC 5h

description:
includes D0 spike-in resting control
act_5_set_1_atac

value: aCD3/CD28 activated


title: male liver, LKO, 20-22month, biorep1

description:
Library name: B1
colname: ../starAligned/B1/Aligned.sortedByCoord.out.bam


title: S48_HiGated_Ruc_24h


title: S43_LoGated_Ruc_24h

value: Lo


title: HDT289_kidney_2

value: Kidney

value: Non-neoplastic kidney

value: contol


title: HDT294_kidney_1

value: M


title: D1 RNA 15h

description:
includes D0 spike-in resting control
act_15_set_1_rna


title: S47_LoGated_Ruc_24h


title: S45_LoGated_Ruc_24h


title: male liver, CRE-, 20-22month, biorep3

description:
Library name: A3
colname: ../starAligned/A3/Aligned.sortedByCoord.out.bam


title: HDT293_kidney_1


title: S44_HiGated_Ruc_24h


title: D1 RNA 5h

description:
includes D0 spike-in resting control
act_5_set_1_rna


title: male liver, LKO, 20-22month, biorep4

description:
Library name: B4
colname: ../starAligned/B4/Aligned.sortedByCoord.out.bam

value: LKO


title: S41_UnGated_Ruc_24h

value: Un


title: HDT289_kidney_1

value: F


title: D1 ATAC 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_1_atac


title: male liver, CRE-, 20-22month, biorep4

description:
Library name: A5
colname: ../starAligned/A5/Aligned.sortedByCoord.out.bam

value: CRE-


title: male liver, LKO, 20-22month, biorep3

description:
Library name: B3
colname: ../starAligned/B3/Aligned.sortedByCoord.out.bam


title: D1 ATAC 0h

description:
includes D0 spike-in resting control
rest_set_1_atac

value: resting


title: D1 RNA 0h

description:
includes D0 spike-in resting control
rest_set_1_rna

value: human lymphocytes


title: BAT EVs, day 28, Sham, rep 1

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description: Library name: MGCF_ACO_38_2_R63_Sham_S2

data_processing:
ACO_38 (miRNASeq): Read quality was assessed with FastQC. Adapter trimming and quality filtering were performed using Cutadapt (v4.1) to remove adapters, poly-A sequences, and bases with Phred scores <28; reads shorter than 18 nt were discarded. Identical reads were collapsed using mapper.pl (miRDeep2 v2.0.1.2) and aligned to the Rattus norvegicus GRCr8 genome (Ensembl v115). miRNAs were identified and novel candidates predicted using miRDeep2. miRNA read counts were extracted and compiled into a count matrix for DESeq2-based normalization and differential expression analysis. miRNAs with FDR-adjusted p ≤ 0.05 were considered significant.
Assembly: ACO_38 (miRNASeq): GRCr8
Supplementary files format and content: csv file (ACO-38)  raw counts for each sample

organism: Rattus norvegicus

source_name: BAT EVs

extract_protocol:
ACO_38 (miRNASeq): RNA was extracted with NORGEN Biotek Exosomal RNA Isolation Kit.
ACO_38 (miRNASeq):  Illumina NextSeq™ 2000 P4 XLEAP-SBS™ Reagent Kit (50 Cycles).

value: BAT EVs

value: Sprague-Dawley

value: Sham

tag: time

value: day 28


title: S42_UnGated_Ruc_24h

value: Ruc


title: D1 RNA 2.5h

description:
includes D0 spike-in resting control
act_2.5_set_1_rna

value: primary

value: effector enriched CD4 T

value: aCD3/CD28 activated


title: S39_UnGated_Veh_24h

value: Veh


title: male liver, CRE-, 20-22month, biorep2

description:
Library name: A2
colname: ../starAligned/A2/Aligned.sortedByCoord.out.bam

value: male liver


title: BAT EVs, day 28, BATsx+Leptin, rep 4

description: Library name: MGCF_ACO_38_9_R132_BATsx_plus_Leptin_S8

value: BAT denervation (BATsx) + Leptin


title: S40_UnGated_Ruc_24h


title: Loucy  ZMIZ1  hairpin knockdown -L15 4

city: Ann Arbor

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: paired-end sample

data_processing:
University of Michigan Bioinformatics Core RNA-seq Pipeline "Watermelon" version 2.3.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3
Trimmed sequence reads were mapped to GRCh38 (ENSEMBL), using STAR v2.7.8a
rlog normalization was performed using DESeq2 (Love et al., 2014)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counds for each sample

source_name: Loucy T lymphoblast cell line

growth_protocol: LOUCY cells were grown in RPMI 1640 (Invitrogen) supplemented with 20% fetal bovine serum (Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Whole RNA was extracted from 1-3 million cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
For creating MYB knockdown libraries, sequencing libraries were prepped with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs #E7490L) and xGen Broad-range RNA Library Prep (IDT #10010145). For ZMIZ1 knockdown libraries, sequencing libraries were prepped with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs #E7490L) and NEBNext Ultra II Directional RNA (New England Biolabs #E7760L) .
% of a NovaSeq S4 2x150 with strand-specific settings

treatment_protocol: LOUCY cells were lentivirally transduced with pLKO.1-based shRNA. Two days later the cells were selected in 0.5-1 ug/ml puromycin. Two days later, the cells were harvested.

value: Loucy T lymphoblast cell line

value: T- cell acute lymphoblastic leukemia

value: short hairpin RNAs shZMIZ1-15

tag: rep/culture

tag: batch


title: BAT EVs, day 28, Sham, rep 2

description: Library name: MGCF_ACO_38_3_R64_Sham_S3

tag: tissue


title: BAT EVs, day 28, BATsx+Leptin, rep 3

description: Library name: MGCF_ACO_38_18_R176_BATsx_plus_Leptin_S16


title: S38_UnGated_Veh_24h

tag: cell line

value: Un


title: Loucy  ZMIZ1  hairpin knockdown -L13 4

description: paired-end sample

tag: cell type

value: short hairpin RNAs shZMIZ1-13


title: P10_GF

description: Library name: GA94465

data_processing:
Sequencing was performed on  NovaSeq X Plus platform in a 101+101 or 151+151 base paired-end mode.
Illumina Real Time Analysis v4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-9.0.1, 10x Genomics) for UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene and cell (barcode) combination

source_name: small intestinal epithelium

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Single Cell 5' Reagent Kits v3 User Guide.

value: small intestinal epithelium

tag: developmental stage

value: neonate

value: GF


title: S36_HiGated_Ruc_2h

value: Hi

tag: treatment

tag: timepoint


title: BAT EVs, day 28, BATsx+Leptin, rep 2

description: Library name: MGCF_ACO_38_15_R169_BATsx_plus_Leptin_S13

value: BAT EVs

value: Sprague-Dawley

value: day 28


title: P10_SPF

description: Library name: GA93745

value: SPF


title: P24_GF

description: Library name: GA93217

value: juvenile


title: Loucy  ZMIZ1  hairpin knockdown -L15 3

description: paired-end sample


title: 20250129_P24SPF

description: Library name: GA92216


title: Loucy  hairpin nontargeting control 4

description: paired-end sample

value: shControl

value: control hairpin


title: male liver, CRE-, 20-22month, biorep1

description:
Library name: A1
colname: ../starAligned/A1/Aligned.sortedByCoord.out.bam

value: male liver

value: CRE-


title: S35_LoGated_Ruc_2h

tag: facs gate

value: Lo

value: Ruc

tag: replicate


title: Loucy  ZMIZ1  hairpin knockdown -L13 3

description: paired-end sample

value: Loucy T lymphoblast cell line

value: T- cell acute lymphoblastic leukemia

tag: genotype


title: Loucy  hairpin nontargeting control 3

description: paired-end sample


title: BAT EVs, day 28, intactBAT+Vehicle, rep 4

description: Library name: MGCF_ACO_38_16_R171_intact_BAT_plus_Vehicle_S14

value: Intact BAT + Vehicle


title: S34_HiGated_Ruc_2h


title: S37_UnGated_Veh_24h

value: Un

value: Veh


title: Loucy  ZMIZ1  hairpin knockdown -L13 2

description: paired-end sample

value: short hairpin RNAs shZMIZ1-13


title: S33_LoGated_Ruc_2h


title: BAT EVs, day 28, BATsx+Leptin, rep 1

description: Library name: MGCF_ACO_38_13_R159_BATsx_plus_Leptin_S12

value: BAT EVs

value: BAT denervation (BATsx) + Leptin


title: SSO+GSI BR3

city: Paris

first: Arndt

middle: Gerhard

last: Benecke

address: 7 quai Saint Bernard

department: Centre of Neurosciences of Sorbonne Université (Neuro-SU)

country: France

institute: Centre National de la Recherche Scientifique

description: SSO+GSI treated HelA cells

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit (P/N 433962)

scan_protocol: Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B)

data_processing: The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement.

label: chemiluminescence

source_name: HeLa cell-line

label_protocol: Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715)

growth_protocol: HeLa cells were grown in DMEM (Dulbecco’s Modified Eagle Medium) containing 2.5% CS (calf serum) and 2.5% FCS (foetal calf serum).

extract_protocol: Quiagen

treatment_protocol: GSI: 15µM in DMSO for 19h; SSO-TAF6delta 100nM using lipofectamine 2000 according to Delannoy A et al. (2018) Cell Death Dis. Jan 22;9(2):70 for 18h.

value: SSO TAF6delta + gamma secretase inhibitor


title: Loucy  ZMIZ1  hairpin knockdown -L15 2

description: paired-end sample

value: short hairpin RNAs shZMIZ1-15


title: BAT EVs, day 28, intactBAT+Vehicle, rep 3

description: Library name: MGCF_ACO_38_12_R138_intact_BAT_plus_Vehicle_S11

value: Sprague-Dawley

value: day 28


title: SSO+GSI BR2

description: SSO+GSI treated HelA cells


title: SSO+GSI BR4

description: SSO+GSI treated HelA cells


title: Loucy  hairpin nontargeting control 2

description: paired-end sample

value: shControl

value: control hairpin


title: BAT EVs, day 28, intactBAT+Vehicle, rep 5

description: Library name: MGCF_ACO_38_7_R125_intact_BAT_plus_Vehicle_S7


title: BAT EVs, day 28, intactBAT+Vehicle, rep 2

description: Library name: MGCF_ACO_38_11_R136_intact_BAT_plus_Vehicle_S10


title: Loucy  ZMIZ1  hairpin knockdown -L15 1

description: paired-end sample


title: S32_HiGated_Ruc_2h

value: Hi


title: SSO TAF6d alone BR 3

description: SSO TAF6delta treted HeLa cells

value: SSO TAF6delta


title: S31_LoGated_Ruc_2h

value: Lo

value: Ruc


title: S30_UnGated_Ruc_2h


title: BAT EVs, day 28, intactBAT+Vehicle, rep 1

description: Library name: MGCF_ACO_38_10_R135_intact_BAT_plus_Vehicle_S9

value: Intact BAT + Leptin


title: BAT EVs, day 28, intactBAT+Leptin, rep 5

description: Library name: MGCF_ACO_38_6_R124_intact_BAT_plus_Leptin_S6


title: SSO TAF6d alone BR 4

description: SSO TAF6delta treted HeLa cells


title: Loucy  hairpin nontargeting control 1

description: paired-end sample

value: Loucy T lymphoblast cell line

value: T- cell acute lymphoblastic leukemia


title: S29_UnGated_Ruc_2h

value: Un


title: Loucy  ZMIZ1  hairpin knockdown -L13 1

description: paired-end sample

value: short hairpin RNAs shZMIZ1-13


title: S28_UnGated_Ruc_2h


title: Loucy MYB KD 4

description: paired-end sample

value: MYB knockdown


title: BAT EVs, day 28, intactBAT+Leptin, rep 4

description: Library name: MGCF_ACO_38_5_R120_intact_BAT_plus_Leptin_S5

value: BAT EVs


title: Loucy shcontrol 4

description: paired-end sample

value: Control


title: GSI tretment alone BR 2

description: GSI tretaed HeLa cells

value: gamma secretase inhibitor


title: BAT EVs, day 28, intactBAT+Leptin, rep 3

description: Library name: MGCF_ACO_38_4_R78_intact_BAT_plus_Leptin_S4

value: Sprague-Dawley


title: Loucy MYB KD 3

description: paired-end sample


title: SSO TAF6d alone BR 2

description: SSO TAF6delta treted HeLa cells


title: GSI tretment alone BR 1

description: GSI tretaed HeLa cells


title: BAT EVs, day 28, intactBAT+Leptin, rep 1

description: Library name: MGCF_ACO_38_1_R61_intact_BAT_plus_Leptin_S1

value: day 28


title: S26_UnGated_Veh_2h

value: Veh


title: Loucy shcontrol 3

description: paired-end sample


title: Loucy MYB KD 2

description: paired-end sample


title: S25_UnGated_Veh_2h


title: GSI tretment alone BR 4

description: GSI tretaed HeLa cells


title: S23_LoGated_Ruc_24h


title: S27_UnGated_Veh_2h


title: Loucy shcontrol 2

description: paired-end sample


title: BAT EVs, day 28, intactBAT+Leptin, rep 2

description: Library name: MGCF_ACO_38_17_R174_intact_BAT_plus_Leptin_S15


title: Heart septum, day 28, BATsx+Leptin, rep 4

description: Library name: 22_Rat132_BATsx_Leptin_S22

data_processing:
P1539 (mRNASeq):   Reads were aligned to the rat genome (mRatBN7) using STAR (v2.7.10a) with default parameters, and uniquely mapped reads were retained. Gene-level counts were generated with featureCounts (v2.0.2). Genes with low expression (<10 counts) were filtered, and normalization and differential expression analysis were performed in DESeq2 (R v4.4.1). Genes with FDR-adjusted p ≤ 0.05 were considered significant.
Assembly: P1539 (mRNASeq): mRatBN7
Supplementary files format and content: txt file (P1539) including raw counts for each sample

source_name: Septum

extract_protocol:
P1539 (mRNASeq): RNA was extracted with the PureLink RNA Mini Kit;
P1539 (mRNASeq): Illumina NextSeq™ 2000 P3 XLEAP-SBS™ Reagent Kit (2 × 100 bp paired-end)

value: Septum

value: BAT denervation (BATsx) + Leptin


title: Control DMSO BR 2

description: DMSO treated HeLa cells


title: Heart septum, day 28, BATsx+Leptin, rep 6

description: Library name: 24_Rat177_BATsx_Leptin_S24


title: Heart septum, day 28, BATsx+Leptin, rep 5

description: Library name: 23_Rat176_BATsx_Leptin_S23


title: Heart septum, day 28, BATsx+Leptin, rep 3

description: Library name: 21_Rat101_BATsx_Leptin_S21


title: Control DMSO BR 3

description: DMSO treated HeLa cells


title: Control DMSO BR 1

description: DMSO treated HeLa cells


title: Loucy shcontrol 1

description: paired-end sample

source_name: Cell Line

value: Cell Line


title: S21_LoGated_Ruc_24h

value: Lo


title: Heart septum, day 28, BATsx+Leptin, rep 2

description: Library name: 20_Rat71_BATsx_Leptin_S20


title: lcs7_0.3Ca, biological rep3

city: Hangzhou

first: Zhihang

last: Feng

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388,Zhejiang Province,P.R.China

country: China

institute: Zhejiang University

description: Gene expression data from 14-day old Arabidopsis shoot tissue under 0.3 mM Ca

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: After reading CEL file and normalization using robust multiarray average using R package oligo (v 1.32.0), the rank products method was performed by using the R package RankProd (v 3.30.0).

label: biotin

organism: Arabidopsis thaliana

source_name: lcs7 grown on 0.3 mM Ca medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were sterilized with 10% NaClO and 1/200 (v/v) detergent followed by 4~5 times washing with sterilized ultra-pure water. After soaking in sterilized ultra-pure water and keeping at 4°C for 2 days in the dark, seeds were sown on 1.5% agar solidified Yamagami medium supplied with 1% sucrose (pH 5.5 adjusted with K2HPO4). plates were vertically positioned in a growth chamber under a 16/8-h light-dark cycle at 22°C.

extract_protocol: Total RNA was prepared from the samples using a RNeasy Plant Mini kit (Qiagen, Valencia, CA, USA) and was treated with RNase-free DNase (Qiagen).

treatment_protocol: Shoot tissue of 14-day old seedlings were collected and immediately freezed in liquid nitrogen. Samples were stored in -80°C freezer before RNA extraction.

value: Shoot

tag: ecotype

tag: agent

value: 0.3 mM Ca

tag: age


title: S20_HiGated_Ruc_24h

value: Hi

value: Ruc


title: Loucy MYB KD 1

description: paired-end sample

value: Loucy T lymphoblast cell line

value: T- cell acute lymphoblastic leukemia


title: S19_LoGated_Ruc_24h


title: CL2

city: Vernon Hills

first: DONGPING

last: WANG

state: IL

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

data_processing:
Based on gene annotation information, reads were mapped into genome resulting as a compressed binary version of the Sequence Alignment Map (BAM files).
To determine the transcriptional abundance for each gene, the number of reads that mapped within each annotated coding sequence (CDS) was determined.
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data, and mean RPKM values were determined for both the control and treatment samples.
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: RPKM

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas cells_clay minerals

growth_protocol: P. aeruginosa PAO1 were started from single colonies located on LB agar plates. All cultures were grown at 37˚C in static plates to an approximate OD600 = 1.2.

extract_protocol:
RNA extraction was performed using Qiagen RNA extraction kit
RNA-Seq analysis was performed at Otogenetics, Atlanta, GA. Strand-specific cDNA libraries were constructed using Illumina TruSeq RNA Sample Preparation Kits.

treatment_protocol: For clay treatment, 2.5 mg Mound clay was added to bacterial cultures at an OD600 of 0.3.

tag: sample type

value: bacterial cultures

value: 2.5 mg Mound clay


title: Heart septum, day 28, BATx+Leptin, rep 6

description: Library name: 18_Rat186_BATx_Leptin_S18

value: BAT ablation (BATx) + Leptin


title: CL1


title: S22_HiGated_Ruc_24h


title: Col-0_0.3Ca, biological rep3

source_name: Col-0 grown on 0.3 mM Ca medium

value: wildtype


title: lcs7_0.3Ca, biological rep2


title: Col-0_0.3Ca, biological rep2


title: S17_UnGated_Ruc_24h

value: Un


title: WT3

source_name: Pseudomonas cells_control

value: none (control)


title: Heart septum, day 28, BATsx+Leptin, rep 1

description: Library name: 19_Rat53_BATsx_Leptin_S19

value: Sprague-Dawley

value: day 28


title: WT2


title: S18_UnGated_Ruc_24h


title: Heart septum, day 28, BATx+Leptin, rep 3

description: Library name: 15_Rat152_BATx_Leptin_S15

value: Septum


title: Heart septum, day 28, BATx+Leptin, rep 5

description: Library name: 17_Rat164_BATx_Leptin_S17


title: lcs7_0.3Ca, biological rep1


title: Heart septum, day 28, BATx+Leptin, rep 4

description: Library name: 16_Rat157_BATx_Leptin_S16


title: S14_UnGated_Veh_24h

value: Veh


title: S15_UnGated_Veh_24h


title: lcs7_2Ca, biological rep3

description: Gene expression data from 14-day old Arabidopsis shoot tissue under 2 mM Ca

source_name: lcs7 grown on 2 mM Ca medium

value: 2 mM Ca


title: Heart septum, day 28, BATx+Leptin, rep 2

description: Library name: 14_Rat148_BATx_Leptin_S14


title: Liver, WHV infection, TLH, rep 8

city: Toronto

first: Zoe

middle: Alixandra

last: Clarke

state: Ontario

address: 27 King's College Cir

department: Molecular Genetics

institute: University of Toronto

description:
Library name: L9666_TLH
Adult female, sampled in 2018

data_processing:
Cell Ranger (v.5.0.0) followed by standard Seurat protocol using SCTransform normalisation and DropletQC filtering.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS file of integrated Seurat objects

organism: Marmota monax

source_name: Liver

growth_protocol: scRNA-seq was performed on freshly isolated liver cells from woodchucks with a woodchuck hepatitis virus (WHV) infection; cells were never cultured.

extract_protocol:
Woodchuck livers were dissociated according to a previously described 2-step collagenase perfusion protocol https://doi.org/10.1038/s41467-018-06318-7.
Single-cell samples were sequenced with 10X Genomics SingleCell 3' v2 chemistry according to manufacturer's instructions.

value: Liver

value: Outbred

value: Liver cells

value: WHV infection

value: paired-end


title: Col-0_0.3Ca, biological rep1

value: Shoot

value: 0.3 mM Ca


title: S13_UnGated_Veh_24h


title: lcs7_2Ca, biological rep1


title: S24_HiGated_Ruc_24h

value: Hi

value: Ruc


title: WT1

value: bacterial cultures


title: S16_UnGated_Ruc_24h

value: Un


title: Liver, WHV infection, TLH, rep 7

description:
Library name: L9649_TLH
Adult male, sampled in 2018


title: S11_LoGated_Ruc_2h

value: Lo


title: Heart septum, day 28, BATx+Leptin, rep 1

description: Library name: 13_Rat95_BATx_Leptin_S13

value: Sprague-Dawley

value: BAT ablation (BATx) + Leptin


title: Heart septum, day 28, intactBAT+Vehicle, rep 4

description: Library name: 10_Rat168_intactBAT_Vehicle_S10

value: Septum

value: Intact BAT + Vehicle

value: day 28


title: S12_HiGated_Ruc_2h


title: Liver, WHV infection, PBMC, rep 7

description:
Library name: L9649_PBMC
Adult male, sampled in 2018

source_name: PBMC

value: PBMC

value: PBMCs


title: lcs7_2Ca, biological rep2

value: 2 mM Ca


title: CAM

city: Sherbrooke

first: Alexis

last: Perreault

state: Quebec

address: 3001 12e avenue Nord

institute: Université de Sherbrooke

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: CAM

data_processing:
The resulting libraries underwent a total of 11 amplification cycles and were purified using 0.9X Ampure XP beads (Beckman Boulter, Mississauga, ON, Canada, cat#A63881).
Quality and size of fragments were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada).
Libraries were then quantified with a Qubit fluorometer (Thermo Fisher Scientific, Mississauga, ON, Canada, cat#Q32866), pooled at equimolar concentrations, diluted to 1.8 pM, and sequenced on an Illumina NextSeq 500 (illumina, San Diego, CA, USA, cat#SY-515-1001) using the NextSeq 500/550 High Output Kit v2.5 (75 cycles) (illumina, cat#20024907) with a 2 × 43 bp paired-end run configuration. RNA preparation and sequencing were performed by the Plateforme RNomique de l’Université de Sherbrooke.
Reads were trimmed using Trimmomatic, and their quality was assessed using FastQC22. Kallisto was used to pseudo-align the reads to the transcriptome and quantify transcript abundance23.
A combined transcriptome reference was generated using gffread from Ensembl v109 annotations and genome file for the human genome (GRCh38)24. Transcript- level abundances were summarized to gene-level counts using the tximport package25.
Assembly: Human genome (GRCh38)24
Supplementary files format and content: tab-delimited text file (raw_counts_All_Samples.txt) includes raw counts for all samples

organism: Gallus gallus

source_name: chick chorioallantoic membrane_host

extract_protocol:
Tissue xenografts extracted from the CAMs were homogenized using a mortar and pestle in liquid nitrogen. Total RNA was isolated using the RNeasy® Mini Kit (Qiagen, Mississauga, ON, Canada, cat#74106) in accordance with the manufacturer’s instructions. Each RNA-seq library was generated from 500 ng of total RNA free of genomic DNA.
RNA libraries were prepared using the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Whitby, ON, Canada, cat#E7760S), following the manufacturer's protocol in combination with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, cat#E7490). The resulting libraries underwent a total of 11 amplification cycles and were purified using 0.9X Ampure XP beads (Beckman Boulter, Mississauga, ON, Canada, cat#A63881).

value: chick chorioallantoic membrane_host


title: Liver, WHV infection, PBMC, rep 8

description:
Library name: L9666_PBMC
Adult female, sampled in 2018

value: Outbred

value: WHV infection

value: paired-end


title: Col-0_2Ca, biological rep1

source_name: Col-0 grown on 2 mM Ca medium

value: Shoot

value: wildtype


title: Heart septum, day 28, intactBAT+Vehicle, rep 3

description: Library name: 9_Rat135_intactBAT_Vehicle_S9


title: Heart septum, day 28, intactBAT+Vehicle, rep 5

description: Library name: 11_Rat169_intactBAT_Vehicle_S11


title: S9_LoGated_Ruc_2h

value: Ruc


title: S10_HiGated_Ruc_2h

value: Hi


title: Heart septum, day 28, intactBAT+Vehicle, rep 2

description: Library name: 8_Rat40_intactBAT_Vehicle_S8


title: Liver, WHV infection, PBMC, rep 6

description:
Library name: L9648_PBMC
Adult female, sampled in 2018


title: Liver, WHV infection, PBMC, rep 5

description:
Library name: L9647_PBMC
Adult male, sampled in 2018


title: Upcyte hepatocytes treated with OP 2:1 0,6 mM biological replicate 3

city: Valencia

first: Ramiro

middle: Jover

last: Atienza

state: Valencia

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-8.11

hyb_protocol: The hybridization cocktail was heated at 99° for 5 minutes followed by 45° for 5 minutes and then centrifuged at max speed for 1 minute. 80µL were transferred to each array. Genechip array was incubated overnight at 45°C while rotating in a Hybridization Oven 645 (Affymetrix). After 16h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station 450, according to the FS450_0007 protocol.

scan_protocol: The distribution of fluorescent signals on the array was obtained using GeneChip Scanner 3000 7G (Affymetrix). GeneChip Operating Software (Affymetrix) was used to generate the CEL files

data_processing:
The data were normalized using the RMA method, and probes were summarized using the revised entrez-based probe annotation. A probe-filtering step excluding those probes that show a lower coefficient of variation, low intensity levels in all observations or that are non-informative (not annotated) was employed. Differential expression analysis was assessed using linear models for microarray data based on empirical Bayes moderated t-statistics for all filtered probe sets. To correct for multiple testing, the false discovery rate was estimated from p-values derived from the moderated t-statistics using the method of Benjamini and Hochberg. The data were also analyzed with Transcriptome Analysis Console version 4.0.2 (TAC 4.0.2) using Affymetrix default analysis settings.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: Upcyte Hepatocytes

label_protocol: The fragmented biotinylated cRNA, using WT Terminal Labeling Kit (Affymetrix), derived from 300 ng of total RNA

growth_protocol: Upcyte hepatocytes were seeded in culture medium obtained from upcyte technologies (ClinicSciences Group) at a density of 5,000 cells/cm2 in collagen-type I-coated flasks (Corning, New York) and were maintained until 80% confluence. Medium was replaced every 2 days. Cells were subcultured with 0.25% trypsin/0.02% EDTA (Gibco BRL, Paisley, Scotland) and were seeded at a density of 70,000 cells/cm2 in collagen-type I precoated 12-well plates in culture medium. After 4-5h, medium wasreplaced with a high-performance medium, also obtained from upcyte technologies (ClinicSciences Group).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Three or four days after seeding, cells were preincubated for 14 h with a 62 µM mixture of oleate and palmitate (2:1 ratio), followed by a change to fatty-acid–free medium containing different concentrations of VPA (CAS nº1069-66-5) or vehicle. To compare the lipogenic effect of VPA with that induced by fatty acids, some cells were incubated in parallel with 0.6 mM oleate: palmitate (O:P, 2:1 ratio).

value: Upcyte Hepatocytes Donor 422


title: S7_LoGated_Ruc_2h

value: Lo


title: S8_HiGated_Ruc_2h


title: Col-0_2Ca, biological rep2


title: Upcyte hepatocytes treated with PBS biological replicate 3

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-8.8

value: PBS


title: Liver, WHV infection, TLH, rep 5

description:
Library name: L9647_TLH
Adult male, sampled in 2018

value: Liver

value: Liver cells


title: Heart septum, day 28, intactBAT+Vehicle, rep 6

description: Library name: 12_Rat171_intactBAT_Vehicle_S12

value: Septum

value: Sprague-Dawley

value: Intact BAT + Vehicle

value: day 28


title: Liver, WHV infection, TLH, rep 4

description:
Library name: L9642_TLH
Adult male, sampled in 2018


title: S5_UnGated_Ruc_2h

value: Un


title: Liver, WHV infection, PBMC, rep 3

description:
Library name: L215_PBMC
Adult male, sampled in 2018

value: PBMC

value: Outbred

value: PBMCs


title: Heart septum, day 28, intactBAT+Leptin, rep 5

description: Library name: 5_Rat120_intactBAT_Leptin_S5

value: Intact BAT + Leptin


title: Liver, WHV infection, PBMC, rep 4

description:
Library name: L9642_PBMC
Adult male, sampled in 2018

value: WHV infection

value: paired-end


title: Liver, WHV infection, TLH, rep 6

description:
Library name: L9648_TLH
Adult female, sampled in 2018


title: S6_UnGated_Ruc_2h

value: Ruc


title: Upcyte hepatocytes treated with VPA 4 mM biological replicate 13

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-8.10

value: Upcyte Hepatocytes Donor 422

value: VPA 4 mM


title: Upcyte hepatocytes treated with VPA 4 mM biological replicate 2

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.11


title: Heart septum, day 28, intactBAT+Leptin, rep 4

description: Library name: 4_Rat56_intactBAT_Leptin_S4


title: S4_UnGated_Ruc_2h


title: Heart septum, day 28, intactBAT+Vehicle, rep 1

description: Library name: 7_Rat36_intactBAT_Vehicle_S7


title: Liver, WHV infection, PBMC, rep 2

description:
Library name: L211_PBMC
Adult female, sampled in 2018


title: S3_UnGated_Veh_2h

value: Veh


title: Upcyte hepatocytes treated with OP 2:1 0,6 mM biological replicate 2

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.12


title: Upcyte hepatocytes treated with PBS biological replicate 2

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.9

value: PBS


title: Heart septum, day 28, intactBAT+Leptin, rep 3

description: Library name: 3_Rat62_intactBAT_Leptin_S3


title: Heart septum, day 28, intactBAT+Leptin, rep 2

description: Library name: 2_Rat61_intactBAT_Leptin_S2


title: Liver, WHV infection, PBMC, rep 1

description:
Library name: L207_PBMC
Adult male, sampled in 2018


title: Heart septum, day 28, intactBAT+Leptin, rep 6

description: Library name: 6_Rat196_intactBAT_Leptin_S6


title: Upcyte hepatocytes treated with OP 2:1 0,6 mM biological replicate 1

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.4


title: Liver, WHV infection, spatial, rep 2

description:
Library name: L215_spatial_D1_VIS
Adult male, sampled in 2018

data_processing:
Space Ranger (v1.2.2) followed by standard Seurat protocol using SCTransform normalisation.
Assembly: Custom woodchuck genome and annotation. Available at https://doi.org/10.5281/zenodo.10855128.
Supplementary files format and content: Filtered data matrices from CellRanger outputs: gene expression matrices, feature lists, and barcode lists.
Supplementary files format and content: .RDS and .Rdata files of integrated Seurat objects
Library strategy: Spatial Transcriptomics

growth_protocol: Spatial transcriptomics data was fresh frozen.

extract_protocol:
Spatial transcriptomics was performed on 16-μM woodchuck liver tissue slices from fresh frozen OCT-embedded tissue of the L212 and L215 woodchucks following the protocol described in DOI: 10.1002/hep4.1854. Woodchuck L215 had a woodchuck hepatitis virus (WHV) infection.
Samples were sequenced with 10X Genomics Spatial 3' v1 chemistry according to manufacturer's instructions.

value: Liver

value: Liver cells

value: WHV Infection


title: Upcyte hepatocytes treated with VPA 4 mM biological replicate 1

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.3


title: Heart septum, day 28, intactBAT+Leptin, rep 1

description: Library name: 1_Rat60_intactBAT_Leptin_S1

value: Septum

value: Sprague-Dawley


title: Liver, WHV infection, spatial, rep 1

description:
Library name: L215_spatial_C1_VIS
Adult male, sampled in 2018


title: S1_UnGated_Veh_2h

value: Un


title: Col0, seedling, SD, biorep1, BSseq

status: Public on Jan 04 2026

city: Neuherberg

first: Martin

last: Groth

address: Ingolstädter Landstr. 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmholtz Munich

description: Library name: BSseq_WT_SD_rep1

library_source: genomic

data_processing:
BS-seq: Raw reads were pre-processed with trimmomatic using the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:1:30:12:3:true CROP:150 HEADCROP:3 (for standard)/12 (for PBAT libraries) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for PE150 reads and ILLUMINACLIP:TruSeq3-SE.fa:1:30:10 CROP:50 HEADCROP:2 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for SE50 reads. Pre-processed reads were mapped to TAIR10 using Bismark (v0.23.1) with parameters N set to 1 (allowing 1 mismatch in seed alignments) and X (maximum insert size for valid paired-end alignments) set to 700. Duplicated reads and reads flagged as unconverted due to three or more consecutive methylated CHH sites were discarded. Methylation ratios were calculated separately for CG, CHG, and CHH sites as #C/(#C+#T). Non-conversion ratios were calculated from chloroplast cytosine methylation ratios. Genome browser tracks showing CG, CHG, and CHH methylation ratios at single cytosine resolution were generated from Bismark genome-wide cytosine methylation output files for cytosine sites with at least 4 reads.
mRNA-seq: mRNA-seq reads were processed using the nf-core/rnaseq pipeline (v3.10.1) in Nextflow  (v22.10.6) executed using singularity containers on the high-performance computing cluster at Helmholtz Munich. Default parameters were used for read trimming/filtering, alignment, and quantification with Trim Galore!, STAR, and Salmon, respectively, except as stated below. TEs and genes were analyzed separately. For TEs, reads were aligned to the TAIR10 reference genome using a transcript-based TE annotation and extra STAR alignment arguments “--outMultimapperOrder Random --outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3”, whereas Araport11 gene models and extra STAR alignment arguments “--outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3” were used for genes. Transcript abundance estimates from Salmon were used to generate TE/gene-level count matrices for visualization and differential expression analysis with DESeq2 (v1.38.3). TEs/genes with less than 6 counts across all samples were removed.
Assembly: TAIR10/Araport11
Supplementary files format and content: BS-seq: wig or bigWig files showing single cytosine methylation ratios for each sequence context.
Supplementary files format and content: mRNA-seq: tab-separated text file containing TPM per gene/TE for all samples of the experiment.

source_name: seedling

growth_protocol: Plants were cultivated in growth chambers (Weiss Technik & Vötsch) at 23/20 °C (day/night), 65 % relative humidity and 100 μmol m-2 s-1 photosynthetically active radiation (PAR, 400–700 nm) under long day (LD), i.e. 16h light, and short day (SD), i.e. 10h light, 24h cycles. Plants were germinated and grown on soil consisting of 4 parts multiplication substrate (Floragard) and 1 part quartz sand.

extract_protocol:
Samples consisted of rosette leave tissue that was harvested 21 and 28 days after germination for LD and SD conditions, respectively. Genomic DNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using DNeasy Plant Mini Kit (Qiagen), except for comparison of DNA methylation under SD and LD conditions, where 14 days old seedlings grown on Phyto agar (RPI Corp.) with half-strength Murashige and Skoog (MS) basal salt mixture (MP Biomedicals) were used. Total RNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using RNeasy Plant Mini Kit (Qiagen) followed by DNA digestion with amplification grade DNase I (Thermo Fisher Scientific).
BS-seq: The isolated DNA was sheared into 200-400bp fragments by ultrasonication (Covaris S2/S220/E220). WGBS of wild type, mthfd1, thfs single and mt double mutants was performed by BGI TECH Solutions (Hong Kong), proceeding with end repair of the sheared DNA, deoxyadenylation, and ligation of methylated sequencing adaptors, followed by bisulfite conversion using EZ DNA Methylation-Gold kit (ZYMO Research), size selection, PCR amplification and final size selection of libraries. Libraries for WGBS of seedlings grown under SD and LD conditions and CRISPR-Cas9 lines were prepared the same way, except using KAPA HyperPrep Kit (Roche), TruSeq DNA LT (Illumina)/NEBNext Multiplex Oligos (New England Biolabs) methylated adaptors, and EpiTect Bisulfite Kit (Qiagen), and sequenced at Novogene. WGBS of wild type and mthfd1 plants grown under cCO2 and hCO2 was performed by Novogene using post-bisulfite adaptor tagging (PBAT) with Accel-NGS Methyl-Seq DNA Library Kit for Illumina (Swift Biosciences).
mRNA-seq: Library construction and sequencing was performed by Novogene. For preparation of non-directional libraries, messenger RNA (mRNA) was purified from total RNA using oligo-dT-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: For analysis of methylome and transcriptome changes upon suppression of photorespiration, plants were grown in a sun simulator climate chamber at the Research Unit for Environmental Simulation, Helmholtz Munich. Growth conditions were controlled with light intensity of 130 µmol m⁻² s⁻¹ (PAR) at plant height, day/night temperature cycle of 23°C (16 h) and 21°C (8 h), and relative humidity of 65%. Plants were grown in two Plexiglas cuvettes of dimensions 55 × 28 × 110 cm (W × D × H). One cuvette was flushed with 60 m³ h⁻¹ of air containing ambient CO₂ concentrations (cCO2), while the other was flushed with air and continuously fumigated with CO₂ (Air Liquide) at ~3000 ppm final concentration (hCO2). Airflows were controlled using a 1L mass flow controller (MKS Instruments GmbH), calibrated with a mass flow meter (ADM 3000, Agilent).

value: seedling

value: wild type

value: short day


title: Col-0_2Ca, biological rep3

description: Gene expression data from 14-day old Arabidopsis shoot tissue under 2 mM Ca

value: Shoot

value: wildtype

value: 2 mM Ca


title: Col0, seedling, SD, biorep2, BSseq

description: Library name: BSseq_WT_SD_rep2


title: Upcyte hepatocytes treated with PBS biological replicate 1

description:
Gene expression data from upcyte hepatocytes cell culture
mi422-7.1


title: mthfd1-1, seedling, SD, biorep1, BSseq

description: Library name: BSseq_m_SD_rep1


title: RSC96 co-cultured with control MenSCs rep3

city: Yinchuan

first: He

last: ZhongYi

address: No. 1160, Shengli Street, Xingqing District

institute: Ningxia Medical University

description: Library name: SCs3

data_processing:
The raw sequencing data were processed against the reference genome with HISAT2, followed by transcript assembly with StringTie.
Assembly: mm10
Supplementary files format and content: xlxs files includes FPKM values for each sample

extract_protocol:
Employing Trizol reagent (Invitrogen, USA), total RNA was isolated from three groups
the quality of RNA was assessed with a Nanodrop spectrophotometer and an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Only high-quality RNA samples were selected for library preparation. Oligo (dT) magnetic beads were used to selectively enrich mRNA, which was then fragmented. cDNA was synthesized using random hexamer primers. The resulting cDNA fragments were then purified, end-repaired, A-tailed, and ligated to sequencing adapters. The libraries underwent paired-end sequencing on the Illumina HiSeq platform (Illumina, USA) after PCR amplification and quality assessment

value: Schwann cells


title: mthfd1-1, seedling, SD, biorep2, BSseq

description: Library name: BSseq_m_SD_rep2


title: Col0, seedling, LD, biorep1, BSseq

description: Library name: BSseq_WT_LD_rep1

value: long day


title: RSC96 co-cultured with MenSCs-CM rep2

description: Library name: M_SCs2


title: Col0, seedling, LD, biorep2, BSseq

description: Library name: BSseq_WT_LD_rep2


title: RSC96 co-cultured with control MenSCs rep1

description: Library name: SCs1


title: RSC96 co-cultured with control MenSCs rep2

description: Library name: SCs2


title: RSC96 co-cultured with MenSCs-CM rep3

description: Library name: M_SCs3


title: S2_UnGated_Veh_2h

data_processing:
Reads were processed using cutadapt v4.7 (Martin 2011) to remove Illumina adapters, trim, and filter on quality with the settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, -n 1, -m 31, --nextseq-trim 20, --max-n 0
Processed reads were quantified against the GRCh38 transcriptome (Ensembl 107 annotations) by Salmon (Patro et al. 2017) with the following settings: -l A, --softclip, --softclipOverhangs, --allowDovetail, --seqBias, --gcBias.
Within DESeq2 v1.44.0 (Love, Huber, and Anders 2014), independent hypothesis weighting was conducted to optimise the power of p value filtering using IHW v1.32.0 (Ignatiadis et al. 2016) and log2 fold-change shrinkage was performed using ashr v2.2-63 (Stephens 2017). Multiple correction testing adjustments were optimised by passing FDR and log2FC thresholds at the point of results generation.
Assembly: GRCh38
Supplementary files format and content: Transcript-level expression estimates

extract_protocol:
After treatment, with or without FACS-sorting to separate rucaparib-high and low (top and bottom 20% of population), cells were washed in ice-cold PBS before extraction RNA using the RNeasy purification kit (Qiagen, 74106) according to manufacturer’s instructions. Unsorted controls cells were scraped directly into lysis buffer (RLT) using a cell scraper.
The NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module was used to generate RNA-Seq libraries according to the manufacturer’s protocol. Library quality was checked using the Agilent 2100 High-Sensitivity DNA assay, before checking concentrations with the Qubit dsDNA HS Assay Kit. Libraries were sequenced on a NextSeq 2000 after pooling in equimolar quantities.


title: RSC96 co-cultured with MenSCs-Exos rep2

description: Library name: EXO_SCs2


title: mthfd1-1, seedling, LD, biorep1, BSseq

description: Library name: BSseq_m_LD_rep1


title: RSC96 co-cultured with MenSCs-Exos rep3

description: Library name: EXO_SCs3


title: RSC96 co-cultured with MenSCs-Exos rep1

description: Library name: EXO_SCs1


title: scRNA-seq of CAR-2

city: West Lafayette

first: Qing

last: Deng

state: IN

address: 915 Mitch Daniels Boulevard

department: Biological Science

institute: Purdue University

data_processing:
Raw Illumina sequencing reads were aligned to the GRCm38 (mm10) reference genome (Mus musculus) using the BeeNetPLUS (Honeycomb) with default parameters. Subsequently, genes were quantified as UMI counts, and count matrices, aligned BAM, and QC files were generated using the BeeNetPLUS workflow on Terra.bio (Honeycomb).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw transcript count matrix for each sample

source_name: Glioblastoma

extract_protocol:
Tumor tissues were transported on ice in DMEM/F-12 medium immediately after surgical resection. The tumor was minced into smaller fragments and dissociated into single-cell suspensions. The single-cell suspensions were then loaded into the HIVE CLX system (Honeycomb), and libraries were prepared using the HIVE system and sequenced by Honeycomb.
RNA libiries for RNA-seq were prepared by using HONEYCOMB designed Transcriptome Recovery & Library Preparation protocol

value: Glioblastoma

value: WT

value: In vivo CAR-2


title: scRNA-seq of CAR-1

value: In vivo CAR-1


title: mthfd1-1, seedling, LD, biorep2, BSseq

description: Library name: BSseq_m_LD_rep2


title: RNA-seq of Huh7 cells transfected with siControl

city: Seoul

first: Su-Yeon

last: Park

state: National Research Foundation of Korea

address: Cancer Molecular Targeted Herbal Research Center, College of Korean Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, South Korea

country: South Korea

institute: Kyung Hee University

description:
Library name: Huh7_siControl_RNAseq
RNA-seq of Huh7 siControl cells

data_processing:
Raw sequencing reads were trimmed for adapters and low-quality bases and aligned to the human genome (GRCh38) using HISAT2. Gene expression levels were quantified using featureCounts.
Assembly: GRCh38

source_name: liver

growth_protocol: Huh7 cells were cultured in RPMI1640 supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's protocol. RNA concentration and purity were assessed using NanoDrop and Bioanalyzer.
RNA-seq libraries were prepared using an Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with control siRNA or QRICH1-targeting siRNA using Lipofectamine RNAiMAX according to the manufacturer's instructions.

value: liver

value: total RNA

value: siControl


title: RNA-seq of Huh7 cells transfected with siQRICH1

description:
Library name: Huh7_siQRICH1_RNAseq
RNA-seq of Huh7 siQRICH1 knockdown cells


title: scRNA-seq of C2

value: Mock Control-2


title: scRNA-seq of C1

value: Mock Control-1


title: HFL-1, GFP-ERG, replicate 3

city: Chengdu

first: Lu

last: Pu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

institute: west china hospital

description:
Library name: Sample13
Column name in All_gene_counts.xls: ERG-3_fpkm

data_processing:
The RNA libraries were sequenced on the Illumina HiSeq 2500 platform.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim-galore
Trimmed sequence reads were mapped to Homo_sapiens.GRCh38 using HISAT2
StringTie was applied to assemble the mapped reads.
FPKM(Fragments Per Kilobase of transcript per Million fragments mapped) was applied to measure the expression level of a gene or transcript by StringTie using maximum flow algorithm.
Assembly: hg38
Supplementary files format and content: FPKM values for each Sample

growth_protocol: F12-K, 10% fetal bovine serum, 1×penicillin-streptomycin. Cells were cultured at 37 ℃ at 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols.

value: Human fetal lung fibroblast

value: GFP-ERG


title: HFL-1, GFP-ERG, replicate 1

description:
Library name: Sample11
Column name in All_gene_counts.xls: ERG-1_fpkm


title: RSC96 co-cultured with MenSCs-CM rep1

description: Library name: M_SCs1


title: HFL-1, GFP-D13, replicate 5

description:
Library name: Sample10
Column name in All_gene_counts.xls: D13-5_fpkm


title: HFL-1, GFP-ERG, replicate 4

description:
Library name: Sample14
Column name in All_gene_counts.xls: ERG-4_fpkm


title: HFL-1, GFP-D13, replicate 3

description:
Library name: Sample8
Column name in All_gene_counts.xls: D13-3_fpkm


title: HFL-1, GFP-D13, replicate 4

description:
Library name: Sample9
Column name in All_gene_counts.xls: D13-4_fpkm


title: HFL-1, GFP-ERG, replicate 2

description:
Library name: Sample12
Column name in All_gene_counts.xls: ERG-2_fpkm


title: HFL-1, GFP-ERG, replicate 5

description:
Library name: Sample15
Column name in All_gene_counts.xls: ERG-5_fpkm


title: HFL-1, GFP, replicate 3

description:
Library name: Sample3
Column name in all_genes_FPKM.xls: GFP-3_fpkm

value: GFP


title: HFL-1, GFP, replicate 5

description:
Library name: Sample5
Column name in all_genes_FPKM.xls: GFP-5_fpkm


title: HFL-1, GFP-D13, replicate 2

description:
Library name: Sample7
Column name in All_gene_counts.xls: D13-2_fpkm


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish J1A1

city: Stanford

first: Jingxun

last: Chen

state: CA

address: 290 Jane Stanford Way, Room E365

department: Genetics

institute: Stanford University - Stanford, CA

description:
Library name: FatM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P5_2

data_processing:
Combine the sequencing data from all the sequencing batches (1-4) for each sample
Raw sequencing data (FASTQ files) were merged for each library pool (2 lanes for the pooled library 1 and 3 lanes for the pooled library 2) and checked for quality using Trim-galore v0.5.0.
The processed reads were aligned to the African turquoise killifish reference genome downloaded from NCBI (Nfu_20140520, GCF_001465895.1) using STAR v2.7.10b83 with the default parameters. Out of all the sequenced samples, 14 samples had >90% of reads mapped to the genome; 252 samples, 80–90% reads mapped; and 178 samples, 75–80% mapped. Samtools v1.16.184, with the parameters of MAPQ < 255 (‘samtools view -q255 -b’), was used to remove the reads mapped to multiple genomic regions. Next, we input the uniquely mapped reads into the ‘featureCounts’ program (with the default parameters) from subread v2.0.685 to generate the read counts for each gene.
We detected three samples as outliers, which were removed from subsequent analyses: J6 (a liver sample), L21 (a testis sample), and H19 (a skin sample). Two samples (J6 and L21) were excluded because they had low total raw counts. One sample (H19) was excluded because it had low mapping performance. As a separate method, we used gene expression connectivity to detect outliers from the WGCNA package v1.73. This method computes sample-to-sample correlations and derives network connectivity for each sample, then standardizes the connectivity scores, and finally identifies samples with Z-scores below -2 as outliers. Through this method, we verified these same three samples (J6, L21, and H19) as ‘outliers,’ validating their removal.
Assembly: NCBI African turquoise killifish reference genome (Nfu_20140520, GCF_001465895.1).
Supplementary files format and content: Comma-separated text files include the transcript per million (TPM) for all files in a matrix.

organism: Nothobranchius furzeri

source_name: fat

growth_protocol: All experiments used the GRZ strain of the African turquoise killifish species Nothobranchius furzeri. Fish were housed in a 26°C circulating water system kept at a conductivity between 3500 and 4500 μS/cm and a pH between 6.5 and 7.5, with a daily water exchange of 10% with reverse-osmosis-treated water. All animals were kept on a 12 h/12 h day/night cycle. The detailed protocol for embryo collection and husbandry of juvenile fish before sexual maturity can be found in the associated publication. The atlas cohort began at the 5th week post-hatching, each fish was transferred to a 2.8 L tank and sexed by caudal fin color: males exhibit vivid colors, but females do not. Fish with severe gill defects, curved spines, and an inability to float (‘belly sliders’) were excluded. A random subset of individuals from each cohort were designated as ‘Lifespan’ animals, and these animals were not selected for harvest. Any other unharvested animals that died from natural causes were also plotted in the lifespan analysis. Cohort 1 fish were enrolled in two batches, 2 weeks apart. Cohort 2 fish were enrolled as an independent cohort, 6 months apart from Cohort 1. All fish from each cohort were randomly assigned to tank locations using the ‘Randomize Range’ function in Google Sheets. Cohort 1 (1A, first enrollment) fish were fed using an automated feeder22 under the ad libitum regimen (5 mg per feeding and fed 7 times a day for a total of 35 mg of Otohime fish pellets). Cohort 1 (1B, second enrollment) and Cohort 2 were fed using a custom-made manual feeder twice a day, 18 mg per feeding, for a total of 36 mg of Otohime fish pellets. The core design of the custom feeder has the same precision as the automated feeder.

extract_protocol:
The RNA isolation protocol was based on the RNeasy Mini RNA extraction protocol from QIAGEN and largely kept consistent between tissues, except for when stated otherwise. Please see the associated publication for the full details of the RNA extraction protocol. To reduce within-tissue batch effects, we processed all samples of the same tissue type on the same day unless otherwise noted. Due to the large number of samples, RNA extraction was performed in 2-3 batches for each tissue, with the order of samples randomized and a roughly equal assignment of age and sex combinations to each batch. The processing order of each sample within a tissue type was randomized using the “Randomize Range” option in Google Sheets. After randomization, tissue samples were assigned unique numerical “RNA_IDs” and split into batches of 12-24 samples for processing.
cDNA libraries were prepared using a SmartSeq-based in-house protocol. Briefly, RNA samples were thawed on ice, and the concentration was measured. RNA sample concentrations were normalized to 25 ng/µL, and 2 µL of each sample was used as input into the cDNA first-strand synthesis reaction. The resulting single-stranded library was amplified using 9 cycles. A portion of the full cDNA library volume (6 µL) was cleaned using Agencourt AMPure XP beads at a 0.7X ratio following the manufacturer’s guidelines. Next, sequencing libraries were made using the Nextera XT DNA Library Preparation Kit and the IDT for Illumina DNA/RNA UD Index Sets A-D (Illumina, 20027213, 20027214, 20042666, 20042667), following the manufacturer’s instructions except for reducing all the reactions by half. Two library pools were ultimately generated, one of 322 samples and the other of 358 samples, with all the samples from the same tissue type assigned unique dual indices in the same library pool to reduce any batch effects. For tagmentation, 0.5 ng of the cDNA (2.5 µL total) was mixed with 5 µL TD buffer and then 2.5 µL ATM buffer from the Nextera kit, incubated at 55°C for 5 min and cooled to 10°C. To stop the tagmentation reaction, we added 2.5 µL of NT buffer for 5 min at room temperature. The cDNA library was indexed and amplified for 12 cycles in a PCR reaction containing 10 µL of tagmented DNA, 5 µL of dual indices, and 7.5 µL NPM buffer. The amplified cDNA library (25 µL total) was split into two 12.5 µL aliquots, each purified using 22.5 µL of AMPure XP beads. The aliquots were re-pooled after the first was eluted in 11 µL of Buffer EB, such that the total elution volume was 10 µL. We performed most pipetting steps using the Dragonfly or Mosquito HV robotic liquid handlers to accelerate sample processing and maintain high pipetting accuracy. Each pooled library was sequenced by Novogene on 2 (pooled library 1, which included 322 tissues) or 3 lanes (pooled library 2, which included 358 tissues) of an Illumina NovaSeq X 25B flow cell (2x150 bp paired-end) with 10% PhiX spike-in control for each lane, at a target sequencing depth of >40 million paired-end reads (20 million single-end) per sample. Novogene performed base calling, demultiplexing, and FASTQ file generation.

treatment_protocol: The harvest dates were randomly assigned to each fish within each cohort. On a harvest day, each fish was fed 18 mg of Otohime fish pellets 7:30 - 8 AM. At ~10:30 AM, the fish were transported from the animal facility to the lab space in their own tanks. Typically, 4 fish (2 males and 2 females) were dissected on each harvest day (~30 min to dissect each fish). Dissection began with perfusion (detailed protocol and sample description can be found in the associated publication) and then tissue collections on top of ice-cold Sylgard-coated Petri dishes. Dissected tissues were placed in 1.5 mL tubes, snap-frozen in liquid nitrogen, and stored at -80°C until RNA extraction. The same operator dissected the same tissues for all fish in this study. Muscle samples were collected from a ~1 cm region immediately anterior to the caudal fin, with skin removed and cuts made above and below the horizontal septum to remove the spinal cord and vertebrae. The spinal cord was collected by dissecting out the vertebrae and gently pulling the spinal cord from the vertebral foramen. Skin samples corresponded to the caudal fin's most posterior ~0.5 cm portion. The retina and retinal pigment epithelium (RPE) were dissected from the eye together. In some cases, the retina/RPE samples were dissected from individual eyes from the same animal, and in other cases, samples were pooled between animals. Only the head kidney was collected for the kidney samples. For the liver samples, the pale green gallbladder was removed whenever it was visible. Total visceral fat was collected (without regional distinction). All oocytes were collected for ovaries, including those that had fallen out of the organ during dissection.

value: fat

value: GRZ wild type

tag: Sex

value: male

tag: age days


title: HFL-1, GFP, replicate 1

description:
Library name: Sample1
Column name in all_genes_FPKM.xls: GFP-1_fpkm


title: HFL-1, GFP, replicate 2

description:
Library name: Sample2
Column name in all_genes_FPKM.xls: GFP-2_fpkm


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish P1B9

description:
Library name: SpinalCordF49_P_1B_9
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P9_2

source_name: spinalcord

value: spinalcord

value: female


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish J04

description:
Library name: FatM162_J04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P6_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish I03

description:
Library name: EyeM162_I03
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P4_2

source_name: eye

value: eye


title: HFL-1, GFP, replicate 4

description:
Library name: Sample4
Column name in all_genes_FPKM.xls: GFP-4_fpkm


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish J1A25

description:
Library name: EyeM103_J_1A_25
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P8_2


title: HFL-1, GFP-D13, replicate 1

description:
Library name: Sample6
Column name in All_gene_counts.xls: D13-1_fpkm


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish H2

description:
Library name: BrainM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P22_2

source_name: brain

value: brain


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish P1A3

description:
Library name: BrainM152_P_1A_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P21_2


title: RNA-Seq of nothobranchius furzeri: adult female spleen from fish P1B3

description:
Library name: SpleenF77_P_1B_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P19_2

source_name: spleen

value: spleen


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish A17

description:
Library name: EyeM78_A17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P16_2


title: RNA-Seq of nothobranchius furzeri: adult female brain from fish J1B6

description:
Library name: BrainF133_J_1B_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P23_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish A06

description:
Library name: BoneF102_A06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P2_2

source_name: bone

value: bone


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish E04

description:
Library name: EyeM102_E04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P12_2


title: RNA-Seq of nothobranchius furzeri: adult female spleen from fish I05

description:
Library name: SpleenF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P18_2


title: RNA-Seq of nothobranchius furzeri: adult female eye from fish J1B7rightEye

description:
Library name: EyeF147_J_1B_7_right
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O8_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish J1A24

description:
Library name: BoneF47_J_1A_24
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P3_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish P1B2

description:
Library name: HeartM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P13_2

source_name: heart

value: heart


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish J1B2

description:
Library name: FatM49_J_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O7_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish J1B13

description:
Library name: HeartM77_J_1B_13
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P15_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish J1B20

description:
Library name: HeartM77_J_1B_20
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P14_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish P1A10

description:
Library name: EyeM103_P_1A_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O4_2


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish J1B7

description:
Library name: SpinalCordF147_J_1B_7
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O9_2


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish J1B5

description:
Library name: SpinalCordF49_J_1B_5
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P11_2


title: RNA-Seq of nothobranchius furzeri: adult female fat from fish P1B1

description:
Library name: FatF77_P_1B_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P7_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish C1

description:
Library name: BoneF155_C1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O2_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish J1A25

description:
Library name: SpleenM103_J_1A_25
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O19_2


title: RNA-Seq of nothobranchius furzeri: adult male spinalcord from fish A01

description:
Library name: SpinalCordM78_A01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P10_2


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish P1B11

description:
Library name: BrainM147_P_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O21_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish P1B8leftEye

description:
Library name: EyeM147_P_1B_8_left
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O16_2


title: RNA-Seq of nothobranchius furzeri: adult female spleen from fish J1B6

description:
Library name: SpleenF133_J_1B_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: P17_2


title: RNA-Seq of nothobranchius furzeri: adult female fat from fish D6

description:
Library name: FatF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O6_2


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish P1B10

description:
Library name: FatM133_P_1B_10
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O5_2


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish J1B4

description:
Library name: BrainM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O23_2


title: RNA-Seq of nothobranchius furzeri: adult female eye from fish NA3

description:
Library name: EyeF103_NA_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O12_2


title: RNA-Seq of nothobranchius furzeri: adult female fat from fish P1A2

description:
Library name: FatF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N7_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish J1B4

description:
Library name: EyeM161_J_1B_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N8_2


title: RNA-Seq of nothobranchius furzeri: adult female brain from fish I05

description:
Library name: BrainF134_I05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O22_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish P1B1

description:
Library name: BoneF77_P_1B_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O1_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish P1A6

description:
Library name: HeartM133_P_1A_6
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O15_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish J1B18

description:
Library name: BoneF133_J_1B_18
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O3_2


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish F05

description:
Library name: FatM102_F05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N6_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish H2

description:
Library name: SpleenM52_H_02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O18_2


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish C1

description:
Library name: SpinalCordF155_C1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O10_2


title: RNA-Seq of nothobranchius furzeri: adult female eye from fish P1A1andJ1A24

description:
Library name: EyeF47_P_1A_1_and_J_1A_24
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N4_2


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish J1A22

description:
Library name: BrainM47_J_1A_22
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N21_2


title: RNA-Seq of nothobranchius furzeri: adult male spinalcord from fish J1A13

description:
Library name: SpinalCordM75_J_1A_13
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O11_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish D6

description:
Library name: BoneF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N2_2


title: RNA-Seq of nothobranchius furzeri: adult female brain from fish D6

description:
Library name: BrainF52_D_06
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N22_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish P1B2

description:
Library name: SpleenM133_P_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O17_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish E1

description:
Library name: HeartM52_E_01
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O13_2


title: RNA-Seq of nothobranchius furzeri: adult male fat from fish J1B11

description:
Library name: FatM161_J_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N5_2


title: RNA-Seq of nothobranchius furzeri: adult male brain from fish J1B13

description:
Library name: BrainM77_J_1B_13
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N23_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish P1B8

description:
Library name: HeartM147_P_1B_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N15_2


title: RNA-Seq of nothobranchius furzeri: adult female spleen from fish D14

description:
Library name: SpleenF52_D_14
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N18_2


title: RNA-Seq of nothobranchius furzeri: adult female eye from fish P1B9andJ1B5

description:
Library name: EyeF49_P_1B_9_and_J_1B_5
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N12_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish P1A4

description:
Library name: HeartM133_P_1A_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: O14_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish A17

description:
Library name: HeartM78_A17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N13_2


title: RNA-Seq of nothobranchius furzeri: adult male bone from fish J1A17

description:
Library name: BoneM47_J_1A_17
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N3_2


title: RNA-Seq of nothobranchius furzeri: adult male spinalcord from fish J1B12

description:
Library name: SpinalCordM49_J_1B_12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N9_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish P1A4

description:
Library name: EyeM133_P_1A_4
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N16_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish P1B3

description:
Library name: BoneF77_P_1B_3
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N1_2


title: RNA-Seq of nothobranchius furzeri: adult female fat from fish P1A8

description:
Library name: FatF75_P_1A_8
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M7_2


title: RNA-Seq of nothobranchius furzeri: adult female fat from fish E02

description:
Library name: FatF78_E02
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M6_2


title: RNA-Seq of nothobranchius furzeri: adult male heart from fish J1B11

description:
Library name: HeartM161_J_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N14_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish J1A1

description:
Library name: SpleenM152_J_1A_1
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N19_2


title: RNA-Seq of nothobranchius furzeri: adult male eye from fish J1B12andJ1B2

description:
Library name: EyeM49_J_1B_12_and_J_1B_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M8_2


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish C04

description:
Library name: SpinalCordF134_C04
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N10_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish J1B11

description:
Library name: SpleenM161_J_1B_11
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: N17_2


title: RNA-Seq of nothobranchius furzeri: adult female spinalcord from fish P1A2

description:
Library name: SpinalCordF103_P_1A_2
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M9_2


title: RNA-Seq of nothobranchius furzeri: adult female bone from fish P1A12

description:
Library name: BoneF75_P_1A_12
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M3_2


title: RNA-Seq of nothobranchius furzeri: adult male spleen from fish D05

description:
Library name: SpleenM162_D05
cDNA libraries were prepared using a SmartSeq-based in-house protocol.
Library_ID: M18_2