title: Day10_EC_Cd31po_Rnf20_Ctr_r1


title: 42_ChIPseq_shGFP_s_H3K27ac_rp2

status: Public on Sep 24 2025

type: SRA

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

description: Library name: Sample 42

library_source: genomic

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Supplementary files format and content: The differential expression file was further provided(tab-delimited file).
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
RNA-seq raw files (fastq, PE150) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
HISAT2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.
Cut and Tag raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. Peaks were called by MACS2. HOMER was then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Bowtie2
DESeq2
HOMER
Adjusted p-value < 0.05
Assembly: mm10
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p-value of each peak.

molecule: genomic DNA

organism: Mus musculus

source_name: monocyte

growth_protocol:
WT RAW264.7 cells, lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7 cells  with lentivirus-medicated knockdown cells were maintained normal 10% FBS DMEM medium.
RAW264.7  cells were maintained normal 10% FBS DMEM medium.
shGFP, shNCOR and shSMRT RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
Fresh cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes, followed by 1% formaldehyde for 10 minutes at room temperature. Nuclei were isolated, sonicated, and incubated with magnetic bead-antibody complexes.  Antibodies to NCOR (bethyl, A301-145A), SMRT (bethyl, A301-147A), and GPS2 (homemade) were used.
ChIP-Seq: ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.
WT RAW264.7 cells were seeded with triplicates in the 12 wells plates with 2×105 cells one day before the experiments. Cells were washed with PBS and then resuspended in lysis buffer. Cell nuclei were spined down and transferred into the transposition reaction buffer and incubated at 37 °C for 30 minutes using 105 cells. Genomic DNA was extracted using Qiagen MinElute PCR Purification Kit. ATAC-seq library was done with the protocol as previously reported (Buenrostro et al., 2015). The Purified ATAC-seq DNA library mix was sequenced on NextSeq 550 (Illumina, 35 SE reads, paired-end) in BEA Core Facility (Karolinska Institutet, Huddinge, Sweden).
ATAC-Seq: The ATAC-seq Library preparation was performed through the manufacturer's introduction.
2×105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
RNA-Seq: The RNA-seq library preparation was followed by the instructions of the NEB Next Ultra II RNA Library kit (NEB, E7770S).
105 shGFP, shNCOR and shSMRT cells were seeded one day before the treatment. Total RNA was extracted from the manufacturer's introduction.
Cut&Tag: The Cut and Tag Library preparation was performed through the manufacturer's introduction (Steven Henikoff lab,Bench top CUT&Tag V.3 ).

treatment_protocol:
No treatment
No treatment
No treatment
RAW264.7 cells were treated with or without LPS (100ng/ml), IL4 (20ng/ml), GW3965 (5uM) for 3 hours. H3K27ac (Abcam, ab4729) was used for the Cut&Tag experiment.

tag: tissue

value: monocyte

tag: cell line

tag: cell type

value: Macrophages

tag: genotype

value: BALB/c

tag: batch

value: ChIP-seq


title: CD8pos_aCD19CAR_4

city: Vienna

first: Jakob

last: Huemer

state: Vienna

address: Zimmermannpl. 10

country: Austria

institute: Children’s Cancer Research Institute

description:
500 aCD19CAR cells that did not interact
processed data file: Counts_CAR.csv

library_source: transcriptomic

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0)
Uniquely mapped reads for each exon were counted using the function summarizeOverlaps from the Ge-nomicAlignments package (version 1.12.0) in R (version 3.4.0)
Gene and exon annotations were obtained from the Ensembl GENCODE Basic set (genome-build GRCh38)
Assembly: hg38
Supplementary files format and content: csv file of read counts

molecule: total RNA

organism: Homo sapiens

source_name: aCD19CAR cells

growth_protocol: Human primary NK cells (‘primary NK cells’) were isolated from buffe coat and enriched using RosetteSep Human NK Cell Enrichment Cocktail (Stemcell technologies) according to manufacturer’s instructions. Enriched NK cells were resuspended in PBS supplemented with 3% heat-inactivated fetal bovine serum and 10mM ultrapure EDTA, pH 8.0 (Invitrogen) and further purified with MagniSort Human NK cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CD19-specific human CAR T cells (‘aCD19CAR cells’) were generated similarly as described before (Salzer et.al., 2020). Normal donor derived T cells were lentivirally transduced following 24 hours of stimulation with T Cell TransAct (Miltenyi Biotec) according to manufacturer’s protocol. Lentiviral supernatant was added at a final dilution of 1:4. Stimulation reagent was removed by centrifugation after 72 hours of activation. Transduced T cells were cultivated in AIM V medium (Thermo Scientific) with 2.5% 1M HEPES (Gibco), 2% heat-inactivated octaplas SD blood type AB (Vienna Red Cross), 1% L-Glutamine was supplemented with 10 ng/ml rh IL- 7 (Miltenyi Biotec) and 5 ng/ml rh IL-15 (Miltenyi Biotec) instead of 200 rh U/ml IL-2. CD19 specific CAR T cells were enriched for CD8+ population using MagniSort Human CD8 T cell Enrichment Kit (Invitrogen) according to manufacturer’s instructions. CAFs (‘CAF cells’) were isolated from a liver metastasis of an individual with colorectal cancer. The tumor metastasis was dissociated with 100 U/ml collagenase IV (Gibco) in DMEM supplemented with 10% fetal bovine serum for 1 hour at 37°C. Cells were strained through 0.45µm filter and grown for 2 hours in EGM-MV2 (PromoCell). Thereafter, cells were cultured in EGM-MV2 supplemented with 0.25 μg/ml amphotericin B (Gibco), 20 mg/ml gentamycin (Gibco), 100 U/ml penicillin/streptomycin (Sigma) with a daily 5 hours antibiotic free incubation period. From passage 2 onwards fibroblast were grown in EGM-MV2 without antibiotics. NK-92 cells (‘NK92 cells’) were cultured in alphaMEM (Sigma) supplemented with 12.5% heat-inactivated fetal bovine serum (Sigma), 12.5% heat-inactivated horse serum (Sigma), 0.2 mM myo-inositol, 0.02 mM folic acid, 10 mM HEPES (Gibco), 100 U/ml Penicillin-Streptomycin (Gibco), 2 mM L-glutamine (Sigma), and 20 U/ml rh IL-2 (Novartis). NK-92 cells were passaged every 2-3 days and given fresh medium 1 day before the experiments. K562 cells (‘K562 cells’) were grown in RPMI-1640 (Gibco) supplemented with 2 mM L-glutamine, 10 mM HEPES, 100 U/ml Penicillin-Streptomycin, and 10% heat-inactivated fetal bovine serum (further described as ‘full RPMI’). Jurkat cells (‘Jurkat cells’) were grown in full RPMI. CD19+ Jurkat cells were generated by CD19 mRNA electroporation similar to the previously described method (Zajc et. al., 2020).

extract_protocol:
RNA was isolated according to Smart-seq2 was performed as described previously (Picelli et.  al., 2014). In brief, cells were lysed in 0.2% Triton X-100 in the presence of RNase inhibitor 40 U/µl RNase inhibitor (Takara) and stored at -80°C until ready to proceed.
RNA was denatured, reverse transcribed and amplified for 22 cycles. After reverse transcription, 1 ng cDNA was tagmented, amplified and barcoded following the Illumina Nextera indexing strategy. Final libraries were pooled to 4 nM for sequencing on HiSeq3000/4000. cDNA and library quality was assessed using TapeStation 4150 instrument and D5000HS or D1000 screening tapes (Agilent), respectively. DNA concentration was determined using Qubit dsDNA HS kit and instrument (Invitrogen). cDNA and Illumina Nextera indexed samples were purified using Ampure XP beads (Beckman Coulter) at 1:1 ratio. Sequencing was performed by the Biomedical Sequencing Facility at CeMM at 50bp single-end configuration.

treatment_protocol: For CIPS application: Cells were brought to high viability and density by spinning at 100 rcf for 3 minutes and subsequent elution in full RPMI. 1 million cells were stained with Hoechst 3334 (Invitrogen) and to discriminate GFP-expressing K562 from NK-92 cells, NK-92 cells were in addition counterstained with CD56-PE (N901, Beckman Coulter) for 30 minutes in full RPMI. Cells were washed with PBS and brought to a density of 1000 cells per µl in full RPMI for loading on a DEPArray Cartridge V2 (Silicon Biosystems). Cells were scanned for brightfield, the corresponding fluorescent markers and Hoechst (DAPI) for doublet/multicell exclusion. For further use, cells were defined with the following parameters: (i) in ‘grid’ (one cell per DEP cage), (ii) Hoechst positive, and (iii) cell size. Cell fulfilling criteria (i) to (iii) were categorized as NK-92: smaller cells, GFP negative, PE positive or K562: bigger cells, GFP positive, PE negative. From this pool, approximately 50-60 cells each were moved the Cartridge ‘park area’, where cells were aligned, collided and separated by changing the electric potential of DEP cages. Cells were assigned and moved to RNase/DNase-free 0.2 ml PCR-tubes (Applied Biosystems). After total four hours of cell-cell interactions cells were washed by adding RNase-free PBS up to a total of 100 µl per sample. Cells were spun and the total volume was reduced to approximately 1 µl using the VRNxT/Silicon Biosystems (‘DEPArray OUT‘ program) according to the manufacturer’s instructions. Enriched primary human NK cells with K562 partner cell were stained and processed the same in the CIPS procedure as described above for NK-92 and K562 cells. Enriched CD8+ CD19 specific CAR T cells with Jurkat partner cell and CAFs processed with following adaptations. Enriched CD8+ CD19 specific CAR T were stained with Hoechst 3334, CD4-APC (clone RPA-T4, BD Biosciences), CD8-PE (clone SK1, BD Biosciences) and GFP-expressing Jurkat cells with Hoechst 3334. Cells were categorized as CD8+ T cells as: smaller cells, APC negative, PE positive or Jurkat: bigger cells, GFP positive, APC negative, PE negative. CAFs were stained with Hoechst 3334, CD90-APC (clone 5E10, Biolegend), FAP-AF488 (clone # 427819, R&D) and categorized as: bigger cells, APC positive, GFP dim. Cell manipulation, recovery was done as described before with longer routing times for primary human NK cells and CD8+ T cells. For FACS application: Enrichment of human primary NK cells, CD8+ CD19 specific CAR T cells and expression of CD19 on Jurkat cells was assessed using 100-200*10^3 cells and controls each. Cells were washed in 2% heat-inactivated fetal bovine serum in PBS after blocking for 10min, 4°C in 10% heat-inactivated fetal bovine serum in PBS. Cells were stained with the following antibodies at 4°C for 30min. Primary human NK cells: CD56-AF700 (clone B159, BD Biosciences) and CD3-FITC (clone SK7, BD Biosciences). CD19 specific CAR T cells: CD3-FITC (clone SK7, BD Biosciences), CD4-APC (clone RPA-T4, BD Biosciences), CD8-V450 (clone RPA-T8, BD Biosciences), and DYKDDDDK (Flag) Tag-PE (clone L5, Biolegend), the latter for CAR expression. CD19+ Jurkat cells: CD19-PECy7 (clone SJ25C1, BD Bioscience). Cells were washed and analyzed as well as  500 cell per well sorted for following populations. Primary NK cells: ‘CD56hi’, ‘CD56dim’; Jurkat cells: ‘Jurkat’, ‘CD19Jurkat’; CD19-specific human CAR T cells: ‘CD4pos’, ‘CD8pos’ using Aria Fusion. Following a degranulation assay NK-92 and K562 cells stained with stained with a CD56-AF700 and CD107a-PE antibody cells were washed, re-suspended, and filtered in 0.5% BSA in PBS. 500 cells of unresponsive NK-92 (CD56+, CD107a-), granule releasing NK-92 (CD56+, CD107a+) and K562 (GFP+) were sorted with Aria Fusion into a 96-well plate for follow-up Smart-seq2 processing. CD107a positivity was defined by NK-92 cells stimulated for two hours with 250 ng/ml Phorbol 12-myristate 13-acetate (PMA) and 1 µg/ml Ionomycin. NK-92 and K562 cells incubated alone were processed as negative controls. For both, CIPS and FACS application cells were further processed with the Smart-Seq2 protocol.

value: aCD19CAR cells

tag: number of cells

tag: interaction duration

tag: experiment id

tag: phenotype

tag: treatment


title: IVP11_EC

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
The read qualities for each fastq file were accessed with FastQC (V 0.11.9), and low-quality bases and adapters were removed with Trimmomatic.
The sequenced reads were mapped to the bovine reference genome (bosTau 9) with the STAR aligner (V 2.7.0b), generating the genome index with the ARS-UCD1.3 assembly.
Read counts were estimated at the gene level, and the counting was done with featureCounts, part of the Subread software (V 2.0.3).
Assembly: bosTau 9
Supplementary files format and content: tab delimited text file containing raw read counts for each sample.

molecule: polyA RNA

organism: Bos taurus

source_name: ED

extract_protocol:
Embryo samples were shipped in dry ice to the BGI TECH SOLUTIONS Company (Hong Kong), which performed the RNA extraction, quality control, library preparation and sequencing.
RNA sequencing (RNAseq) was run in the RNA samples through non-stranded & polyA-selected mRNA library preparation and PE100 sequencing with 5Gb clean data per sample on DNBSEQ. After library preparation and sequencing, raw data with adapter sequences or low-quality sequences were filtered to remove contamination and obtain valid data. This step was completed by the SOAPnuke software developed by BGI Company.

treatment_protocol: For IVP embryos, oocytes aspirated from slaughterhouse ovaries were matured, fertilized, and cultivated in serum-free medium until transfer at day 7. IVV embryos (n=8) were generated after ovarian super-stimulation and artificial insemination. For both procedures, animals were flushed at day 15 of gestation, and sections of the ED and EEM were snap-frozen in 0,1% PVA PBS until shipment.

value: ED

tag: developmental stage

value: Day 15 elongated embryo

tag: condition

value: IVP


title: 48_ChIPseq_shNCOR_H3K27ac_rp2

description: Library name: Sample 48


title: CD8pos_aCD19CAR_2


title: Liver_AI_Female_4

city: Dublin

first: Laura

last: Thompson

address: Belfield

country: Ireland

institute: University College Dublin

description:
Library name: Sample_16
Liver_16

source_name: Calf liver

extract_protocol:
Blood and tissues samples were shipped on dry ice to Macrogen Europe (Amsterdam, Netherlands), which performed the RNA extraction, quality control, library preparation, and sequencing.
Libraries were prepared with Truseq-stranded mRNA for all tissue samples and SMARTer Stranded RNA library for the blood samples, followed by PE100 sequencing with the NovaSeq platform, generating ~30 million raw reads per sample in FASQ format.

value: Calf liver

tag: Sex

value: Female

value: AI

tag: age at_biopsy

value: 121 days


title: Liver_IVP_Female_2

description:
Library name: Sample_10
Liver_10

value: 130 days


title: Jurkat_1225_single_0min_JH0028

description:
1 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

source_name: Jurkat cells

value: Jurkat cells

value: WT

value: GFP


title: Liver_IVP_Female_1

description:
Library name: Sample_9
Liver_9

value: 143 days


title: CD8pos_aCD19CAR_1


title: 01E11_5_Cdh5_Rnf20_WT_r1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

library_source: transcriptomic single cell

data_processing:
Raw fastq files were mapped and de-multiplexed by the use of cellRanger (v.7.1.0) count function (settings –expected-cells 3000 and refdata-gex-mm10-2020-A genome.
The filtered feature matrixes were used as input files to merge the data using the Seurat (v. 4.3.0). Low-quality cells were discarded by filtering selected only cells expressing genes higher than 900 genes per cells. Clusters were found with the function FindClusters (resolution=0.5, random.seed=1 and algorithm=1). The UMAP or TSNE plots were generated using RunUMAP and RunTSNE (dims=1.30, n.neighbors= 30).
To select the cardiomyocyte (CM) subpopulation of cells, we selected those cells with the expression of CM markers Nebl, Tnni3, and Myh6. FindClusters with a resolution of 0.8 was used to cluster the CMs. In the case of the endothelial cell populations, the Isl1cre/+-Rnf20fl/fl KO and the EC were obtained after clustering cells with the expression of Pecam1. In the E11.5 of control and Cdh5CreERT2-Rnf20fl/fl KO, EC was obtained after clustering Pecam1 positive cells and excluding in both datasets the Immune cell clusters. In both EC sub-populations, FindClusters with a resolution of 0.2 was used to cluster the ECs.
In all of the single-cell data sets, the marker genes were identified using the FindAllMarkers function (min.pct=0.25, logfc.threshold = 0.25, test.use= Wilcox). Differentially regulated genes between wt and Rnf20 Ko in each cluster were identified with FindMarkers (ident.1= Ko_cells, ident.2= wt_cells, min.pct= 0.05 and logfc.threshold= 0.25, test.use= Wilcox).
Assembly: refdata-gex-mm10-2020-A genome.
Supplementary files format and content: txt demultiplexed files output from CellRanger (barcodes.tsv, features.tsv, matrix.mtx).

source_name: 5 whole heart from E11.5

growth_protocol: E14 Tg(Nkx2–5-EmGFP) ES cells were differentiated according to Rui et al. 2018 and at day3.7 cells were differentiated towards EC. At day10, cells were selected by CD31 positive cells for RNA extraction.

extract_protocol:
5 hearts were isolated in PBS and tail was taken for genotyping of the embryos. Positive sorting of DAPI for living cells from the hearts whole cells were further sorted with 10x genomics machine.
RNA preparation kit according to BGI RNA-seq preparation kit.

treatment_protocol: Mother were injected at E8.5-E10.5 with 4-Hydroxytamoxifen to induce the deletion of Rnf20 in ECs.

value: 5 whole heart from E11.5

value: Rnf20_deletion_Endothelial cells

value: tamoxifen


title: SCG male flea 1

city: Seville

first: Angela

middle: M.

last: García Sánchez

address: Profesor García González, 2

country: Spain

institute: Universidad de Sevilla

description: Library name: Sample SCG.m.1

data_processing:
Paired-end reads were merged using FLASH V1.2.7
Quality filtering on the raw tags was performed according to QIIME V1.9
Chimeric merged reads were detected and removed using UCHIME
Multiple sequence alignment was conducted using MUSCLE V 3.8.31
Assembly: NCBI genome assembly ASM342690v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Spilopsyllus cuniculi

extract_protocol:
Total DNA was extracted from fleas using flea abdomen by the DNeasy Blood  and Tissue Kit (Qiagen, Valencia, CA, U.S.A.) in accordance with the manufacturer’s instructions
Sequencing libraries were generated using TruSeq DNA PCR- Free Sample Preparation Kit (Illumina, USA) following manufacturer's recommendations

tag: host

value: Cat

tag: gender

value: Male


title: 44_ChIPseq_shSMRT_H3K27ac_rp2

description: Library name: Sample 44

value: monocyte

value: Macrophages

value: BALB/c

value: ChIP-seq


title: 02E11_5_Cdh5_Rnf20_KO_r1


title: Liver_AI_Male_4

description:
Library name: Sample_8
Liver_8

value: Calf liver

value: 114 days


title: CD4pos_aCD19CAR_4

value: aCD19CAR cells


title: Liver_IVP_Female_4

description:
Library name: Sample_12
Liver_12

value: Female

value: IVP

value: 118 days


title: SCG female flea 3

description: Library name: Sample SCG.f.3


title: CD4pos_aCD19CAR_3


title: bE10_5_heart_Isl1_Rnf20_KO

data_processing:
Raw fastq files were mapped and de-multiplexed by the use of cellRanger (v.7.1.0) count function (settings –expected-cells 3000 and refdata-gex-mm10-2020-A genome.
The filtered feature matrixes were used as input files to merge the data using the Seurat (v. 4.3.0). Low-quality cells were discarded by filtering selected only cells expressing genes higher than 900 genes per cells. Clusters were found with the function FindClusters (resolution=0.5, random.seed=1 and algorithm=1). The UMAP or TSNE plots were generated using RunUMAP and RunTSNE (dims=1.30, n.neighbors= 30).
To select the cardiomyocyte (CM) subpopulation of cells, we selected those cells with the expression of CM markers Nebl, Tnni3, and Myh6. FindClusters with a resolution of 0.8 was used to cluster the CMs. In the case of the endothelial cell populations, the Isl1cre/+-Rnf20fl/fl KO and the EC were obtained after clustering cells with the expression of Pecam1. In both EC sub-populations, FindClusters with a resolution of 0.2 was used to cluster the ECs.
In all of the single-cell data sets, the marker genes were identified using the FindAllMarkers function (min.pct=0.25, logfc.threshold = 0.25, test.use= Wilcox). Differentially regulated genes between wt and Rnf20 Ko in each cluster were identified with FindMarkers (ident.1= Ko_cells, ident.2= wt_cells, min.pct= 0.05 and logfc.threshold= 0.25, test.use= Wilcox).
Assembly: refdata-gex-mm10-2020-A genome.
Supplementary files format and content: txt demultiplexed files output from CellRanger (barcodes.tsv, features.tsv, matrix.mtx).

source_name: 5 whole heart from E10.5

treatment_protocol: Mother were injected at E7.5-E19.5 with 4-Hydroxytamoxifen to induce the deletion of Rnf20 in progenitor cells.

value: 5 whole heart from E10.5

value: Rnf20_deletion_Progenitor cells


title: SCG female flea 2

description: Library name: Sample SCG.f.2


title: Liver_AI_Male_3

description:
Library name: Sample_7
Liver_7

value: AI

value: 133 days


title: CD4pos_aCD19CAR_2


title: CD8pos_aCD19CAR_3


title: aE10_5_heart_Isl1_Rnf20_WT

value: tamoxifen


title: Liver_IVP_Female_3

description:
Library name: Sample_11
Liver_11

value: 120 days


title: SCG female flea 1

description: Library name: Sample SCG.f.1

value: Cat


title: CD4pos_aCD19CAR_1


title: RNA-seq of Rattus norvegicus, adult male hippocampus E (DG) rep3

city: Berkeley

first: Daniela

last: Kaufer

state: California

address: 430E LKS, Univ of California - Berkeley

department: Integrative Biology, Neuroscience

country: USA

institute: University of California, Berkeley

description:
Library name: HPC_E_CTRLLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

data_processing:
Reads were aligned to the Rattus norvegicus Rn5 genome assembly using Spliced Transcripts Alignment to a Reference aligner (STAR/2.6.0a)29 with gene annotations provided from the ensemble build 75
Transcript/gene level quantification and differential gene expression were performed using rsem/1.3.1 + ebseq
Assembly: Rattus norveegicus Rn5, annotation from ensembl build 75
Supplementary files format and content: raw_counts_TPM_hpc.txt and raw_counts_TPM_amg.txt contain expected_counts, TPM and FPKM values
Supplementary files format and content: degs_hpc_amg.xlsx contain the results of differential gene expression at FDR 0.05

organism: Rattus norvegicus

source_name: brain, hippocampus

extract_protocol:
On day 9 after stress, animals were anesthetized with isoflurane and rapidly decapitated. Brains were extracted, flash frozen by floating on liquid nitrogen, and stored at -80°C. A subset of 12 animals were selected for RNA sequencing based on composite anxiety-like behavior scores: 3 stress-exposed animals with low scores (0-2), 3 stress-exposed animals with high scores (13-15), and 6 control animals from across the spectrum (0-6, average = 3.67). Sections of 200 µm  thickness were collected under sterile conditions on a Leica cryostat, and punches of 0.75 mm diameter were taken from the dorsal dentate gyrus and basolateral amygdala (rat AP coordinates -2.9 to -5.28  relative to Bregma) using a Rapid-Core Sampling Tool (Electron Microscopy Sciences, Hatfield, PA). Punches were separated by hemisphere, and 7-9 punches were collected per hemisphere. Samples were stored at -80°C until processing. Tissue punches from the left hemisphere were homogenized in TRIzol reagent (Invitrogen, Waltham, MA), and RNA was extracted and treated with DNase (DNase I, RNase-free, New England Biolabs, Ipswich, MA) according to the TRIzol reagent user guide (Pub. No. MAN0001271, Rev. A.0). The left hemisphere was chosen for the purposes of standardization and consistency across animals.
For RNA sequencing, all postprocessing (including cDNA library preparation) and sequencing was performed by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. RNA quality scores were determined for each sample on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). One sample (from a control animal with composite behavior score of 0) had low RNA quality, and RNA was re-extracted but later excluded from analysis (see Statistical Analysis section). RNA was poly-A selected, and library preparation was conducted on a Biomek FXp with Kapa Biosystems reagents.

value: brain, hippocampus

tag: strain

value: Sprague-Dawley

value: male

value: WT

value: undistrubed control

tag: unique animal_id


title: Liver_AI_Male_1

description:
Library name: Sample_5
Liver_5

tag: tissue

value: Calf liver

value: Male

value: 136 days


title: RNA-seq of Rattus norvegicus, adult male hippocampus K (DG) rep3

description:
Library name: HPC_K_STRESSLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: 3 h immob with predator scent


title: HAP1, Targeting iTOP, 1440min, rep3

city: Leiden

first: Niels

last: Geijsen

address: Einthovenweg 20

department: Anatomy and Embryology

institute: LUMC

description: Library name: 1440T3

data_processing:
Adapters were trimmed from the reads with TrimGalore 0.6.6
STAR 2.7.11b was used to align trimmed reads to the combined GRCh38 human genome, dEGFP-PuroR construct and the ERCC spike in RNA sequences
A count table was generated with featureCounts version 2.0.3 using the -M -O --fraction flags.
Assembly: GRCh38 + ERCC spike-in RNA sequences + dEGFP expression construct
Supplementary files format and content: tab-delimeted text file includes raw counts for each sample

growth_protocol: HAP1-dEGFP cells were cultured in IMDM 10% FBS supplemented with 10 ug/ml puromycin. Cells were grown in a 37C, 5% CO2 incubator with humidified atmosphere.

extract_protocol:
Cells were collected in TRIZOL. RNA was purified with the Zymo direct-zol 96-well RNA kit. 2 µl of 1:1000 diluted ERCC RNA Spike-In Mix 1 (ThermoFisher #4456740) was added to 100ng total RNA of each sample. This was used as input for library prep.
The Watchmaker RNA library prep kit with Polaris Depletion - rRNA/Globin (HMR) was used for library prep

treatment_protocol: Cells were either left untreated, transfected with an empty iTOP transfection, transfected with LbuCas13a and a non-targeting gRNA by iTOP, or transfected with LbuCas13a and a dEGFP targeting gRNA by iTOP. Cells were harvested at 50, 200 and 1440 minutes after transfection.

tag: cell line

tag: cell type

value: near haploid chronic myelogenous leukemia KBM-7 derived

value: LbuCas13a and dEGFP targeting gRNA transfection


title: CD19Jurkat_9350_p5_22_5min_JH0026

description:
1 Jurkat cells that interacted for 22.5min
processed data file: Counts_CAR.csv

value: Jurkat cells

tag: genotype

value: GFP


title: Liver_IVP_Male_4

description:
Library name: Sample_4
Liver_4

value: IVP

value: 117 days


title: 41_ChIPseq_shGFP_s_H3K27ac_rp1

description: Library name: Sample 41

value: monocyte

value: Macrophages

value: BALB/c

tag: batch

value: ChIP-seq


title: HAP1, Targeting iTOP, 1440min, rep2

description: Library name: 1440T2


title: HAP1, Targeting iTOP, 1440min, rep1

description: Library name: 1440T1


title: RNA-seq of Rattus norvegicus, adult male hippocampus J (DG) rep3

description:
Library name: HPC_J_CTRLHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: brain, hippocampus

value: Sprague-Dawley

value: male


title: Liver_IVP_Male_2

description:
Library name: Sample_2
Liver_2

value: Calf liver

value: 137 days


title: RNA-seq of Rattus norvegicus, adult male hippocampus C (DG) rep2

description:
Library name: HPC_C_STRESSLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: WT


title: Liver_IVP_Male_3

description:
Library name: Sample_3
Liver_3

value: Male

value: 136 days


title: CD19Jurkat_8172_single_0min_JH0026

tag: number of cells

tag: interaction duration


title: RNA-seq of Rattus norvegicus, adult male hippocampus I (DG) rep2

description:
Library name: HPC_I_CTRLLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: undistrubed control


title: HAP1, Non-targeting iTOP, 1440min, rep2

description: Library name: 1440NT2

value: near haploid chronic myelogenous leukemia KBM-7 derived

value: LbuCas13a and non-targeting gRNA transfection


title: Liver_AI_Male_2

description:
Library name: Sample_6
Liver_6

value: AI


title: CD19Jurkat_5589_p8_14min_JH0026

description:
1 Jurkat cells that interacted for 14min
processed data file: Counts_CAR.csv

value: Jurkat cells

tag: experiment id

tag: phenotype

value: GFP


title: RNA-seq of Rattus norvegicus, adult male hippocampus G (DG) rep1

description:
Library name: HPC_G_STRESSLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

tag: treatment

value: 3 h immob with predator scent


title: Drosophila S2 cells, ppp1r15 dsRNA #2 transfected, 2days, rep3

city: Shenzhen

first: Zhaowei

last: Wang

state: Guangdong

address: No.66, Gongchang Road, Guangming District

department: School of Ecology

institute: Sun Yat-sen University

description: Library name: dsppp1r15#2-3

data_processing:
Paired-end Illumina reads were adapter- and quality-trimmed with Trimmomatic v0.39 (parameters- ILLUMINACLIP:adapter.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36)
Trimmed reads were then aligned to the Drosophila melanogaster reference genome(dm6) using STAR v2.7.10a (parameters- twopassMode:Basic)
Read count extraction and normalization were performed using featureCounts.
Assembly: dm6
Supplementary files format and content: csv file include Transcripts Per Million (TPM) values for each sample

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Thermo Fisher Scientific, Cat #21720024)/10% fetal bovine serum (FBS), and incubated at 27°C.

extract_protocol:
48 hours after dsRNA transfection, total RNA was extracted from the cells using the RNA isolater Total RNA Extraction Reagent (Vazyme, Cat #R401-01).
(1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within certain size range. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

treatment_protocol: Drosophila S2 cells were grown to reach 70% confluence. After that, dsRNAs were transfected into the cells using FuGene HD transfection reagent (Promega, Cat #2311), following the manufacturer’s protocol.

value: embryonic cell

value: ppp1r15 dsRNA #2


title: CD19Jurkat_6128_p9_14min_JH0026


title: Liver_IVP_Male_1

description:
Library name: Sample_1
Liver_1

value: IVP

value: 143 days


title: RNA-seq of Rattus norvegicus, adult male hippocampus H (DG) rep2

description:
Library name: HPC_H_STRESSHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: brain, hippocampus

value: Sprague-Dawley

value: male


title: HAP1, Non-targeting iTOP, 1440min, rep1

description: Library name: 1440NT1


title: HAP1, Empty iTOP, 1440min, rep3

description: Library name: 1440EmptyTrt3

value: empty iTOP transfection


title: CD19Jurkat_5560_p7_13min_JH0025

description:
1 Jurkat cells that interacted for 13min
processed data file: Counts_CAR.csv


title: Drosophila S2 cells, ppp1r15 dsRNA #2 transfected, 2days, rep2

description: Library name: dsppp1r15#2-2


title: Drosophila S2 cells, ppp1r15 dsRNA #2 transfected, 2days, rep1

description: Library name: dsppp1r15#2-1


title: RNA-seq of Rattus norvegicus, adult male hippocampus L (DG) rep2

description:
Library name: HPC_L_STRESSHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: WT


title: CD19Jurkat_5170_p12_10min_JH0025

description:
1 Jurkat cells that interacted for 10min
processed data file: Counts_CAR.csv


title: HAP1, Empty iTOP, 1440min, rep2

description: Library name: 1440EmptyTrt2


title: RNA-seq of Rattus norvegicus, adult male hippocampus B (DG) rep2

description:
Library name: HPC_B_CTRLHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name


title: CD19Jurkat_5126_p16_10min_JH0026


title: CD19Jurkat_8896_p5_18_5min_JH0025

description:
1 Jurkat cells that interacted for 18.5min
processed data file: Counts_CAR.csv


title: RNA-seq of Rattus norvegicus, adult male hippocampus F (DG) rep1

description:
Library name: HPC_F_CTRLHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name


title: HAP1, Empty iTOP, 1440min, rep1

description: Library name: 1440EmptyTrt1


title: Drosophila S2 cells, ppp1r15 dsRNA #1 transfected, 2days, rep3

description: Library name: dsppp1r15#1-3

value: ppp1r15 dsRNA #1


title: HAP1, Non-targeting iTOP, 1440min, rep3

description: Library name: 1440NT3


title: HAP1, Untreated, 1440min, rep3

description: Library name: 1440Untrt3

value: untreated


title: CD19Jurkat_4821_single_0min_JH0026


title: CD19Jurkat_4

description:
500 Jurkat cells that did not interact
processed data file: Counts_CAR.csv


title: Drosophila S2 cells, ppp1r15 dsRNA #1 transfected, 2days, rep2

description: Library name: dsppp1r15#1-2


title: RNA-seq of Rattus norvegicus, adult male hippocampus D (DG) rep1

description:
Library name: HPC_D_STRESSHI
raw_counts_TPM_hpc.txt name in colum "sample" same as library name


title: HAP1, Untreated, 1440min, rep2

description: Library name: 1440Untrt2

value: near haploid chronic myelogenous leukemia KBM-7 derived


title: RNA-seq of Rattus norvegicus, adult male hippocampus A (DG) rep1

description:
Library name: HPC_A_CTRLLO
raw_counts_TPM_hpc.txt name in colum "sample" same as library name

value: undistrubed control


title: CD19Jurkat_3


title: Drosophila S2 cells, ppp1r15 dsRNA #1 transfected, 2days, rep1

description: Library name: dsppp1r15#1-1


title: HAP1, Untreated, 1440min, rep1

description: Library name: 1440Untrt1


title: RNA-seq of Rattus norvegicus, adult male amygdala 35 (BLA) rep4

description:
Library name: CTRL_LOW_AMG_35_S13
raw_counts_TPM_amg.txt name in colum "sample" same as library name

source_name: brain, amygdala

value: brain, amygdala


title: CD19Jurkat_2163_p14_12min_JH0025

description:
1 Jurkat cells that interacted for 12min
processed data file: Counts_CAR.csv

value: Jurkat cells


title: RNA-seq of Rattus norvegicus, adult male amygdala 34 (BLA) rep3

description:
Library name: STRESS_LOW_AMG_34_S12
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: CD19Jurkat_21156_p15_5min_JH0025

description:
1 Jurkat cells that interacted for 5min
processed data file: Counts_CAR.csv

value: GFP


title: Drosophila S2 cells, GFP dsRNA transfected, 2days, rep2

description: Library name: dsGFP-2

value: GFP dsRNA


title: HAP1, Targeting iTOP, 200min, rep2

description: Library name: 200T2

value: LbuCas13a and dEGFP targeting gRNA transfection


title: HAP1, Targeting iTOP, 200min, rep3

description: Library name: 200T3


title: RNA-seq of Rattus norvegicus, adult male amygdala 32 (BLA) rep3

description:
Library name: CTRL_HI_AMG_32_S11
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: Drosophila S2 cells, GFP dsRNA transfected, 2days, rep1

description: Library name: dsGFP-1

value: embryonic cell


title: CD19Jurkat_2


title: ACHN cells, passage 39, rep2

first: Wei

last: Yang

address: Shenzhen 6082 longgang Road

institute: Shenzhen Longgang Central Hospital

description: Library name: ACHN-P39-2

data_processing:
Raw reads were processed with fastp to remove low-quality reads, adapter contaminants, and reads with excessive N content, yielding clean reads.
rRNA contamination was eliminated by aligning reads to an rRNA database using bowtie2.
The remaining reads were mapped to the reference genome using HISAT2, and mapping efficiency was calculated.
Gene expression levels (FPKM and TPM) were estimated with StringTie and RSEM.
Assembly: GRCh38 for Homo sapiens; GRCm39 for Mus musculus
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: ACHN

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA purity was assessed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), concentration was measured using a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and integrity (RIN value) was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). After quality control, mRNA was enriched using Oligo(dT) magnetic beads, and first-strand cDNA was synthesized with M-MuLV Reverse Transcriptase. RNA templates were degraded by RNase H, and second-strand cDNA was synthesized. Subsequent steps included end repair, poly-A tailing, adapter ligation, and size selection (~200 bp) using AMPure XP beads, followed by PCR amplification for library construction.
RNA libraries for RNA-seq were prepared using New England Biolabs (#E7530 ) following manufacturer's protocols.

value: ACHN

value: Renal Cell Adenocarcinoma Cell

value: Routine Passaging


title: HAP1, Targeting iTOP, 200min, rep1

description: Library name: 200T1


title: RNA-seq of Rattus norvegicus, adult male amygdala 30 (BLA) rep2

description:
Library name: STRESS_LOW_AMG_30_S10
raw_counts_TPM_amg.txt name in colum "sample" same as library name

value: Sprague-Dawley

value: 3 h immob with predator scent


title: ACHN cells, passage 39, rep1

description: Library name: ACHN-P39-1


title: CD19Jurkat_16771_p2_5_5min_JH0026

description:
1 Jurkat cells that interacted for 5.5min
processed data file: Counts_CAR.csv


title: HAP1, Non-targeting iTOP, 200min, rep3

description: Library name: 200NT3

value: LbuCas13a and non-targeting gRNA transfection


title: CD19Jurkat_16475_p1_4_5min_JH0026

description:
1 Jurkat cells that interacted for 4.5min
processed data file: Counts_CAR.csv


title: RNA-seq of Rattus norvegicus, adult male amygdala 27 (BLA) rep2

description:
Library name: CTRL_LOW_AMG_27_S8
raw_counts_TPM_amg.txt name in colum "sample" same as library name

value: male

value: WT


title: HAP1, Non-targeting iTOP, 200min, rep2

description: Library name: 200NT2


title: RNA-seq of Rattus norvegicus, adult male amygdala 28 (BLA) rep3

description:
Library name: CTRL_LOW_AMG_28_S9
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: CD19Jurkat_16257_single_0min_JH0025

description:
1 Jurkat cells that did not interact
processed data file: Counts_CAR.csv


title: ACHN cells, passage 24, rep1

description: Library name: ACHN-P24-1


title: ACHN cells, passage 24, rep2

description: Library name: ACHN-P24-2


title: Drosophila S2 cells, GFP dsRNA transfected, 2days, rep3

description: Library name: dsGFP-3


title: ACHN cells, passage 17, rep2

description: Library name: ACHN-P17-2


title: HAP1, Non-targeting iTOP, 200min, rep1

description: Library name: 200NT1


title: CD19Jurkat_14722_p10_4_5min_JH0026


title: HAP1, Empty iTOP, 200min, rep3

description: Library name: 200EmptyTrt3

value: empty iTOP transfection


title: RNA-seq of Rattus norvegicus, adult male amygdala 20 (BLA) rep3

description:
Library name: STRESS_HI_AMG_20_S6
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: ACHN cells, passage 17, rep1

description: Library name: ACHN-P17-1


title: HAP1, Empty iTOP, 200min, rep2

description: Library name: 200EmptyTrt2

value: near haploid chronic myelogenous leukemia KBM-7 derived


title: CD19Jurkat_13868_p14_10min_JH0026

description:
1 Jurkat cells that interacted for 10min
processed data file: Counts_CAR.csv


title: RNA-seq of Rattus norvegicus, adult male amygdala 19 (BLA) rep2

description:
Library name: STRESS_HI_AMG_19_S5
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: HAP1, Empty iTOP, 200min, rep1

description: Library name: 200EmptyTrt1


title: ACHN cells, passage 10, rep2

description: Library name: ACHN-P10-2


title: CD19Jurkat_14372_p1_4_5min_JH0025


title: HAP1, Untreated, 200min, rep3

description: Library name: 200Untrt3

value: untreated


title: RNA-seq of Rattus norvegicus, adult male amygdala 17 (BLA) rep2

description:
Library name: CTRL_HI_AMG_17_S4
raw_counts_TPM_amg.txt name in colum "sample" same as library name

value: brain, amygdala

value: undistrubed control


title: RNA-seq of Rattus norvegicus, adult male amygdala 14 (BLA) rep1

description:
Library name: CTRL_HI_AMG_14_S3
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: ACHN cells, passage 3, rep2

description: Library name: ACHN-P3-2


title: CD19Jurkat_1

description:
500 Jurkat cells that did not interact
processed data file: Counts_CAR.csv

value: Jurkat cells

value: GFP


title: HAP1, Untreated, 200min, rep2

description: Library name: 200Untrt2


title: RNA-seq of Rattus norvegicus, adult male amygdala 7 (BLA) rep1

description:
Library name: STRESS_HI_AMG_7_S2
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: CAF_8245_single_0min_JH0022

description:
1 CAF cells that did not interact
processed data file: Counts_CAR.csv

source_name: CAF cells

value: CAF cells


title: RNA-seq of Rattus norvegicus, adult male amygdala 22 (BLA) rep1

description:
Library name: STRESS_LOW_AMG_22_S7
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: ACHN cells, passage 3, rep1

description: Library name: ACHN-P3-1


title: HAP1, Untreated, 200min, rep1

description: Library name: 200Untrt1


title: HAP1, Targeting iTOP, 50min, rep3

description: Library name: 50T3

value: LbuCas13a and dEGFP targeting gRNA transfection


title: CAF_7394_single_0min_JH0022


title: RNA-seq of Rattus norvegicus, adult male amygdala 2 (BLA) rep1

description:
Library name: CTRL_LOW_AMG_2_S1
raw_counts_TPM_amg.txt name in colum "sample" same as library name


title: breast cancer cell exosomes, Treat3

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

data_processing:
Firstly, fastp software (v0.20.0) was used to trim adaptor and filter low-quality reads to get high-quality clean reads. Then, clean reads from all samples were merged, and miRdeep2 software (v0.1.3) was used to predict novel miRNAs.
The clean reads were then aligned to the merged human miRNA databases (miRNA from miRbase v22.1 plus the newly predicted novel miRNAs) using Novoalign software (v3.09.04) with at most one mismatch.
The mapped miRNA read counts were defined as the raw expression levels of that miRNA. The read counts were then normalized by DESeq2 R packages (v1.30.1). Differentially expressed miRNAs between two groups were filtered through fold change and pvalue.
Genome_build: miRBase v22.1
Supplementary_files_format_and_content: miRNA Expression Profiling.xlsx

source_name: cell supernatant

extract_protocol: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on following the manufacturer's instructions.

value: breast cancer cells

value: DOX treatment

tag: sample type

value: exosome


title: HAP1, Targeting iTOP, 50min, rep2

description: Library name: 50T2


title: CAF_5582_single_0min_JH0022


title: breast cancer cell exosomes, Treat2


title: CAF_515_single_0min_JH0022


title: CD19Jurkat_13190_396_p13_11min_JH0026

description:
1 Jurkat cells that interacted for 11min
processed data file: Counts_CAR.csv


title: breast cancer cell exosomes, Treat1


title: breast cancer cell exosomes, Con3

value: Control


title: CAF_2905_single_0min_JH0022


title: HAP1, Non-targeting iTOP, 50min, rep3

description: Library name: 50NT3


title: ACHN cells, passage 10, rep1

description: Library name: ACHN-P10-1

value: ACHN

value: Renal Cell Adenocarcinoma Cell

value: Routine Passaging


title: breast cancer cell exosomes, Con2


title: CAF_16741_single_0min_JH0029


title: HAP1, Non-targeting iTOP, 50min, rep2

description: Library name: 50NT2

value: LbuCas13a and non-targeting gRNA transfection


title: CAF_15831_single_0min_JH0029


title: HAP1, Non-targeting iTOP, 50min, rep1

description: Library name: 50NT1


title: CAF_14577_single_0min_JH0030


title: breast cancer cell exosomes, Con1


title: HAP1, Empty iTOP, 50min, rep3

description: Library name: 50EmptyTrt3

value: empty iTOP transfection


title: collagen domain, M-1

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

description: Library name: 1275

data_processing:
STAR was used to align FASTQ files to genome.
BAM files were used to generate gene counts using Rsamtools and the summarize overlaps function with the Genomic Alignments package.
Differential gene expression analysis was performed with the DESeq2 package.
Assembly: GRCm39.107
Supplementary files format and content: comma-separated files include count values for each sample

source_name: brain

extract_protocol:
RNA was extracted from frozen, pulverized forebrains using TRIzol reagent (Invitrogen) followed by an RNeasy mini column (Qiagen) with an on-column DNase treatment.
RNA sequencing libraries were contructed using Illumina's TruSeq RNA Library Prep kit version 2; libraries were sequenced on paired-end, 75-bp runs on a NextSeq 500 using a pooled strategy to minimize batch effects.

treatment_protocol: Neonatal mice were injected intracerebralventricularly with rAAV encoding Collagen Domain constructs or PBS (control) were aged 3 months and euthanized,brains were harvested. One hemibrain was snap-frozen in isopentane on dry ice and then stored at -80 degrees C until pulverized and  homogenized for RNA extractions.

value: brain

value: collagen domain

tag: Sex

value: M

tag: age

value: 3 months


title: CAF_13925_single_0min_JH0030


title: HAP1, Empty iTOP, 50min, rep2

description: Library name: 50EmptyTrt2

value: near haploid chronic myelogenous leukemia KBM-7 derived


title: K20_m_47

type: RNA

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix Expression Console 1.4.1.46 for normalization (SST-RMA); BRB Array (https://brb.nci.nih.gov/BRB-ArrayTools/) tools for statistical analysis

label: Biotin

extract_protocol: Blood samples were collected in PAXgene® Blood RNA tubes and stored according to manufacturer’s protocol at –80-degree Celsius. RNA was then extracted using the MagNA Pure 96 Cellular RNA Large Volume Kit following the manufacturer’s instructions.

value: male

tag: group

value: Healthy Control


title: K22_f_52

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

value: female


title: PBS, M-3

description: Library name: 1321

value: PBS


title: collagen domain, F-2

description: Library name: 1282

value: F


title: K8_f_41


title: K3_f_29


title: K25_m_33


title: HAP1, Targeting iTOP, 50min, rep1

description: Library name: 50T1

value: LbuCas13a and dEGFP targeting gRNA transfection


title: K21_m_39


title: PBS, F-3

description: Library name: 1294


title: CAF_10406_single_0min_JH0022

value: CAF cells


title: aCD19CAR_9249_p7_13min_JH0025

description:
1 aCD19CAR cells that interacted for 13min
processed data file: Counts_CAR.csv

value: aCD19CAR cells


title: CAF_1147_single_0min_JH0029


title: PBS, F-2

description: Library name: 1281


title: aCD19CAR_9193_single_0min_JH0025

description:
1 aCD19CAR cells that did not interact
processed data file: Counts_CAR.csv


title: HAP1, Untreated, 50min, rep3

description: Library name: 50Untrt3

value: untreated


title: HAP1, Empty iTOP, 50min, rep1

description: Library name: 50EmptyTrt1


title: K30_m_29


title: K18_f_25


title: PBS, M 2

description: Library name: 1285


title: HAP1, Untreated, 50min, rep1

description: Library name: 50Untrt1


title: K2_m_28


title: aCD19CAR_874_p13_9_5min_JH0028

description:
1 aCD19CAR cells that interacted for 9.5min
processed data file: Counts_CAR.csv


title: PBS, M-1

description: Library name: 1300


title: K26_f_24


title: 10x Visium, Ciona_brain_No.4

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

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in a 28+100-base paired-end mode.
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger version: 2.0.0 (10X Genomics).
Assembly: genome: Ciona intestinalis HT (Hoya T-line) assembly 2019 (NCBI GenBank GCA_009617815.1), gene model: KY21 Gene Model (http://ghost.zool.kyoto-u.ac.jp/download_ht.html)
Supplementary files format and content: matrix_Ciona_brain_No_*.csv: the filtered matrix of UMI counts for each gene-spatial barcode combination
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene ID
Supplementary files format and content: matrix.mtx.gz: non-zero gene expresion raw UMI count data in Matrix Market Exchange Formats
Supplementary files format and content: tissue_positions.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue
Library strategy: Visium Spatial Transcriptomics

organism: Ciona intestinalis

source_name: neural complex

extract_protocol:
Vase tunicate brain slide gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard MGI protocols.

tag: type

value: Type A

value: neural complex

value: WT

tag: developmental stage

value: Adult


title: K24_f_24


title: aCD19CAR_8314_p5_22_5min_JH0026

description:
1 aCD19CAR cells that interacted for 22.5min
processed data file: Counts_CAR.csv


title: collagen domain, F-3

description: Library name: 1292

value: brain

value: collagen domain


title: K17_m_24


title: 10x Visium, Ciona_brain_No.3


title: HAP1, Untreated, 50min, rep2

description: Library name: 50Untrt2


title: 10x Visium, Ciona_brain_No.2


title: collagen domain, M-2

description: Library name: 1345

value: M

value: 3 months


title: collagen domain, F-1

description: Library name: 1284


title: aCD19CAR_8133_single_0min_JH0024


title: coro1a-DsRed cells,ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 hpf, atac-seq, rep2

city: Chongqing

first: he

last: yuepeng

state: Chongqing

address: No.266 Fangzheng Avenue,Shuitu Hi-tech Industrial Park, Shuitu Town, Beibei District, Chongqing

institute: Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences

description: Library name: sample16

data_processing:
RNA-seq was performed using the PE100 strategy on the Illumina HiSeq 2500 (Anoroda Corporation). Reads were aligned to the zebrafish reference genome (Danio rerio, GRCz11), and differentially expressed genes (DEGs) were identified with DESeq2 (v1.32.0) using P < 0.05. Functional enrichment of DEGs was analyzed with ClusterProfiler.  For ATAC-seq, adapters and low-quality bases (phred < 10) were removed with Trimmomatic (v0.38). Clean reads were aligned to the reference genome using Bowtie2 (v2.4.3), and properly paired reads (MAPQ ≥ 30) were retained with Samtools (v1.9). PCR duplicates were removed with Picard, and organelle contamination was excluded. Chromatin integrity was evaluated by insertion size distribution (R v3.5.1) and TSS enrichment scores following ENCODE guidelines. Peaks were called with MACS2 using parameters --nomodel --shift 75 --extsize 150. Reproducibility was assessed with pseudo-replicates, and differential peaks were analyzed with DiffBind (v3.4.5) and DESeq2.  For scRNA-seq, low-quality cells were filtered out (200–6,000 genes, UMI > 1,000, mitochondrial content < 10%). Data were normalized with Seurat (LogNormalize), and the top 2,000 variable genes were identified with the vst method. After regressing out nCount_RNA and percent.mito, PCA was performed, followed by UMAP and t-SNE using the top 50 PCs. Clustering was performed with Seurat (resolution = 1.2) using the Louvain algorithm on a shared nearest-neighbor graph. Cell trajectory and pseudotime analyses were performed with Monocle 2.
Assembly: GRCz11
Supplementary files format and content: Matrix Market format files (.mtx) containing gene-by-cell UMI count matrix, accompanied by cell annotation file (.tsv) with cell barcodes, and gene annotation file (.tsv) with gene IDs and names.

organism: Danio rerio

source_name: coro1a-DsRed cells, ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 hpf

extract_protocol:
Tg(coro1a:DsRed) embryos from WT, Tg(coro1a:HA-ikzf1), Tg(coro1a:FLAG-myb), and ikzf1Δ4+3/Δ4+3; mybhkz3/hkz3 (DM) embryos were collected at 24–30 hpf. Embryos were dissociated with a Papain Dissociation Kit (Worthington) in DPBS at 37 °C for 20–30 minutes to obtain single-cell suspensions, which were generated by gentle trituration, filtered through 40–70 μm strainers, and sorted by FACS. Sorted coro1a-DsRed+ cells (about 5,000 for ATAC-seq, larger pools for Smart-seq) were subsequently processed using established protocols, with single-cell suspensions loaded onto Single Cell G Chips (v3.1 chemistry, PN1000120).
RNA-seq libraries were prepared from total RNA extracted with the TRIzol Reagent Kit (Invitrogen) following the manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer and agarose gel electrophoresis. Eukaryotic mRNA was enriched with Oligo(dT) beads, and prokaryotic mRNA by rRNA depletion (Ribo-Zero Magnetic Kit, Epicentre). Enriched mRNA was fragmented, reverse-transcribed, and converted to double-stranded cDNA. After end repair, A-tailing, and adapter ligation, libraries were size-selected, PCR-amplified, and sequenced on an Illumina NovaSeq 6000 (Gene Denovo, Guangzhou, China).  For ATAC-seq, nuclei were isolated with cell lysis buffer, and Tn5 transposase was used to fragment accessible DNA. After PCR amplification, libraries were sequenced on the Illumina platform using a PE150 strategy, generating ~20 Gb of raw data.  Single-cell RNA-seq libraries were generated using the Chromium Single Cell Gene Expression system (10x Genomics) with the v3.1 reagent kit (PN-1000121). Single-cell suspensions were loaded onto Chromium Chips, processed on the Chromium Controller to form GEM partitions, and libraries were prepared according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 using the S4 Reagent Kit v1.5 (PN-20028312).

value: embryos coro1a-DsRed positive myeloid cells

value: myeloid cell

value: ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM)


title: aCD19CAR_671_p3_4_5min_JH0028

description:
1 aCD19CAR cells that interacted for 4.5min
processed data file: Counts_CAR.csv


title: 10x Visium, Ciona_brain_No.1


title: PBS, F-1

description: Library name: 1244

value: PBS


title: aCD19CAR_7593_p11_10min_JH0025

description:
1 aCD19CAR cells that interacted for 10min
processed data file: Counts_CAR.csv


title: 6_m_63

value: male

value: Suicide Attempt


title: aCD19CAR_4687_p2_4_5min_JH0028


title: coro1a-DsRed cells,ikzf1del4+3/del4+3; mybhkz3/hkz3 (DM), 30 hpf, atac-seq, rep1

description: Library name: sample15


title: K1_f_18

value: female

value: Healthy Control


title: aCD19CAR_440_single_0min_JH0028

value: aCD19CAR cells


title: aCD19CAR_8255_single_0min_JH0024


title: coro1a-DsRed cells, ikzf1+/+;myb+/+ (WT), 30 hpf, atac-seq, rep1

description: Library name: sample13


title: 19_f_60


title: 13_m_58


title: aCD19CAR_4241_p9_14min_JH0026

description:
1 aCD19CAR cells that interacted for 14min
processed data file: Counts_CAR.csv


title: 1Et_S2

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: Library name: 1Et_S2

data_processing:
Genome alignment, quality control, and differential gene expression were analyzed using Partek Flow (Partek, St. Louis, MO, USA).
Contaminants were removed using Bowtie 2 v2.2.5, and the reads were aligned to the reference genome (mm10) using STAR 2.7.8a.
Aligned reads were quantified using RefSeq Transcripts 96. Features (genes) were filtered to retain only those with at leats 10 reads.
Normalization was done with TMM, followed by transformation by log2 (+0.0001 -TMM - log2)
Assembly: mm10
Supplementary files format and content: .txt

growth_protocol: ATDC5 cells were grown in maintenance medium (DMEM/F-12) containing 5% FBS and 1% Pen/Strepto. The media is thenenriched by adding 50 µg/mL sodium ascorbate, 10 mM beta-glycero phosphate, and 1 X Insulin-Transferrin-Selenium an dexposed to the treatments.

extract_protocol:
RNA from ATDC5 cell culture was isolated using Trireagent
The libraries were generated using the Illumina Stranded mRNA Prep kit

treatment_protocol: For in vivo analyses, C57BL/6 female mice were purchased from Charles River laboratory and were blindly randomized into 4 groups with 10 mice in each group as follows: lean (L), lean+estrogen-pelleted (L+P), obese (O), and obese+estrogen-pelleted (O+P). Two groups were fed a normal chow diet while the other two groups were fed a high fat diet (HFHSD; 29% Fat Kcal, Teklad) for 3 months, and the body weight of each mouse was recorded until the experiments were completed. The obese mice were administered with a subcutaneous 17 β Estradiol tablet 800 µg/mouse (Innovative Research of America; E-121, FL, USA). Livers were collected. For in vitro assays, HepG2 (1x106) cells were seeded out into a 6-well plate and allowed to attach overnight and treated with β-Estradiol (25 nM) and CoCl2 (50 µM) for 4 hours. RNA was extracted

value: chondrogenic cell line

value: Ethanol


title: collagen domain, M-3

description: Library name: 1280


title: coro1a-DsRed cells, Tg(coro1a:FLAG-myb), 30 hpf, atac-seq, rep2

description: Library name: sample12


title: aCD19CAR_410_single_0min_JH0028


title: 3Ac_S9

description: Library name: 3Ac_S9

value: Acetate


title: coro1a-DsRed cells, Tg(coro1a:FLAG-myb), 30 hpf, atac-seq, rep1

description: Library name: sample11


title: 22_f_53


title: 20_m_47


title: K27_m_23


title: 3Et_S8

description: Library name: 3Et_S8


title: aCD19CAR_396_p13_11min_JH0026

description:
1 aCD19CAR cells that interacted for 11min
processed data file: Counts_CAR.csv


title: coro1a-DsRed cells, ikzf1+/+;myb+/+ (WT), 30 hpf, atac-seq, rep2

description: Library name: sample14


title: 16_f_45


title: coro1a-DsRed cells, Tg(coro1a:HA-ikzf1), 30 hpf, atac-seq, rep2

description: Library name: sample10


title: 2Et_S5

description: Library name: 2Et_S5


title: 1Ac_S3

description: Library name: 1Ac_S3


title: aCD19CAR_33418_p5_18_5min_JH0025

description:
1 aCD19CAR cells that interacted for 18.5min
processed data file: Counts_CAR.csv


title: coro1a-DsRed cells, Tg(coro1a:HA-ikzf1), 30 hpf, atac-seq, rep1

description: Library name: sample9


title: coro1a-DsRed cells, WT, 30 hpf, atac-seq, rep2

description: Library name: sample8

source_name: coro1a-DsRed cells, WT, 30 hpf

value: WT


title: 3cntrl_S7

description: Library name: 3cntrl_S7

value: Control


title: aCD19CAR_3331_p11_9min_JH0028

description:
1 aCD19CAR cells that interacted for 9min
processed data file: Counts_CAR.csv


title: aCD19CAR_2944_p11_15min_JH0024

description:
1 aCD19CAR cells that interacted for 15min
processed data file: Counts_CAR.csv


title: 21_m_37


title: 2cntrl_S4

description: Library name: 2cntrl_S4


title: coro1a-DsRed cells, WT, 30 hpf, atac-seq, rep1

description: Library name: sample7


title: 1cntrl_S1

description: Library name: 1cntrl_S1


title: 10_f_55


title: aCD19CAR_28413_p8_16min_JH0025

description:
1 aCD19CAR cells that interacted for 16min
processed data file: Counts_CAR.csv


title: CIK_GCRV-2

city: WuHan

first: Wang

middle: Yang

address: IHB

institute: IHB

description: Library name: CIK_GCRV-2

data_processing:
HISAT2
Assembly: ASM1834038v1
Supplementary files format and content: tab-delimited text fle includes raw fpkm for each Sample

organism: Ctenopharyngodon idella

source_name: Ctenopharyngodon idellus kidney cells

extract_protocol:
Total RNAs were extracted using the Trizol reagent (Invitrogen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kit followingmanufacturer's protocols.

value: Ctenopharyngodon idellus kidney cells

value: GCRV infected


title: 11_m_27


title: 2Ac_S6

description: Library name: 2Ac_S6


title: 5_f_43


title: CIK_GCRV-1

description: Library name: CIK_GCRV-1


title: 30_m_34


title: 24_f_26


title: CIK_GCRV_PZC10-2

description: Library name: CIK_GCRV_PZC10-2

value: Cortisol; GCRV infected


title: 7_m_24


title: SCA6, cerebellum, 19 months, sample 3

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
FastQC for raw read quality
Trimmomatic for trimming reads and adapters
STAR for read alignment to MM10 genome
DESeq2 analysis for DEGs
GO analysis using ToppFunn and SynGO
Assembly: MM10
Supplementary files format and content: TXT, Count table

source_name: cerebellum

extract_protocol:
RNA extraction
150 bp paired end reads

value: cerebellum

value: HET

value: 19 months


title: Hypothalamus, spring, resident junco_rep7

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

description: Library name: Res_8

data_processing:
Sequenced reads were de-multiplexed using bcl2fastq version v2.20.0.422.
Raw reads were adapter trimmed and quality filtered using Trimmomatic version 0.33 (Bolger et al. 2014) requiring a minimum base quality score of 20 averaged across a sliding window of 3 bases. Reads shorter than 20 bases post trimming were discarded.
Trimmed reads were mapped to the dark-eyed junco draft genome assembly sequence using the RNA-Seq read aligner STAR version 2.5.3a (Dobin et al., 2013).
Regions within the dark-eyed junco draft genome assembly that shared homology with protein sequences from the zebra finch (Taeniopygia guttata, ENSEMBL release 80, version taeGut3.2.4 — https://may2015.archive.ensembl.org/Taeniopygia_guttata/Info/Index) were identified and annotated as putative transcribed elements using GMAP (version gmap-gsnap-2018-03-25; Wu, 2005).
The expression of these transcribed elements was quantified by counting the number reads mapping to each of these regions using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple transcribed elements were excluded. (parameters: -s 2 -p -B -C)
Assembly: Dark-eyed junco draft genome assembly
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with putative transcribed elements annotated on the Junco genome assembly.

organism: Junco hyemalis

source_name: Brain (Hypothalamus)

extract_protocol:
A total of 6 migrant and 7 resident junco hypothalamii were punched and homogenized in RLT buffer containig 1% 2-Mercaptoethanol on ice. Total RNA was prepared using AllPrep DNA/RNA Universal Kit (Qiagen, Cat. # 80224). RNA integrity and concentration were determined using Agilent 2200 Tapestation System.
The RNAseq libraries were generated using the TruSeq Stranded mRNA kit protocol. The integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were used for library preparation. The mRNA was purified from 200ng of total RNA for each sample, after cDNA synthesis and adapter ligation, the library was amplified with 12 rounds of PCR cycles. The enriched and cleaned libraries were pooled and loaded on the sequencer.

value: Brain (Hypothalamus)

value: Male

value: Spring sample (March 2017)


title: CIK_GCRV_PZC10-1

description: Library name: CIK_GCRV_PZC10-1


title: Hypothalamus, spring, resident junco_rep6

description: Library name: Res_5


title: SCA6, cerebellum, 19 months, sample 4


title: aCD19CAR_2544_p5_18min_JH0028

city: Vienna

first: Jakob

last: Huemer

address: Zimmermannpl. 10

institute: Children’s Cancer Research Institute

description:
1 aCD19CAR cells that interacted for 18min
processed data file: Counts_CAR.csv

data_processing:
Raw reads were trimmed using trimmomatic (version 0.32)
aligned to the mouse reference genome (mm10) using HISAT2 (version 2.1.0)
Uniquely mapped reads for each exon were counted using the function summarizeOverlaps from the Ge-nomicAlignments package (version 1.12.0) in R (version 3.4.0)
Gene and exon annotations were obtained from the Ensembl GENCODE Basic set (genome-build GRCh38)
Assembly: hg38
Supplementary files format and content: csv file of read counts

source_name: aCD19CAR cells

extract_protocol:
RNA was isolated according to Smart-seq2 was performed as described previously (Picelli et.  al., 2014). In brief, cells were lysed in 0.2% Triton X-100 in the presence of RNase inhibitor 40 U/µl RNase inhibitor (Takara) and stored at -80°C until ready to proceed.
RNA was denatured, reverse transcribed and amplified for 22 cycles. After reverse transcription, 1 ng cDNA was tagmented, amplified and barcoded following the Illumina Nextera indexing strategy. Final libraries were pooled to 4 nM for sequencing on HiSeq3000/4000. cDNA and library quality was assessed using TapeStation 4150 instrument and D5000HS or D1000 screening tapes (Agilent), respectively. DNA concentration was determined using Qubit dsDNA HS kit and instrument (Invitrogen). cDNA and Illumina Nextera indexed samples were purified using Ampure XP beads (Beckman Coulter) at 1:1 ratio. Sequencing was performed by the Biomedical Sequencing Facility at CeMM at 50bp single-end configuration.


title: SCA6, cerebellum, 19 months, sample 2


title: CIK_GCRV_RS10-2

description: Library name: CIK_GCRV_RS10-2

value: Lactate; GCRV infected


title: 1_f_20

value: female

value: Suicide Attempt


title: aCD19CAR_23105_p15_5min_JH0025

description:
1 aCD19CAR cells that interacted for 5min
processed data file: Counts_CAR.csv

value: aCD19CAR cells


title: SCA6, cerebellum, 19 months, sample 1


title: aCD19CAR_26979_p12_10min_JH0025


title: Hypothalamus, spring, resident junco_rep5

description: Library name: Res_4


title: aCD19CAR_21887_p14_12min_JH0025

description:
1 aCD19CAR cells that interacted for 12min
processed data file: Counts_CAR.csv


title: Hypothalamus, spring, resident junco_rep4

description: Library name: Res_14


title: CIK_GCRV_RS10-1

description: Library name: CIK_GCRV_RS10-1


title: aCD19CAR_2018_p10_14_5min_JH0024

description:
1 aCD19CAR cells that interacted for 14.5min
processed data file: Counts_CAR.csv


title: aCD19CAR_2010_p9_10min_JH0024


title: SCA6, cerebellum, 19 months, sample 5


title: wild-type, cerebellum, 19 months, sample 5


title: CIK_PZC2-2

description: Library name: CIK_PZC2-2

value: Cortisol


title: Hypothalamus, spring, resident junco_rep3

description: Library name: Res_13


title: aCD19CAR_18489_p1_4_5min_JH0025


title: CIK_PZC2-1

description: Library name: CIK_PZC2-1


title: Hypothalamus, spring, resident junco_rep2

description: Library name: Res_11


title: wild-type, cerebellum, 19 months, sample 4


title: aCD19CAR_1808_p10_9min_JH0028


title: CIK_RS10-2

description: Library name: CIK_RS10-2

value: Lactate


title: Hypothalamus, spring, resident junco_rep1

description: Library name: Res_10


title: aCD19CAR_1492_p10_4_5min_JH0026


title: CIK_RS10-1

description: Library name: CIK_RS10-1


title: wild-type, cerebellum, 19 months, sample 2

value: WT


title: Hypothalamus, spring, migrant junco_rep6

description: Library name: Mig_9


title: CIK_Null-2

description: Library name: CIK_Null-2


title: wild-type, cerebellum, 19 months, sample 1


title: aCD19CAR_14867_p8_14min_JH0026


title: aCD19CAR_1366_single_0min_JH0025


title: Hypothalamus, spring, migrant junco_rep5

description: Library name: Mig_7


title: SCA6, cerebellum, 12 months, sample 5

value: 12 months


title: CIK_Null-1

description: Library name: CIK_Null-1

value: Ctenopharyngodon idellus kidney cells


title: Hypothalamus, spring, migrant junco_rep4

description: Library name: Mig_6


title: drmy1 Biol Rep 2

city: Villa Park

first: Byron

last: Rusnak

state: IL

address: 128 E Division st

department: Plant Biology

institute: Cornell University

description:
Library name: drmy1-2
10x Genomics

data_processing:
Raw single cell data reads were converted to fastq format with cellranger v7.0.1 mkfastq and biological replicates were aggregated and converted to feature matrices with cellranger count using default settings
Assembly: TAIR10 v6.0.2 Arabidopsis genome
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in matrix

organism: Arabidopsis thaliana

source_name: flower bud

growth_protocol: 16 degrees celsius, 24 hour light, 100 µmol m−2 s−1

extract_protocol:
Once ap1 cal AP1-GR  and drmy1 ap1 cal AP1-GR plants began to bolt, they were induced with 10 μM Dexamethasone in 0.015% Silwet (vol/vol) three times at roughly 24 hour intervals. About 108 hours (4 ½ days) after the first induction, when flower buds had reached stages 2-3, whole cauliflower-like inflorescences were cut and incubated in protoplasting solution, filtered, pelleted, and washed as described in Satterlee et al. 2020 with the following adjustments: cells were incubated in protoplasting solution for 90 minutes, were passed through a 70 micron filter once and a 40 micron filter twice, and 5 μg/mL final concentration of fluorescein diacetate (FDA) was added after the final resuspension in 50-100 µL wash solution to stain live cells for counting. Two biological replicates were protoplasted per genotype using 0.25-0.6 g of tissue per replicate.
Library was constructed according to manufacturers protocol (10x Genomics 3' single cell RNAseq pipeline HT kit v3)

treatment_protocol: AP1-GR induced in 10 uM Dexamethasone once daily for 3 days (1 minute each day).

value: flower bud


title: aCD19CAR_13359_p16_10min_JH0026


title: SCA6, cerebellum, 12 months, sample 3


title: drmy1 Biol Rep 1

description:
Library name: drmy1-1
10x Genomics


title: Hypothalamus, spring, migrant junco_rep2

description: Library name: Mig_2


title: aCD19CAR_13482_p14_10min_JH0026


title: SCA6, cerebellum, 12 months, sample 4


title: aCD19CAR_1219_single_0min_JH0026


title: SCA6, cerebellum, 12 months, sample 2


title: Hypothalamus, spring, migrant junco_rep3

description: Library name: Mig_3


title: WT Biol Rep 2

description:
Library name: WT2
10x Genomics


title: Hypothalamus, spring, migrant junco_rep1

description: Library name: Mig_1


title: aCD19CAR_1074_single_0min_JH0026


title: wild-type, cerebellum, 19 months, sample 3


title: SCA6, cerebellum, 12 months, sample 1


title: WT Biol Rep 1

description:
Library name: WT1
10x Genomics


title: aCD19CAR_1049_p4_19min_JH0028

description:
1 aCD19CAR cells that interacted for 19min
processed data file: Counts_CAR.csv


title: 210310_A00902_A_L002_ALPZ-5-9_R1.fastq.gz

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

data_processing:
Only reads R1 from paired reads (R1, R2) were used for the data analysis for each sample.
Data analyses were performed using CLC Genomics Workbench 21.0.5 (QIAGEN Aarhus A/S). Adapters were removed in two steps: firstly by automatic adapter read-through trimming together with low quality sequence removal (limit=0.05) and ambiguous nucleotides removal (max. 2 ambiguous nucleotides), secondly by adapter sequences trimming together with low quality sequence removal (limit=0.05), ambiguous nucleotides removal (max. 2 ambiguous nucleotides) and removal of sequences on length: minimum length 18 nucleotides and maximum length 25 nucleotides.
Counts were normalized per 1 000 000 reads. Experiment was performed by two group comparison (samples treated by high temperature vs. control temperature for 1h, 3h and 6h).
Annotation (strand specific, without mismatches) was carried out using miRbase Sequence database, release 22. Then statistical analyses were performed using EDGE method (Empirical analysis of DGE).
Assembly: miRBase, release 22
Supplementary files format and content: .xlsx, two group comparison (samples treated by high temperature vs. control temperature for 1h)
Supplementary files format and content: .xlsx, two group comparison (samples treated by high temperature vs. control temperature for 3h)
Supplementary files format and content: .xlsx, two group comparison (samples treated by high temperature vs. control temperature for 6h)

organism: Hordeum vulgare

source_name: shoot

growth_protocol: Seeds of spring barley, line Rolap, were germinated on wet, sterile Whatman filter paper for 2 days in a plant growth chamber under long-day (16h) condition, at 22°C. Then three germinated seedlings were transferred to a pot with soil/sand (7:2). Pots were kept at BDW120 High-Light Plant Growth Room (Conviron) with 600 mmol/(m2×s) light. Plants were grown up to two weeks at 21 ºC day/15 ºC night temperature and were watered to maintain optimal growth conditions of 70% SWC (Soil Water Content). Samples were collected at 1h, 3h and 6h from heat treated and control plants.

extract_protocol:
Shoots of two-week-old barley plants were collected in three biological replicates. The extraction of total RNA was performed using 100 mg of the ground material and 1 ml of extraction buffer (described previously: Smoczynska A, Sega P, Stepien A, Knop K, Jarmolowski A, Pacak A, Szweykowska-Kulinska Z. miRNA Detection by Stem-Loop RT-qPCR in Studying microRNA Biogenesis and microRNA Responsiveness to Abiotic Stresses. Methods Mol Biol. 2019;1932:131-150. doi: 10.1007/978-1-4939-9042-9_10) supplemented with 70 µl of Plant RNA Isolation Aid reagent (Invitrogen). Further steps were carried out using Direct-zol RNA Mini Prep Kit (Zymo Research) without DNase treatment according to the manufacturer’s protocol.
Libraries were constructed using the TruSeq Small RNA Library Preparation Kit (Illumina) according to the manufacturer's protocol. Libraries were sequenced at FASTERIS SA, 1228 Plan-les-Ouates, Switzerland. Nine libraries were pooled and placed on one lane.

treatment_protocol: Two-week-old barley were exposed to high temperature 35.5°C and control temperature (21°C). The analysed samples were derived from plants exposed for 1h, 3h and 6h of high temperature, and parallelly from plants grown in control temperature.

value: shoot

value: Rolap

value: control temperature, 6 hours


title: wild-type, cerebellum, 12 months, sample 5

value: cerebellum


title: aCD19CAR_10223_p2_5_5min_JH0026

description:
1 aCD19CAR cells that interacted for 5.5min
processed data file: Counts_CAR.csv


title: 210310_A00902_A_L002_ALPZ-5-8_R1.fastq.gz


title: Heart_tissue_TOF_49

city: Mannheim

first: Gergana

last: Dobreva

address: Ludolf-Krehl-Str. 7-11

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: TOF_49

data_processing:
RNA-Seq reads were mapped to the mm10 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000)
Samples were quantified using featureCounts with the default setting.
Assembly: hg38
Supplementary files format and content: Excel file include genename, gene length, row counts

source_name: RV Heart

extract_protocol:
Total RNA was isolated using the RNeasy Plus Universal Mini kit from Qiagen. RNA quality were performed by BGI. Only qualified samples were used for library construction.
RNA libraries were prepared by BGI for sequencing using standard DNBSEQ protocols

value: RV Heart


title: wild-type, cerebellum, 12 months, sample 4


title: Heart_tissue_TOF_48

description: Library name: TOF_48


title: 20_cells_NK92_WT_MF224

description:
20 NK92 cells that did not interact
processed data file: Counts_NK92.csv

source_name: NK92 cells

value: NK92 cells


title: wild-type, cerebellum, 12 months, sample 3


title: Heart_tissue_TOF_44

description: Library name: TOF_44


title: Heart_tissue_TOF_40

description: Library name: TOF_40


title: 210310_A00902_A_L002_ALPZ-5-6_R1.fastq.gz

value: high temperature, 6 hours


title: wild-type, cerebellum, 12 months, sample 2


title: 210310_A00902_A_L002_ALPZ-5-5_R1.fastq.gz


title: 20_cells_K562_MF232

description:
20 K562 cells that did not interact
processed data file: Counts_NK92.csv

source_name: K562 cells

value: K562 cells


title: 210310_A00902_A_L002_ALPZ-5-4_R1.fastq.gz


title: 20_cells_K562_MF224


title: Heart_tissue_TOF_38

description: Library name: TOF_38


title: wild-type, cerebellum, 12 months, sample 1


title: SCA6, cerebellum, 6 months, sample 5

value: HET


city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

description: Library name: AIYT-326_Total-Input_HA-UzcR_Caulobacter_crescentus_NA1000∆uzcR;xylX::Pxyl_HA-uzcR;yjbI::Tn

data_processing:
The single-end sequence reads stored in FastQ files were mapped against the genome of C. crescentus NA1000 (NC_011916.1) using Bowtie2 Version 2.4.5+galaxy1 available on the web-based analysis platform Galaxy (https://usegalaxy.org) to generate the standard genomic position format files (BAM). Then, BAM files were imported into SeqMonk version 1.47.2 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) to build ChIP-Seq normalized sequence read profiles. Briefly, the genome was subdivided into 50 bp, and for every probe, we calculated the number of reads per probe as a function of the total number of reads (per million, using the Read Count Quantitation option). Using the web-based analysis platform Galaxy (https://usegalaxy.org), HA-ChvI and HA-UzcR ChIP-Seq peaks were called using MACS2 Version 2.2.7.1+galaxy0 (No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05. Peaks were rank-ordered according to their fold-enrichment values. Consensus sequences common to the top 130 HA-ChvI peaks and to the top 134 HA-UzcR peaks (identified in yjbI::Tn backgrounds) were respectively identified by scanning peak sequences (+ or - 150 bp relative to the coordinates of the peak summit) for conserved motifs using MEME-ChIP (Version 5.5.0; http://meme-suite.org/).
Base calling: NextSeq Control Software 4.0.2.7, RTA2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.73+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.5+galaxy1)
Peak calling: MACS2 (Galaxy Version 2.2.7.1+galaxy0 , No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
Motif-based sequence analysis: MEME-ChIP (Version 5,5,0; http://meme-suite.org/)
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Assembly: NC_011916.1
Supplementary files format and content: The processed data file named “ChIP-Seq analysis_Viollierlab.xlsx” is an Excel spreadsheet that compiles the alignment statistics generated by Bowtie2 and SeqMonk (including Total Read Count (PFa), Mapped Read Count, % Mapped Reads, Read Length, and Genome Fold Coverage).  In addition, the file contains the normalized ChIP-Seq read profiles for each of the eight ChIP-Seq samples, generated with SeqMonk. For this, the genome was subdivided into 50 bp probes, and the number of reads per probe was calculated as a function of the total number of reads (per million, using the Read Count Quantitation option).  HA-ChvI and HA-UzcR ChIP-Seq peaks were identified using MACS2 (with the No broad regions option, relative to the total input DNA samples). MACS2 tables list the peak intervals, peak summits and statistics (-log10 of p- and q- values, fold enrichment) for all HA-ChvI statistical peaks detected (q = 0.05). Peaks were rank-ordered according to their fold-enrichment values (Peaks with a fold-enrichment values >4 were retained for further analysis: MEME-ChIP).

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus

growth_protocol: Cultures of exponentially growing Caulobacter crescentus (NA1000) ∆uzcR; xylX::Pxyl-HA-uzcR, the yjbI mutant derivative  ∆uzcR; xylX::Pxyl-HA-uzcR; yjbI::Tn (GmR), as well as ∆bla; xylX::Pxyl-HA-chvI and the yjbI mutant derivative ∆bla; xylX::Pxyl-HA-chvI; yjbI::Tn (GmR), were grown in PYE medium supplemented with 0.3% xylose until they reached an OD660 of 0.5 (80 mL per sample).

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl), the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor Pico) at 4°C using 15 bursts of 30 seconds to shear DNA fragments to an average length of 0.3–0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 minutes at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μL of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. Five percent of the pre-cleared lysates were kept as total input samples (negative control samples). The rest of the pre-cleared lysates was then incubated overnight at 4°C with monoclonal rabbit Anti-HA Tag antibodies (Millipore, clone 114-2C-7) at a 1:400 dilution. Immuno-complexes were captured by incubation with Protein-A agarose beads (pre-saturated with BSA) during a 2 hour period at 4°C and then, washed with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). Immuno-complexes were then eluted from the Protein-A beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like the total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 30 μL of DNAse/RNAse free water.
The immunoprecipitated chromatin was used to prepare sample libraries used for deep sequencing by Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions. Single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles (for HA-uzcR) and 75 cycles (HA-chvI), respectively, were performed and yielded several million reads per sequenced sample.

treatment_protocol: When the OD660 reached 0.5, each culture was supplemented with 10 μM sodium phosphate buffer (pH 7.6) and subsequently treated with formaldehyde (1% final concentration) at room temperature for 10 minutes to achieve crosslinking. The cultures were then incubated for an additional 30 minutes on ice and washed three times with phosphate-buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at –80 °C.

tag: strain

value: Caulobacter crescentus

value: uzcR knockdown xylX::Pxyl-HA-uzcR yjbI::Tn

value: PYE supplemented with xylose 0.3%


description: Library name: AIYT-310_ChIP-Seq_HA-UzcR_Caulobacter_crescentus_NA1000∆uzcR;xylX::Pxyl_HA-uzcR;yjbI::Tn


title: SCA6, cerebellum, 6 months, sample 4

tag: tissue


title: 210310_A00902_A_L002_ALPZ-5-1_R1.fastq.gz

value: control temperature, 3 hours


title: 210310_A00902_A_L002_ALPZ-5-7_R1.fastq.gz


title: Heart_tissue_TOF_32

description: Library name: TOF_32


title: SCA6, cerebellum, 6 months, sample 3

tag: cell line


title: Heart_tissue_TOF_28

description: Library name: TOF_28


title: 210310_A00902_A_L001_ALPZ-4-9_R1.fastq.gz

value: high temperature, 3 hours


title: 210310_A00902_A_L002_ALPZ-5-2_R1.fastq.gz


description: Library name: AIYT-328_Total-Input_HA-UzcR_Caulobacter_crescentus_NA1000∆uzcR;xylX::Pxyl_HA-uzcR

tag: cell type

value: uzcR knockdown xylX::Pxyl-HA-uzcR


title: Heart_tissue_TOF_37

description: Library name: TOF_37


title: Heart_tissue_TOF_29

description: Library name: TOF_29


title: 210310_A00902_A_L002_ALPZ-5-3_R1.fastq.gz

tag: genotype


title: Heart_tissue_TOF_23

description: Library name: TOF_23


description: Library name: ADPB-72_Total-Input_HA-ChvI_Caulobacter_crescentus_NA1000∆bla;xylX::Pxyl_HA-chvI;yjbI::Tn

value: bla knockdown xylX::Pxyl-HA-chvI yjbI::Tn


title: SCA6, cerebellum, 6 months, sample 2


description: Library name: AIYT-312_ChIP-Seq_HA-UzcR_Caulobacter_crescentus_NA1000∆uzcR;xylX::Pxyl_HA-uzcR


title: SCA6, cerebellum, 6 months, sample 1


description: Library name: ADPB-69_ChIP-Seq_HA-ChvI_Caulobacter_crescentus_NA1000∆bla;xylX::Pxyl_HA-chvI;yjbI::Tn


title: wild-type, cerebellum, 6 months, sample 4

value: WT


title: Heart_tissue_TOF_22

description: Library name: TOF_22


title: Heart_tissue_TOF_20

description: Library name: TOF_20


title: wild-type, cerebellum, 6 months, sample 3


description: Library name: ADPB-66_ChIP-Seq_HA-ChvI_Caulobacter_crescentus_NA1000∆bla;xylX::Pxyl_HA-chvI

value: bla knockdown xylX::Pxyl-HA-chvI


title: wild-type, cerebellum, 6 months, sample 2


title: 210310_A00902_A_L001_ALPZ-4-4_R1.fastq.gz

value: shoot

value: Rolap

value: control temperature, 1 hour


title: Heart_tissue_TOF_27

description: Library name: TOF_27

value: RV Heart


title: 210310_A00902_A_L001_ALPZ-4-8_R1.fastq.gz


title: 210310_A00902_A_L001_ALPZ-4-3_R1.fastq.gz

value: high temperature, 1hour


title: Heart_tissue_TOF_18

description: Library name: TOF_18


title: Renca cells, passage 39, rep1

description: Library name: Renca-P39-1

source_name: Renca

value: Renca

value: Renal Cell Adenocarcinoma Cell

value: Routine Passaging


description: Library name: ADPB-70_Total-Input_HA-ChvI_Caulobacter_crescentus_NA1000∆bla;xylX::Pxyl_HA-chvI

value: Caulobacter crescentus


title: 210310_A00902_A_L001_ALPZ-4-7_R1.fastq.gz


title: wild-type, cerebellum, 6 months, sample 5

value: cerebellum


title: wild-type, cerebellum, 6 months, sample 1


title: Heart_tissue_TOF_17

description: Library name: TOF_17


title: Renca cells, passage 24, rep2

description: Library name: Renca-P24-2


title: SCA6, cerebellum, 3 months, sample 4

value: HET

value: 3 months


title: Heart_tissue_TOF_15

description: Library name: TOF_15


title: 210310_A00902_A_L001_ALPZ-4-2_R1.fastq.gz


title: 210310_A00902_A_L001_ALPZ-4-6_R1.fastq.gz


title: SCA6, cerebellum, 3 months, sample 5


title: Heart_tissue_TOF_13

description: Library name: TOF_13


title: Renca cells, passage 39, rep2

description: Library name: Renca-P39-2


title: Renca cells, passage 17, rep1

description: Library name: Renca-P17-1


title: Renca cells, passage 24, rep1

description: Library name: Renca-P24-1


title: Heart_tissue_TOF_16

description: Library name: TOF_16


title: 210310_A00902_A_L001_ALPZ-4-5_R1.fastq.gz


title: Renca cells, passage 10, rep2

description: Library name: Renca-P11-2


title: Renca cells, passage 17, rep2

description: Library name: Renca-P17-2


title: SCA6, cerebellum, 3 months, sample 3


title: patient3_pre

city: Houston

first: Oluwadara

last: Coker

address: 6767 Bertner Ave

department: GI Medical Oncology

institute: MD Anderson Cancer Center

description: Fresh frozen parafilm embedded spatial transcriptome imaging. 10X Genome Analyzer was used to process the samples. Xenium Explorer was used to analyze the imaging and Xenium data of these files. All the files in the processed folder were loaded into the Seurat object using LoadXenium function

hyb_protocol: Automated imaging and cyclic probe hybridization were performed on the Xenium Analyzer across 15 hybridization cycles. Fluorescent-labeled detection probes were hybridized, imaged, and removed sequentially in each cycle. Z-stack images were acquired at 0.75 µm step size to cover the entire tissue thickness for each round of imaging, across four fluorescent channels.

scan_protocol: Z-stack images from all cycles and channels were stitched, aligned to DAPI counterstains, and used to construct spatial maps of transcript localization within each region of interest. Transcript puncta were identified as fluorescent spots quantified by photon counts, and their spatial registration across cycles was achieved using Gaussian fitting. Each transcript was assigned a unique optical signature based on the combined fluorescence intensities across cycles and channels. A Phred-scaled quality score (Q-score) was calculated for each decoded transcript, and only transcripts with Q ≥ 20 were retained for downstream spatial gene expression analysis

data_processing: Cell segmentation was performed using a nuclear (DAPI-based) seed expansion algorithm, where cell boundaries were defined by expanding 15 µm radially from the nucleus or until adjacent cell boundaries were encountered. The Xenium Onboard Analysis (XOA) pipeline generated output files including the feature-cell expression matrix, transcript spatial coordinates, and cell boundary files (CSV format).

label: DAPI

source_name: Liver

label_protocol: Nuclei was counterstained with DAPI

growth_protocol: Patient samples in the form of FFPE were obtained from ITB at MDA with approval from the IRB and with written consent from patients

extract_protocol: FFPE tissue sections were cut (5uM thick) from tumor biopsies and mounted onto Xenium slides. Sections then underwent deparaffinization, antigen retrieval, and permeabilization steps to expose RNA transcripts.

treatment_protocol: These samples came from patients who were treated with G12Ci/EGFRi during clinical trials

value: Liver


title: Heart_tissue_TOF_8

description: Library name: TOF_8


title: Heart_tissue_TOF_10

description: Library name: TOF_10


title: Mouse_lung_ko_vg1_pos cells

city: Hannover

first: Ziqing

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description:
Library name: Mouse_lung_ko_vg1_pos
10x Genomics

data_processing:
The scRNAseq libraries were sequenced on the NovaSeq X platform, targeting 25,000 read pairs per cell.  the gene expression matrix was generated using Cell Ranger 7.0 (10x Genomics).
Assembly: Mouse mm10
Supplementary files format and content: gene expression matrix

source_name: lung

extract_protocol:
Freshly collected lung cells from mice, then flow cytometrically sorted lung Vγ1+ T cells isolated from Vγ4-/- / Vγ6-/- mice (KO) and Vγ1- T cells isolated from C57BL/6NCrl mice(WT)
Library was performed according to the manufacter's instructions(single cell 3' v1.1 protocol, 10x Genomics)

value: lung

value: gamma delta T cells

value: 5-7 weeks

value: uninfected


title: wild-type, cerebellum, 3 months, sample 4

value: WT


title: patient2_post

source_name: Colon

value: Colon


title: Mouse_lung_wt_vg1_neg cells

description:
Library name: Mouse_lung_wt_vg1_neg
10x Genomics


title: patient3_post

source_name: Abdominal wall

value: Abdominal wall


title: Heart_tissue_TOF_9

description: Library name: TOF_9

value: RV Heart


title: SCA6, cerebellum, 3 months, sample 1


title: Renca cells, passage 10, rep1

city: Shenzhen

first: Wei

address: Shenzhen 6082 longgang Road

institute: Shenzhen Longgang Central Hospital

description: Library name: Renca-P11-1

data_processing:
Raw reads were processed with fastp to remove low-quality reads, adapter contaminants, and reads with excessive N content, yielding clean reads.
rRNA contamination was eliminated by aligning reads to an rRNA database using bowtie2.
The remaining reads were mapped to the reference genome using HISAT2, and mapping efficiency was calculated.
Gene expression levels (FPKM and TPM) were estimated with StringTie and RSEM.
Assembly: GRCh38 for Homo sapiens; GRCm39 for Mus musculus
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent. RNA purity was assessed with a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), concentration was measured using a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), and integrity (RIN value) was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). After quality control, mRNA was enriched using Oligo(dT) magnetic beads, and first-strand cDNA was synthesized with M-MuLV Reverse Transcriptase. RNA templates were degraded by RNase H, and second-strand cDNA was synthesized. Subsequent steps included end repair, poly-A tailing, adapter ligation, and size selection (~200 bp) using AMPure XP beads, followed by PCR amplification for library construction.
RNA libraries for RNA-seq were prepared using New England Biolabs (#E7530 ) following manufacturer's protocols.


title: 210310_A00902_A_L001_ALPZ-4-1_R1.fastq.gz

value: shoot

value: Rolap

value: high temperature, 1hour


title: Heart_tissue_TOF_7

description: Library name: TOF_7


title: SCA6, cerebellum, 3 months, sample 2


title: Heart_tissue_TOF_5

description: Library name: TOF_5


title: Renca cells, passage 3, rep2

description: Library name: Renca-P3-2

value: Renca

value: Renal Cell Adenocarcinoma Cell

value: Routine Passaging


title: patient1_post

source_name: Retroperitoneal

value: Retroperitoneal