title: cVO3

city: Stanford

first: Oscar

last: Abilez

state: CA

address: Clark Center E276, 318 W Campus Dr

department: Cardiothoracic Surgery

institute: Stanford University

description: Library name: Sample 5

data_processing:
The read counts of each cell was calculated by using Cellranger The analysis of single cell RNAseq data was performed by Seurat
genome build hg38
Supplementary files format and content: mtx, tsv

source_name: hPSC-derived cardiac vascularized organoid

growth_protocol: Human embryonic  stem cells (hESCs) were maintained through daily feeding with Essential 8 (E8) medium (A1517001, Thermo Fisher Scientific). The medium was changed daily, and cells were passaged every 3-4 days with 0.5 mM EDTA (15575-020, Thermo Fisher Scientific) between a 1:6 and 1:12 split ratio. hESCs were passaged on to tissue culture plates coated with Corning Matrigel membrane matrix (354234, Thermo Fisher Scientific) at a dilution of 1:100 for either maintenance or differentiation. To aid in passaging, we cultured cells for 24 hours with 10 uM of the ROCK inhibitor Y-27632 (HY-10583, MedChem Express). Prior to differentiation, hESCs were micropatterned as single 2 mm diameter round colonies.

extract_protocol:
cVO samples (day 16, n = 9 pooled organoids per sample) were dissociated using the Pierce™ Primary Cardiomyocyte Isolation Kit (88281 Thermo Fisher Scientific) according to the manufacturer’s instructions.
Single cells (with an end-target of ~5000 cells per sample) were used to create Gel Bead-In EMulsions (GEMs) by using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 kit (PN-120267, 10X Genomics). Libraries were generated according to the manufacturer’s instructions and sequenced using the HiSeq2500 instrument (Illumina) with a read length of PE150 base pairs at each end and ~50 M reads per sample.

treatment_protocol: cVO: 5 uM CHIR + 5 ng/mL FGF2 + 5 uM IWR + 50 ng/mL VEGF + 10 uM SB + 50 ng/mL ANG1 + 50 ng/mL ANG2 + 10 ng/mL PDGFBB + 2 ng/mL TGFB

value: Human H9 WT hESC (WA09)

value: hESC-3R triple reporter line


title: NK (W to N)_LMB2_#2 (Native kidney_LMB2_2-R)

status: Public on Jun 04 2025

type: SRA

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

library_source: transcriptomic

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 10.1.1 (Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

molecule: total RNA

organism: Mus musculus

source_name: Mouse kidney

extract_protocol:
Eight- to 12-week-old male mice that expresses human CD25 limited to the podocytes (NEP25 mice: http://www.informatics.jax.org/allele/MGI:3762500) were used in this study. We performed kidney transplantation between NEP25 mice and their wild-type littermates which have the same genetic background (C57BL/6N). Then anti-human CD25 antibodies (LMB2, 1.75 ng/g per body weight) or vehicle was injected into tail vein. Kidneys were harvested at day 8. Samples were frozen in liquid nitrogen and were crushed into powder with a Multi-beads Shocker (Yasui Kikai Co.). Total RNA was extracted from powdered kidney samples using ISOGEN II reagent (Nippon Gene). The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: Kidney

tag: Sex

value: Male


title: cVO2

country: USA

description: Library name: Sample 4

library_source: transcriptomic single cell

organism: Homo sapiens

tag: cell type

tag: cell line

tag: treatment


title: NK (W to N)_LMB2_#1 (Native kidney_LMB2_1-R)


title: cVO1

description: Library name: Sample 3


title: RC-77T/E_MMC_Method1

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description:
Library name: Sample 5
Methyl-Micro-C library is generated from RC-77T/E cell line.

library_source: genomic

data_processing:
Methyl-Micro-C and NOMe-HiC data were processed using bhmem [PMID: 31384045]. Chromatin interaction of Methyl-Micro-C and NOMe-HiC were processed using 4DN pipeline [PMID: 28905911] as previously done [PMID: 36544209]. To analyze DNA methylation, Methyl-Micro-C and NOMe-HiC data were aligned using bwameth (https://github.com/brentp/bwa-meth) and quantified using biscuit [PMID: 38412294]. Bistools [PMID: 25747664] and IGV [PMID: 22517427] tools were used to visualize DNA methylation signals.
Assembly: hg38
Supplementary files format and content: .hic
Supplementary files format and content: .bedGraph

molecule: genomic DNA

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) cells were obtained from ATCC and were cultured according to the suggested protocols using RPMI (Corning, 10-040-CV) supplemented with 10% FBS plus 1% penicillin and 1% streptomycin.RC-77T/E cells were received from Dr. Johng S. Rhim and were cultured using Keratinocyte SFM medium plus supplement reagents (ThermoFisher, 17005042) as previously reported [PMID: 21042716].

extract_protocol:
Cells were harvested, crosslinked, and lysed to isolate intact nuclei.
Methyl-Micro-C library: Nuclei were treated with MNase and proximity ligation was performed with a biotinylated bridge. Ligated DNA products underwent end preparation (NEB, E7546S) and methylated adapters (NEB, E7165AAVIAL) are added. After enriching ligated products, oxidation of methylated and hydroxy-methylated cytosines and deamination of unprotected unmethylated cytosines were performed using EM-seq conversion module (NEB, E7125S). Methyl-Micro-C library was generated by performing indexing PCR and sequenced using Illumina NovaSeq sequencing systems, following the guidelines of the manufacturer.
NOMe-HiC library: After reaching 70~80 confluence, 22Rv1 cells were detached with 0.5% Trypsin and harvested by centrifuge at 300g for 5min. Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then quenched by adding 0.2M Glycine. After washing with ice-cold PBS, cells were suspended in the nuclei isolation buffer with RNase inhibitors and incubated on ice for 1hr. Subsequent to nuclei membrane permineralization, chromatin was digested using 100U DpnII (NEB, R0543L) overnight at 37 ℃ with RNase inhibitors. The next day, DpnII was inactivated, and nuclei suspension was cooled to room temperature and subjected to biotin fill-in. Proximal segments were in situ ligated using T4 DNA ligase (NEB, M0202) supplemented with RNase inhibitors. Then GpC methyltransferase footprint was performed by incubating the nuclei with M.CviPI (NEB, M0227L), and PBS was added to stop the reaction. The nuclei were reverse crosslinked, DNA was precipitated and sonicated to average 400bp followed by 1xAMPure beads cleanup. Biotin pulldown was performed using streptavidin beads, DNA on beads was end-repaired, d-A tailed, and ligated with EM-seq adaptor (NEB). Bisulfite conversion was conducted using the EZ DNA Methylation-Gold Kit (D5006). Bisulfite converted DNA library was amplified using NEB EM-seq primers and KAPA HiFi Uracil+ ReadyMix (Roche, KK2801).

value: Prostate

value: Prostate Cancer Cell

tag: library type

value: cell line


title: 22Rv1_NOMe-HiC_4

description:
Library name: Sample 4
NOMe-HiC library is genearted from 22Rv1 cell line.


title: hs-Bam_16hr-PHS

type: RNA

city: Ithaca

first: Jongmin

middle: J

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

hyb_protocol: Fragmented cRNA was hybridized to the Drosophila genome 2.0 arrays (Affymetrix, Cat# 900532). All microarray experiments were performed by the Stanford Protein and Nucleic Acid (PAN) facility.

scan_protocol: Affymetrix

data_processing: All the raw CEL files were background adjusted and quantile normalized together by using R/BioConductor (v3.0.2) package GCRMA. Gene annotation was based on the Affymetrix file: Drosophila_2.na32.annot.csv.

label: biotin

organism: Drosophila melanogaster

source_name: Drosophila melanogaster testes

label_protocol: Reverse transcription was performed with oligo(dT)24 primer with a T7 promoter using ~200 ng of total RNA per Affymetrix protocol. The second strand was synthesized from the cDNA, and cRNA was produced by in vitro transcription.

growth_protocol: Flies were raised on molasses food at 25C.

extract_protocol: RNA was extracted from about 30 pairs of dissected testes without accessory glands using Trizol (Invitrogen).

treatment_protocol: For the heat shock timecourse, flies were raised at 25˚C until there were mid- and late-stage pupa. Then bottles were placed in a 37˚C water bath for 30 minutes to induce heat shock and returned to 25˚C, as spelled out in Kim et al., (PMID: 28522526)

tag: genotype

value: hs-bam; bam[1]/bam[86]

tag: time course

value: 16 hours after Bam pulse expression by 30 minutes heat shock


title: Neonate_Spleen_CD8+_T_cell_2

first: Andrew

last: Grimson

address: 445 Biotechnology Bldg

department: Molecular Biology and Genetics

data_processing:
Fastq files were aligned to the mouse mm10 reference genome with bwa. Unmapped, unpaired, and mitochondrial reads were removed usingsamtools. PCR duplicates were removed using Picard. Peak calling was performed on four replicates with MACS2 with a FDR q-value< 0.05. A union peak list of each data set was created by combining all peaks in all samples, merging overlapping peaks using MACS2 and keeping peaks that were called in more than one sample as a saf file. The number of reads in each peak was determined with featurecounts subread package130. Peaks were annotated using HOMER. Each peak was assigned to the nearest gene based on the shortest distance between the peak and gene’s promoter, on either strand; promoters were defined as 1 kb upstream and 100 bp downstream of annotated transcription start site (TSS). Each gene was assigned to a peak cluster that had the greatest number of gene associated peaks; for ties, genes were randomly assigned to one of the tied clusters.
Assembly: mouse mm10 reference genome
Supplementary files format and content: Peak calls are provided in .saf file,Peak visualization can be done using .bedGraph files, Peak read counts for three replicates are provided as a .txt file

source_name: Thymus

extract_protocol:
Thymi and spleens from adult or neonatal mice were collected in RPMI+10% FBS and mashed through a 40µM cell strainer to create a single-cell suspension. Spleens and thymi underwent magnetic enrichment with CD8a and CD4 MicroBeads (Miltenyi Biotec; cat# 130-117-044; cat# 130-117-043), respectively, per the manufacturer’s instructions. The bound thymic fraction was sorted for double positive thymocytes, while the eluted fraction underwent CD8a magnetic enrichment as described previously, after which the bound fraction was sorted for SP8 thymocytes, while the eluted fraction was sorted for DN thymocytes. Thymocyte counts were taken by diluting a single-cell thymus suspension and counting on a MoxiZ cell counter.
The ATAC-seq libraries were prepared based on the Omni-ATAC-seq protocols  with some minor modifications. Briefly, 100,000 FACS-sorted cells were used to prepare nuclei. The transposition reaction was performed by incubating 25,000 nuclei with Nextera Tn5 transposase (Illumina) at 37°C for 1 hour. The transposition mixture was purified using a Zymo DNA Clean and Concentrator kit. The ATAC libraries were amplified for 11 cycles using NEBNext 2X MasterMix and Nextera Index primers. The amplified libraries were size-selected using AMPure beads, to remove large DNA fragments.

value: Thymus

value: CD8+ T cells

value: C57BL/6 mice


title: 22Rv1_NOMe-HiC_3

description:
Library name: Sample 3
NOMe-HiC library is genearted from 22Rv1 cell line.


title: Hepatic_Sample9

description: 1 timepoint x 3 replicates/timepoint = 3 total files

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
FPKM of each gene was counted by RSEM
Assembly: hg38
Supplementary files format and content: FPKM value in XLSX format

source_name: hPSC-derived hepatic vascularized organoid-D6

extract_protocol:
Samples were prepared with the Direct-zol RNA Microprep w/ Zymo-Spin IC Columns (R2060, Zymo Research) and sequenced.
Each replicate had an average of 24.4 million 150 bp long paired-end reads. FastQC v0.11.2 was used for sequencing quality assessment. Reads were then aligned to the GRCh38(hg38) reference genome using STAR v2.5.3a with splice junctions being defined in GTF file (obtained from GRCh38). An average of 85.3% of reads was aligned to the reference transcriptome.

treatment_protocol: hESC-3R: day 0 undifferentiated cells for both Cardiac and Hepatic systems; (Cardiac) Control: baseline cardiac differentiation to day 16; cVO: baseline cardiac differentiation + vascular factors added starting day 5; (Hepatic) Control: baseline hepatic differentiation to day 20; hVO-D3: baseline hepatic differentiation + vascular factors added starting day 3; hVO-D6: baseline hepatic differentiation + vascular factors added starting day 6.

value: Baseline hepatic differentiation + vascular factors added Day 6


title: Neonate_Thymus_Single_Positive_ATAC_4

value: Single Positive


title: Neonate_Spleen_CD8+_T_cell_1


title: TK (N to N)_Vehicle_#3 (Transplated kidney_Vehicle_15-D)


title: Hepatic_Sample8


title: TK (N to N)_Vehicle_#4 (Transplated kidney_Vehicle_16-D)


title: 22Rv1_NOMe-HiC_2

description:
Library name: Sample 2
NOMe-HiC library is genearted from 22Rv1 cell line.


title: Hepatic_Sample6

source_name: hPSC-derived hepatic vascularized organoid-D3

value: Baseline hepatic differentiation + vascular factors added Day 3


title: Hepatic_Sample7


title: Hepatic_Sample5


title: Neonate_Thymus_Single_Positive_ATAC_2


title: TK (N to N)_Vehicle_#2 (Transplated kidney_Vehicle_14-D)


title: Neonate_Spleen_CD8+_T_cell_3


title: TK (N to N)_Vehicle_#1 (Transplated kidney_Vehicle_13-D)


title: Ovarian Tumour Epithelial cells - 29

city: Oxford

first: Lena

last: Rai

address: Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: AA-11641-BR-02-92
11641-Bulk

data_processing:
Raw sequencing data from Brescia ovarian tumour samples was subjected to adapter trimming using Trim Galore v0.6.5, clipping 12bp from the 5' end of reads and discarding reads that were shorter than 60bp.
Transcript expression was quantified in transcripts per million (TPM) using Kallisto v0.46.2 with cDNA annotations from Ensembl release 75.
Transcript-level abundance from Brescia Ovarian Tumour sequences was imported and summarised at the gene level using tximport v1.14.2. Whole transcriptome data from ovarian tumour epithelial cells were aligned to hg19 using STAR and then counted using FeatureCount tool.
Assembly: GRCh37
Supplementary files format and content: TPM_BresciaSamples contains Transcripts Per Million data for all Brescia ovarian tumour samples. FeatureCounts_TumourEpithelialCells.csv contains Feature counts data for all Ovarian Tumour epithelial cells.

source_name: Ovarian Tumour

extract_protocol:
RNA from Brescia Ovarian tumour samples was extracted using Trizol reagent (ThermoFisher Scientific, CA, USA) followed by clean-up with RNeasy MinElute Cleanup Kit (Qiagen, CA, USA) according to manufacturer’s instructions. Single cell RNA purification kit (Norgen Biotek Corp., Canada) was used for extracting RNA from ovarian tumour epithelial cells.
Libraries from total RNA samples from Brescia samples were prepared using NEB Next® Ultra RNA Library Prep Kit for Illumina (NEB, UK) using manufacturer’s recommendations. . SMARTer Stranded total RNA-Seq kit v2 Pico input (Takara Bio USA) was used for ovarian tumour epithelial cells according to manufacturer’s protocol.

value: Ovarian Tumour

value: epithelial cells


title: Neonate_Thymus_Single_Positive_ATAC_1


title: Ovarian Tumour Epithelial cells - 28

description:
Library name: AA-11641-BR-01-92
11641-Bulk


title: Hepatic_Sample4

value: Human H9 WT hESC (WA09)


title: Neonate_Thymus_Double_Positive_ATAC_4

value: Double Positive


title: TK (N to N)_LMB2_#4 (Transplated kidney_LMB2_12-D)

value: Kidney


title: Hepatic_Sample3

source_name: hPSC-derived hepatic organoid

value: hESC-3R triple reporter line

value: Baseline hepatic differentiation Day 20


title: Ovarian Tumour Epithelial cells - 27

description:
Library name: SB-11624-TR-03-64
11624-TICs


title: TK (N to N)_LMB2_#3 (Transplated kidney_LMB2_11-D)

value: Male


title: Neonate_Thymus_Single_Positive_ATAC_3


title: 22Rv1_NOMe-HiC_1

description:
Library name: Sample 1
NOMe-HiC library is genearted from 22Rv1 cell line.

value: Prostate

value: Prostate Cancer Cell

value: cell line


title: Hepatic_Sample2


title: Neonate_Thymus_Double_Positive_ATAC_3

value: Thymus


title: Ovarian Tumour Epithelial cells - 25

description:
Library name: SB-11624-TR-01-64
11624-TICs


title: TK (N to N)_LMB2_#2 (Transplated kidney_LMB2_10-D)


title: TK (N to N)_LMB2_#1 (Transplated kidney_LMB2_9-D)


title: Ovarian Tumour Epithelial cells - 26

description:
Library name: SB-11624-TR-02-64
11624-TICs


title: Hepatic_Sample1


title: Neonate_Thymus_Double_Positive_ATAC_1


title: TK (W to N)_Vehicle_#4 (Transplated kidney_Vehicle_8-D)


title: Cardiac_Sampl36

description: 6 timepoints x 3 replicates/timepoint = 18 total files

source_name: hPSC-derived cardiac organoid

value: Baseline cardiac differentiation Day16


title: Neonate_Thymus_Double_Negative_ATAC_4

value: Double Negative

value: C57BL/6 mice


title: Ovarian Tumour Epithelial cells - 24

description:
Library name: SB-11624-BR-03-64
11624-Bulk


title: Cardiac_Sampl35


title: Ovarian Tumour Epithelial cells - 22

description:
Library name: SB-11624-BR-01-64
11624-Bulk


title: Neonate_Thymus_Double_Positive_ATAC_2


title: Neonate_Thymus_Double_Negative_ATAC_2


title: Cardiac_Sampl33

value: Baseline cardiac differentiation Day12


title: TK (W to N)_LMB2_#4 (Transplated kidney_LMB2_4-D)


title: Cardiac_Sampl34


title: TK (W to N)_Vehicle_#1 (Transplated kidney_Vehicle_5-D)


title: TK (W to N)_LMB2_#3 (Transplated kidney_LMB2_3-D)


title: Adult_Spleen_CD8+_T_cell_4

value: CD8+ T cells


title: Cardiac_Sampl31


title: Ovarian Tumour Epithelial cells - 21

description:
Library name: SB-11619-TR-03-64
11619-TICs

value: Ovarian Tumour


title: Ovarian Tumour Epithelial cells - 20

description:
Library name: SB-11619-TR-02-64
11619-TICs

value: epithelial cells


title: Cardiac_Sampl32

value: Human H9 WT hESC (WA09)


title: Adult_Spleen_CD8+_T_cell_3


title: Ovarian Tumour Epithelial cells - 19

description:
Library name: SB-11619-TR-01-64
11619-TICs


title: TK (W to N)_LMB2_#2 (Transplated kidney_LMB2_2-D)


title: Neonate_Thymus_Double_Negative_ATAC_1


title: Ad-NEXN+high-Pi, rep3

city: Guangzhou

first: Canzhao

last: Liu

address: Gongye Street

country: China

institute: Southern Medical University

description: Library name: sample 7

data_processing:
Step 1: Use Fastp software (https://github.com/OpenGene/fastp) to filter out reads with adapter contamination, low quality, and undetermined bases, and verify sequence quality.
Step 2: Employ HISAT2 (https://ccb.jhu.edu/software/hisat2) for read mapping to the Homo sapiens GRCh38 reference genome.
Step 3: Use StringTie (https://ccb.jhu.edu/software/stringtie) to assemble the mapped reads and merge transcriptomes across samples to reconstruct a comprehensive transcriptome, which was further refined using gffcompare (https://github.com/gpertea/gffcompare/).
Step 4: Estimate expression levels with StringTie, calculating FPKM values for mRNAs.
Step 5: Conduct differential expression analysis with edgeR, identifying mRNAs with a |log2(FC)|>1 (fold change > 2 or < 0.5) and a P - value < 0.05 from parametric F - tests.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: human aortic isolated SMCs (HASMCs)

growth_protocol: Primary human aortic smooth muscle cells (HASMCs) were sourced from iCell Bioscience Inc. (catalog number: HUM-iCell-c010) and cultured in proprietary low-serum medium (PriMed-iCell-004) in strict adherence to the manufacturer's guidelines. These cells were meticulously cultivated under controlled conditions in a humidified incubator at a temperature of 37°C, with an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted and purified using TRIzol Reagent (Invitrogen, 15596026). Its quantity and purity were measured with a NanoDrop ND - 1000. RNA integrity was ensured with a RIN score above 7.0, assessed by Bioanalyzer 2100 and agarose gel electrophoresis. Poly(A) RNA was selected from total RNA using Dynabeads Oligo (dT) 25 - 61005.
The selected poly(A) RNA fragments were reverse - transcribed into cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649). Then, it was converted into U - labeled second - stranded DNAs. An A - base was added to the ends for adapter ligation. Indexed adapters were ligated to the A - tailed DNA, and products were size - selected with AMPureXP beads. After UDG enzyme (NEB, cat.m0280) treatment, the products were amplified by PCR. The final cDNA library had an average insert size of 300±50 bp.

treatment_protocol: HASMCs were pre-transfected with NC or Ad-NEXN. and then followed by high-Pi stimulation.

value: human aortic isolated SMCs (HASMCs)

value: Pre - transfect with Ad-NEXN, then stimulate with high-Pi


title: TK (W to N)_Vehicle_#3 (Transplated kidney_Vehicle_7-D)

value: Kidney


title: Ovarian Tumour Epithelial cells - 18

description:
Library name: SB-11619-BR-03-64
11619-Bulk


title: Cardiac_Sampl30

value: hESC-3R triple reporter line

value: Baseline cardiac differentiation Day10


title: TK (W to N)_LMB2_#1 (Transplated kidney_LMB2_1-D)

value: Male


title: Adult_Spleen_CD8+_T_cell_2


title: Ovarian Tumour Epithelial cells - 23

description:
Library name: SB-11624-BR-02-64
11624-Bulk


title: Ovarian Tumour Epithelial cells - 17

description:
Library name: SB-11619-BR-02-64
11619-Bulk


title: Cardiac_Sampl29


title: Adult_Spleen_CD8+_T_cell_1


title: Ovarian Tumour Epithelial cells - 16

description:
Library name: SB-11619-BR-01-64
11619-Bulk


title: M.orygis-infected lung,rep3

city: Hyderabad

first: Bappaditya

last: Dey

state: Telangana

address: Survey No. 37, Extended Q City Road, Gachibowli

country: India

institute: National Institute of Animal Biotechnology

data_processing:
The raw fastq reads were preprocessed using Fastp v.0.20.1 (parameters: --trim_front1 9 --trim_front2 9 --length_required 50 --correction--trim_poly_g --qualified_quality_phred 30)
The processed reads were aligned to the STAR indexed Bos taurus ARS-UCD1.2 genome using STAR aligner v 2.7.9a (parameters:’--outSAMtype’ BAM SortedByCoordinate, ‘--outSAMunmapped’ Within, ‘--quantMode’, TranscriptomeSAM, '--outSAMattributes' Standard)
The alignment file (sorted BAM) from individual samples were quantified using featureCounts v. 0.46.1 based on the rRNA filtered GTF file to obtain gene counts
Gene counts were used as inputs to DESeq2  for differential expression estimation (parameters: threshold of statistical significance --alpha 0.05; p-value adjustment method: BH). The DESeq2 result files were filtered based on adjusted p-value <= 0.05 and Log2FoldChange ∓ 1.
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Bos taurus

source_name: Lung

extract_protocol:
RNA was isolated from bovine lung using the RNeasy Plus Mini Kit (QIAGEN) in accordance with the manufacturer’s instructions.
The library preparation was carried out using TrueSeq stranded Total RNA kit following manufacturing protocol.

value: Lung

value: M.orygis-infected lung


title: Cardiac_Sampl28


title: M.orygis-infected lung,rep2


title: Ctrl_8hr-PHS

value: 8 hours after 30 minutes heat shock but no Bam expression


title: TK (W to N)_Vehicle_#2 (Transplated kidney_Vehicle_6-D)


title: Ovarian Tumour Epithelial cells - 15

description:
Library name: SB-11617-TR-06-64
11617-TICs


title: Ovarian Tumour Epithelial cells - 14

description:
Library name: SB-11617-TR-05-64
11617-TICs


title: Cardiac_Sampl27

value: Baseline cardiac differentiation Day8


title: Adult_Thymus_Single_Positive_ATAC_3

value: Thymus

value: Single Positive


title: Cardiac_Sampl26


title: Adult_Thymus_Single_Positive_ATAC_2

value: C57BL/6 mice


title: M.orygis-infected lung,rep1


title: Healthy lung,rep3

value: Normal lung

value: Healthy


title: Ovarian Tumour Epithelial cells - 13

description:
Library name: SB-11617-TR-04-64
11617-TICs

value: Ovarian Tumour

value: epithelial cells


title: Cardiac_Sampl25

value: Human H9 WT hESC (WA09)


title: Cardiac_Sampl24

value: Baseline cardiac differentiation Day5


title: Adult_Thymus_Double_Positive_ATAC_4

value: Double Positive


title: Adult_Thymus_Single_Positive_ATAC_1


title: Healthy lung,rep2


title: Ovarian Tumour Epithelial cells - 12

description:
Library name: SB-11617-TR-03-64
11617-TICs


title: Cardiac_Sampl23

value: hESC-3R triple reporter line


title: Healthy lung,rep1


title: Ovarian Tumour Epithelial cells - 11

description:
Library name: SB-11617-TR-02-64
11617-TICs


title: Adult_Thymus_Double_Positive_ATAC_3


title: Ovarian Tumour Epithelial cells - 10

description:
Library name: SB-11617-TR-01-64
11617-TICs


title: Cardiac_Sampl22


title: JET_3

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin, Madison

data_processing:
Adapters and low-quality reads were trimmed in each sample using Trimmomatic
Trimmed reads were aligned to the bovine reference genome (ARS-UCD1.3) using HISAT2
The number of reads per gene in each sample was calculated by HTSeq-count
Gene counts were normalized based on the trimmed mean of M-values method using the 'edgeR' R package
Assembly: ARS-UCD1.3
Supplementary files format and content: CSV file containing raw read counts for each sample

source_name: Endometrial Epithelial Cells

growth_protocol: Bovine endometrial epithelial cells were maintained in Bovine Endometrial Cell Growth Medium (Cell Applications) and incubated at 37C in a humidified 5% CO2 containing atmosphere

extract_protocol:
Total RNA was extracted using TRIzol followed by DNAse treatment
Libraries were prepared using the IDT xGen RNA Library Kit following manufacturer's protocols

treatment_protocol:
24 hours after seeding, cells were transfected with jetMESSENGER (Polyplus) and 500ng of in-vitro produced DPPA3 mRNA
24 hours after seeding, cells were subjected to jetMESSENGER alone

value: Endometrial Epithelial Cells

value: transfection reagent exposure


title: JET_2


title: Adult_Thymus_Double_Positive_ATAC_2


title: Ovarian Tumour Epithelial cells - 9

description:
Library name: SB-11617-BR-03-64
11617-Bulk


title: JET_1


title: Adult_Thymus_Double_Positive_ATAC_1


title: Ovarian Tumour Epithelial cells - 8

description:
Library name: SB-11617-BR-02-64
11617-Bulk


title: Adult_Thymus_Double_Negative_ATAC_4

description: Pooled DN1-DN3

value: Double Negative


title: Cardiac_Sampl20

description: 6 timepoints x 3 replicates/timepoint = 18 total files

value: Baseline cardiac differentiation Day2


title: Cardiac_Sampl19


title: Ovarian Tumour Epithelial cells - 7

description:
Library name: SB-11617-BR-01-64
11617-Bulk


title: Cardiac_Sampl18

value: Baseline cardiac differentiation + vascular factors added Day16


title: Adult_Thymus_Double_Negative_ATAC_2

description: Pooled DN1-DN3


title: Ovarian Tumour Epithelial cells - 5

description:
Library name: SB-11611-TR-02-83
11611-TICs


title: DPPA3_1

value: mRNA transfection


title: Ovarian Tumour Epithelial cells - 6

description:
Library name: SB-11611-TR-03-83
11611-TICs


title: DPPA3_2


title: hs-Bam_noHS

description: Column name: H00

data_processing:
Raw fastq reads were trimmed using trim_galore (version 0.4.3) to remove low-quality (Phred score 20) and adapter-containing (stringency 1) reads (29). Trimmed reads were mapped to the Drosophila melanogaster genome (BDGP6.46) with default parameters using STAR (version 2.5.3) (30). Mapped reads with quality scores smaller than 10 (-q 10) or not properly paired reads (-f 2) were discarded using SAMtools (version 1.4.1) (31). Counts per gene were obtained using the featureCounts function of the subread package (version 1.5.0) (32). Expression levels in different time points were TMM-normalized (Trimmed Mean of M-values), assuming the majority of housekeeping genes have the same expression levels in different time points using the R (version 4.1.0) package edgeR (version 3.34.0) (33). Analyses scripts are available in: https://github.com/jongminkmg/HeldOutWings2024
Assembly: Drosophila melanogaster genome (BDGP6.46)
Supplementary files format and content: Normalized CPM

molecule: polyA RNA

source_name: Testes

extract_protocol:
10~20 μg of total RNA was extracted from ~100 pairs of testes for each time point using Trizol (Invitrogen) followed by RNeasy cleanup (Qiagen) according to kit instructions.
PolyA-tailed RNA was purified using the Oligotex mRNA kit (Qiagen, Cat#70022). Purified PolyA RNA was fragmented in the presence of random hexamer primers in first strand synthesis buffer (Invitrogen, Cat# 18080093) at 85˚C for 8 minutes. Fragmented RNAs were reverse transcribed using Superscript III reverse transcriptase (Invitrogen, Cat# 18080093) in the presence of RNaseOUT (Invitrogen Cat#  10777019) at 50˚C for one hour. From this step, we followed the directions in the NEBNext mRNA Library Prep Master Mix Set for Illumina (E6110s) to make libraries. DNA was purified using a QIAquick PCR purification kit (Qiagen Cat# 28104) after second strand synthesis, end repair, dA tailing, and adapter ligation. After adapter ligation, 300~500 bp fragments were size-selected by gel extraction (1.5% low-melt NUSIEVE gel in TBE).

value: Testes

value: Not a cell line

value: Primarily germ cells

value: hs-bam; bam[1]/bam[86]

value: no heat shcok (HS)


title: Control_3


title: Cardiac_Sampl17


title: Ovarian Tumour Epithelial cells - 4

description:
Library name: SB-11611-TR-01-83
11611-TICs

value: Ovarian Tumour


title: Adult_Thymus_Double_Negative_ATAC_1

description: Pooled DN1-DN3

value: Thymus

value: C57BL/6 mice


title: Ovarian Tumour Epithelial cells - 3

description:
Library name: SB-11611-BR-03-64
11611-Bulk

value: epithelial cells


title: Cardiac_Sampl16

value: Human H9 WT hESC (WA09)


title: Control_2


title: CLP+5-MTP3

first: Gong

last: Jiacheng

address: Shatai South Road, Baiyun District

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. StringTie v2.2.1 --merge -F 0.1 -T 0.1 Hisat2 tools soft were used to map with reference genome.
Assembly: not provided
Supplementary files format and content: tab-delimited text file includes FPKM and raw counts for each sample

source_name: Ileum

extract_protocol:
A total amount of 1 ug RNA per sample was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). for the RNA sample preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.)

value: Ileum

value: WT


title: Cardiac_Sampl15

value: hESC-3R triple reporter line

value: Baseline cardiac differentiation + vascular factors added Day12


title: iSLK cells, delta_circ-vIRF4 mutant virus, lytic infection, 72 hours, biol rep 2

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

description:
Library name: iSLK delta_circ-vIRF4, lytic, biol rep 2
test_lytic.deseq2.results.tsv

data_processing:
Paired-end RNA-seq reads were filtered of rRNA using SortMeRNA (v4.3.2) using the “sensitive” database (v4.3.4) with additional (RNA45SN2) transcript sequence
Read quality was assessed using FASTQC (v0.11.7)
Fastq reads were aligned to a combined human (GRCh38.p13; Ensembl release 103) and KSHV (HHV8; NC\_009333) reference genome using STAR (v.2.5.2a)
Abundance estimates of human and KSHV transcripts were generated using Kallisto (v0.46.0)
Differential expression testing was performed using DESeq2 (v1.32.0) and gene set enrichment analysis was performed using GSEA (v.3.0).
Assembly: Combined human (GRCh38.p13; Ensembl release 103) and KSHV (HHV8; NC\_009333) reference genome
Supplementary files format and content: tsv files containing TPM values for each sample

source_name: iSLK

extract_protocol:
RNA was extracted with RNA-Bee (phenol-chloroform extraction) according to the manufacturer’s protocol. 1 ug of total RNA was used as input to construct sequencing libraries
Lytic libraries were prepared by the authors using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L); Latent libraries were prepared by University of Florida ICBR using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: iSLK


title: Control_1

value: Endometrial Epithelial Cells


title: Ovarian Tumour Epithelial cells - 2

description:
Library name: SB-11611-BR-02-64
11611-Bulk


title: Adult_Thymus_Double_Negative_ATAC_3

description: Pooled DN1-DN3

value: Double Negative


title: Cardiac_Sampl14


title: CLP+5-MTP1


title: Cardiac_Sampl13


title: canINS cryopreserved cells

city: Hatfield

first: Floryne

middle: Ottilie

last: Buishand

address: Hawkshead Lane

department: Clinical Science and Service

institute: Royal Veterinary College

description: Library name: canINS-cryo

data_processing:
CellRanger (version 7.1.0, 10x Genomics) was used to process raw FASTQ files and to align reads to either the canine CanFam3.1, human GRCh38, murine GRMch38/mm10, or rat mRatBN7.2 genome.
Assembly: CanFam3.1 for canINS-fresh and canINS-cryo, human GRCh38 for CM-fresh and CM-cryo, murine GRMch38/mm10 for MIN6, or rat mRatBN7.2 for INS-1
Supplementary files format and content: Cell Ranger software output files: barcodes.tsv, features.tsv, matrix.mtx

organism: Canis lupus familiaris

source_name: canINS

extract_protocol:
The canine insulinoma cell line canINS was cultured in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 1% penicillin-streptomycin (Invitrogen) and 200 ng/mL growth hormone (GH) (ProSpec). The human insulinoma cell line CM was cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin. The mouse insulinoma cell line MIN6 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) containing 25 mM glucose, supplemented with 15% FBS, 0.05 mM beta-mercaptoethanol (Life Technologies) and 1% penicillin-streptomycin. The rat insulinoma cell line INS-1 was cultured in RPMI-1640 + Glutamax (Gibco) supplemented with 10% FBS, 1mM sodium pyruvate (Life Tech), 10mM HEPES (Life Tech), and 0.05 mM beta-mercaptoethanol. All cell lines were cultured at 37°C with 5% CO2, and cells were passaged on reaching 70–80% confluence.
Cell cryopreservation
Freezing medium, consisting out of 90% FCS and 10% dimethyl sulfoxide (DMSO) (Sigma-Aldrich) was added to aliquots of 1 x 106 cells/mL of the canINS and CM cell lines and cells were transferred to cryogenic vials. The vials were put into a CoolCell cell freezing vial container (Corning) and stored at -80°C overnight. Vials of the frozen cell lines were then taken out of the CoolCell containers and stored at -80°C for four weeks until use.
Sample preparation
Cryopreserved cells were thawed in a 37 °C water bath, after which they were washed using pre-warmed 1x phosphate-buffered saline (PBS) (Gibco) supplemented with 0.04% bovine serum albumin (BSA) (Sigma-Aldrich). Single cell suspensions of both fresh and cryopreserved cells were created at a concentration of 1 x 106 cells/mL in 1x PBS + 0.04% BSA according to the Cell Preparation for Single Cell Protocols Handbook CG00053 (10x Genomics). Using trypan blue exclusion, all cell suspensions were confirmed to have a viability greater than 90%. Samples were partitioned on a Chromium Controller (10x Genomics) within 30 min of preparation.
Single-cell 3’ gene expression libraries were prepared for each sample using a Chromium NEXT Gem Single Cell 3 v3.1 Kit and dual index library construction kit (10x Genomics) targeting 10,000 cells per sample. Sequencing was performed on a NovaSeq 6000 sequencer (Illumina) using a 28 x 10 x 10 x 90 bp configuration.

value: canINS

value: insulinoma


title: Ovarian Tumour Epithelial cells - 1

description:
Library name: SB-11611-BR-01-64
11611-Bulk


title: Cardiac_Sampl12

source_name: hPSC-derived cardiac vascularized organoid

value: Baseline cardiac differentiation + vascular factors added Day10


title: Brescia Ovarian Tumour - 139

description:
Library name: R144
counts.R144


title: canINS fresh cells

description: Library name: canINS-fresh


title: CLP+PBS2

value: CLP+PBS


title: CLP+PBS3


title: DPPA3_3

value: mRNA transfection


title: cVO0

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Genome_build: Genome_build: hg38

extract_protocol:
Control and cVO samples (day 16, n = 6 pooled organoids per sample) were dissociated using the Pierce™ Primary Cardiomyocyte Isolation Kit (88281 Thermo Fisher Scientific) according to the manufacturer’s instructions.
Single cells (with an end-target of ~4000 cells per sample) were used to create Gel Bead-In EMulsions (GEMs) by using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 kit (PN-120267, 10X Genomics). Libraries were generated according to the manufacturer’s instructions and sequenced using the HiSeq2500 instrument (Illumina) with a read length of PE150 base pairs at each end and ~50 M reads per sample.

treatment_protocol: Control: 5 uM CHIR + 5 ng/mL FGF2 + 5 uM IWR; cVO: 5 uM CHIR + 5 ng/mL FGF2 + 5 uM IWR + 50 ng/mL VEGF + 10 uM SB + 50 ng/mL ANG1 + 50 ng/mL ANG2 + 10 ng/mL PDGFBB + 2 ng/mL TGFB


title: Cardiac_Sampl11


title: CLP+5-MTP2


title: Brescia Ovarian Tumour - 138

description:
Library name: R143
counts.R143

value: Ovarian Tumour


title: CLP+PBS1


title: Brescia Ovarian Tumour - 137

description:
Library name: R142
counts.R142


title: Cardiac_Sampl10


title: Cardiac_Sampl9

value: Baseline cardiac differentiation + vascular factors added Day8


title: Brescia Ovarian Tumour - 135

description:
Library name: R139
counts.R139


title: Cardiac_Sampl8


title: Control


title: Brescia Ovarian Tumour - 134

description:
Library name: R138
counts.R138


title: O940

city: Ann Arbor

first: Benjamin

middle: H.

last: Singer

state: Mi

address: 109 Zina Pitcher Place

department: Internal Medicine Division of Pulmonary and Critical Care Medicine

institute: University of Michigan

description: Sample 85

data_processing:
Raw count data were processed by the University of Michigan Advanced Genomics Core.
Read files were concatenated into a fastq file for each sample. Raw read quality was checked using the program FastQC version v0.11.3 to identify potential quality problems from features of the data (e.g. low quality score, over-expressed sequences, and inappropriate GC content).
Reads were aligned to the reference genome including mRNAs and lncRNAs (ENSEMBL GRCm38) using Trim_Galore (v 0.5.0) to trim reads and aligned with STAR (v 2.6.0).
Mapped reads were collapsed using Lexogen's supplied collapse_UMI_bam binary
Reads were counted using the R package Rsubread and featureCounts function
Genome_build: Raw count data were then used for analysis in DESeq2 (v 1.22.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include count data for each Sample and has been filtered and normalized VST using the R package deseq2 (v 1.22.2)

source_name: Brain

extract_protocol:
RNA was isolated from post-mortem lung tissues using TRIzol following the manufacturer's recommended protocol.
cDNA libraries were prepared using theQuantseq 3' mRNA FWD kit (Lexogen, Vienna, Austria) with the UMI Second strand synthesis Module (Lexogen), RNA libraries were subsequently prepared for sequencing using standard Illumina protocols
Quantseq

value: Brain

value: CLP

value: Male

tag: group


title: O939

description: Sample 84

value: Anesthesia

value: FxFAD


title: Brescia Ovarian Tumour - 133

description:
Library name: R137
counts.R137


title: Cardiac_Sampl6

value: Human H9 WT hESC (WA09)

value: hESC-3R triple reporter line

value: Baseline cardiac differentiation + vascular factors added Day5


title: O938

description: Sample 83

value: Female

value: WT


title: ABX, eWAT, scRNAseq

city: Shanghai

first: Lizhi

last: Guan

address: 573 Xujiahui Road

department: Department of Endocrine and Metabolic Diseases

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline. The pipeline also determined protein expression of every single cells via algorithm according to the sequencing reads of Abseq library.
The quality-filtered R1 reads were analyzed to identify the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence.
Putative cells information were combined together with RSEC/DBEC-adjusted molecules to generate a single-cell expression matrix.
Raw gene expression matrices from two cartridges were read into R (version 3.6.0) separately and converted to Seurat objects using the Seurat R package (version 3.0.1).
Assembly: mm10
Supplementary files format and content: *.csv: Matrix files

source_name: Visceral adipose tissue

extract_protocol:
Tissues were cut into about 1-mm2 pieces and digested in SoloTM Tumor Dissociation Kit (JZ-SC-58201) at 37 °C for 90min.
Briefly, cells from each sample were labeled by different AbSeq antibodies against respectively and washed three times with Stain Buffer (FBS). Labeled samples were loaded in one BD Rhapsody micro-well cartridge and proceed to single-cell capture. Microbeads-captured single cell transcriptome and Ab tagged index sequences targeting immune cell-associated surface antigens were generated into cDNA library and Abseq library separately containing cell labels and unique molecular identifiers (UMI) information. All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) on the NovaSeq 6000 platform (Illumina).

value: Visceral adipose tissue

value: CD45+ cells

value: Wildtype (WT)

tag: age

value: 15 weeks

value: Antibiotics


title: Brescia Ovarian Tumour - 136

description:
Library name: R141
counts.R141

value: Ovarian Tumour


title: O937

description: Sample 82


title: Brescia Ovarian Tumour - 131

description:
Library name: R135
counts.R135


title: Cardiac_Sampl4


title: NW, eWAT, scRNAseq

value: Normal water


title: O936

description: Sample 81

value: Brain


title: Brescia Ovarian Tumour - 130

description:
Library name: R134
counts.R134


title: Cardiac_Sampl7

value: Baseline cardiac differentiation + vascular factors added Day8


title: Cardiac_Sampl3

value: Baseline cardiac differentiation + vascular factors added Day2


title: O935

description: Sample 80

value: Anesthesia


title: Brescia Ovarian Tumour - 129

description:
Library name: R133
counts.R133


title: Cardiac_Sampl2


title: O934

description: Sample 79

value: Male

value: FxFAD


title: Brescia Ovarian Tumour - 128

description:
Library name: R132
counts.R132


title: Brescia Ovarian Tumour - 132

description:
Library name: R136
counts.R136


title: Cardiac_Sampl1

value: Human H9 WT hESC (WA09)

value: hESC-3R triple reporter line


title: O933

description: Sample 78

value: CLP


title: hESC_Sample3

description: 1 timepoint x 3 replicates = 3 total files

source_name: hESC-3R triple reporter line

value: Undifferentiated/pluripotent


title: Brescia Ovarian Tumour - 127

description:
Library name: R131
counts.R131


title: Adult_Thymus_Single_Positive_ATAC_4

source_name: Thymus

value: Thymus

value: Single Positive

value: C57BL/6 mice


title: O932

description: Sample 77

value: WT


title: RBM38

city: Toronto

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street, Room 1350

department: Terrence Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

description:
raw data file:
C54_2.txt
channel:
2
RNCMPT01687

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on an microarray scanner at 5 micron resolution (Axon Instruments GenePix 4000B). Images were quantified using Imagene 3.0 or 8.0.

data_processing: The experiment was represented with a matrix where rows correspond to probes and columns are the intensities of the Cy5- or Cy3-labeled RNA from the GST-RBP pulldown assay. First, low quality spots due to spatial trends or other problems related to image analysis are discarded. Next, quantile normalization was applied to calibrate multiple arrays. Background signal and other nonspecific binding effects are removed by subtracting from each spot the row median value across all experiments, and dividing by the robust estimate of standard deviation calculated across all the experiments. Finally, the same robust z-score transformation is applied to each column (i.e. experiment). NOTE: The N in the headers of the raw data file (linked below as a supplementary file) stands for Normalized. The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, therefore the data under the headings should be interpreted without the N (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

organism: synthetic construct

source_name: Pulldown RNA labeled with Cy5

label_protocol: Manufacturer's recommended protocol (Kreatech).

extract_protocol: Bound RNA from an RNA pulldown assay is eluted in STE Buffer (1% SDS, 10 mM Tris pH 7.5, 2 mM EDTA) by heating at 90°C for 5 minutes and purifyied by phenol-chloroform extraction followed by ethanol precipitation.

tag: protocol

value: GST-tagged RNA-binding protein pulldown

tag: rna binding protein


title: PUB1

description:
raw data file:
C53_2.txt
channel:
2
RNCMPT01685


title: Brescia Ovarian Tumour - 126

description:
Library name: R130
counts.R130

value: Ovarian Tumour


title: hESC_Sample2


title: srsf3_Cy3_2

description:
raw data file:
C50_2.txt
channel:
1
RNCMPT01680

source_name: Pulldown RNA labeled with Cy3


title: O931

description: Sample 76


title: O930

description: Sample 75

value: Female


title: Cardiac_Sampl5

value: Baseline cardiac differentiation + vascular factors added Day5


title: Brescia Ovarian Tumour - 125

description:
Library name: R129
counts.R129

source_name: Ovarian Tumour


title: INS-1 fresh cells

description: Library name: INS-1

organism: Rattus norvegicus

value: insulinoma


title: hESC_Sample1


title: O929

description: Sample 74

value: Brain


title: tia1_Cy3_2

description:
raw data file:
C47_2.txt
channel:
1
RNCMPT01674


title: RBM24

description:
raw data file:
C49_2.txt
channel:
2
RNCMPT01677


title: hnrpkl

description:
raw data file:
C50_2.txt
channel:
2
RNCMPT01679

value: hnrpkl


title: Neonate_Thymus_Double_Negative_ATAC_3

value: Double Negative


title: khdrbs1b

description:
raw data file:
C47_2.txt
channel:
2
RNCMPT01673


title: Brescia Ovarian Tumour - 124

description:
Library name: R128
counts.R128


title: Brescia Ovarian Tumour - 123

description:
Library name: R127
counts.R127


title: 95PC, Unpaired-retrieval, rep 2, ATAC

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

library_source: genomic single cell

data_processing:
The raw sequencing data were demultiplexed using Cell Ranger ARC (10x Genomics, version 2.0.2). Processed FASTQ files for both gene expression and chromatin accessibility were aligned to the rat genome (mRatBN7.2). Post-alignment, libraries derived from the same brain region (BLA or pPC) were aggregated using Cell Ranger ARC with normalization for sequencing depth.
Processed data were imported into R for analysis using the ‘Seurat’ and ‘Signac’ packages62. Quality control metrics, including total reads, unique molecular identifiers (UMIs), and the fraction of reads mapping to mitochondrial DNA, were evaluated. Gene expression (RNA) and chromatin accessibility (ATAC) data were integrated into Seurat objects corresponding to BLA and pPC. Initial quality control filtering was applied to exclude cells with low-quality metrics, including those with more than 5% mitochondrial content and fewer than 200 RNA or ATAC counts.
RNA and ATAC data from BLA and pPC were integrated using Seurat and Signac. RNA data underwent normalization and variance stabilization via SCTransform, followed by dimensionality reduction using Principal Component Analysis (PCA) on the first 50 principal components. ATAC data were processed using Term Frequency-Inverse Document Frequency (TF-IDF) normalization and Singular Value Decomposition (SVD) to identify the most variable genomic regions. A Weighted Nearest Neighbor (WNN) analysis was conducted to create a joint RNA-ATAC UMAP for integrated visualization of the multi-omic data.
After library preparation, 25,098 UMIs were captured in the BLA and 30,759 UMIs in the PC using Gel Beads-in-emulsions (GEMs). Following quality control and filtering, 23,385 UMIs were retained in the BLA and 25,211 UMIs in the PC. Cell types were identified using a graph-based clustering approach, followed by UMAP visualization of both RNA and ATAC datasets.
Assembly: Rn7
Supplementary files format and content: H5 file contains snRNA data, the fragments.tsv.gz file contains snATAC data.

source_name: brain, piriform cortex

extract_protocol:
single nuclei from the tissues were isolated using the 10x Genomics Chromium Nuclei Isolation with RNAse Inhibitor Kit (PN-1000494). The tissues were immediately immersed in pre-chilled lysis buffer post-extraction to facilitate dissociation and nuclei release. Nuclei were isolated by passing the suspension through a 40 μm cell strainer (Bel-Art™) to remove clumps and aggregates. The quality and concentration of nuclei were assessed by staining with a Trypan blue and ethidium bromide mixture, using a hemocytometer (NanoEntek) and fluorescence microscopy (Invitrogen™ EVOS™ M5000). The final nuclei concentration was optimized by diluting the nuclei buffer.
Single-nucleus ATAC and RNA-seq libraries were constructed using the 10X Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, User Guide Rev F, CG000338). Approximately 2,000 nuclei per sample were loaded onto the Chromium Next GEM Chip G. Libraries were prepared in parallel for ATAC-seq and RNA-seq, comprising double- strand DNA with standard Illumina paired-end construction. Sequencing was performed on an Illumina NovaSeq 6000 platform (Sickkids, Canada) to achieve a target depth of ~20,000 read pairs per cell for ATAC-seq and ~25,000 read pairs per cell for RNA-seq.

treatment_protocol: Twelve rats divided into four behavior groups, unpaired encoding (UE), paired encoding (PE), unpaired retrieval (UR) and paired retrieval (PR); corresponding to 2 phases of the SOC learning

value: brain, piriform cortex

value: Sprague-Dawley

value: Unpaired-retrieval

value: ATAC


title: TIA1_Cy3_1

description:
raw data file:
C46_2.txt
channel:
1
RNCMPT01672


title: Brescia Ovarian Tumour - 122

description:
Library name: R126
counts.R126


title: 95BLA, Unpaired-retrieval, rep 2, ATAC

source_name: brain, basolateral amygdala

value: brain, basolateral amygdala


title: u2af2b_Cy3

description:
raw data file:
C45_2.txt
channel:
1
RNCMPT01670


title: Brescia Ovarian Tumour - 121

description:
Library name: R125
counts.R125


title: Cardiac_Sampl21

description: 6 timepoints x 3 replicates/timepoint = 18 total files

source_name: hPSC-derived cardiac organoid

value: Human H9 WT hESC (WA09)

value: hESC-3R triple reporter line

value: Baseline cardiac differentiation Day2


title: O926

description: Sample 71

value: CLP

value: WT


title: 93PC, Unpaired-retrieval, rep 3, ATAC


title: Brescia Ovarian Tumour - 120

description:
Library name: R124
counts.R124

value: Ovarian Tumour


title: 94BLA, Unpaired-encoding, rep 2, ATAC

value: Unpaired-encoding


title: O925

description: Sample 70

value: Anesthesia

value: Female

value: FxFAD


title: O924

description: Sample 69

value: Brain

value: Male


title: 94PC, Unpaired-encoding, rep 2, ATAC

value: brain, piriform cortex


title: tardbp

description:
raw data file:
C42_2.txt
channel:
1
RNCMPT01664

value: GST-tagged RNA-binding protein pulldown

value: tardbp


title: tra2b

description:
raw data file:
C45_2.txt
channel:
2
RNCMPT01669


title: ENSTNIG00000011257

description:
raw data file:
C46_2.txt
channel:
2
RNCMPT01671


title: Brescia Ovarian Tumour - 119

description:
Library name: R123
counts.R123


title: O923

description: Sample 68


title: O928

description: Sample 73


title: 91PC, Paired-retrieval, rep 2, ATAC

value: Sprague-Dawley

value: Paired-retrieval

value: ATAC


title: O922

description: Sample 67


title: 93BLA, Unpaired-retrieval, rep 3, ATAC

value: brain, basolateral amygdala

value: Unpaired-retrieval


title: Brescia Ovarian Tumour - 117

description:
Library name: R121
counts.R121


title: SCHCODRAFT_104251

description:
raw data file:
A281_2.D.txt
channel:
2
RNCMPT00866


title: Brescia Ovarian Tumour - 118

description:
Library name: R122
counts.R122


title: 91BLA, Paired-retrieval, rep 2, ATAC


title: hnrnpa0b

description:
raw data file:
C44_2.txt
channel:
2
RNCMPT01667


title: PK05280.1

description:
raw data file:
A279_2.D.txt
channel:
2
RNCMPT00862


title: Brescia Ovarian Tumour - 114

description:
Library name: R118
counts.R118


title: O846

description: Sample 64

value: CLP


title: Brescia Ovarian Tumour - 113

description:
Library name: R117
counts.R117


title: O845

description: Sample 63


title: Brescia Ovarian Tumour - 115

description:
Library name: R119
counts.R119


title: 89PC, Paired-retrieval, rep 2, ATAC


title: Brescia Ovarian Tumour - 116

description:
Library name: R120
counts.R120


title: 90PC, Unpaired-retrieval, rep 1, ATAC


title: Brescia Ovarian Tumour - 112

description:
Library name: R116
counts.R116


title: O847

description: Sample 65

value: WT


title: O921

description: Sample 66


title: O844

description: Sample 62


title: 90BLA, Unpaired-retrieval, rep 1, ATAC


title: 85PC, Unpaired-encoding, rep 3, ATAC


title: Brescia Ovarian Tumour - 111

description:
Library name: R115
counts.R115

value: Ovarian Tumour


title: CBG00421

description:
raw data file:
A268_2.D.txt
channel:
2
RNCMPT00840


title: Brescia Ovarian Tumour - 110

description:
Library name: R114
counts.R114


title: O842

description: Sample 60


title: 89BLA, Paired-retrieval, rep 2, ATAC


title: CG4887

description:
raw data file:
A267_2.D.txt
channel:
2
RNCMPT00838


title: 82PC, Paired-retrieval, rep 1, ATAC


title: O841

description: Sample 59


title: Tb927.5.810

description:
raw data file:
A267_2.D.txt
channel:
1
RNCMPT00837


title: O843

description: Sample 61


title: Tb927.7.2140

description:
raw data file:
A265_2.D.txt
channel:
2
RNCMPT00834


title: O840

description: Sample 58


title: 82BLA, Paired-encoding, rep 3, ATAC

value: Paired-encoding


title: Brescia Ovarian Tumour - 107

description:
Library name: R111
counts.R111


title: O839

description: Sample 57


title: Tb927.6.4960

description:
raw data file:
A265_2.D.txt
channel:
1
RNCMPT00833


title: 81PC, Paired-encoding, rep 1, ATAC


title: 85BLA, Unpaired-encoding, rep 3, ATAC

value: Unpaired-encoding


title: PK21303.1

description:
raw data file:
A264_2.D.txt
channel:
1
RNCMPT00831


title: Brescia Ovarian Tumour - 108

description:
Library name: R112
counts.R112


title: PK21151.1

description:
raw data file:
A263_2.D.txt
channel:
2
RNCMPT00830


title: NCU04254

description:
raw data file:
A266_2.D.txt
channel:
1
RNCMPT00835


title: Brescia Ovarian Tumour - 109

description:
Library name: R113
counts.R113


title: 81BLA, Paired-encoding, rep 1, ATAC


title: O838

description: Sample 56


title: Brescia Ovarian Tumour - 106

description:
Library name: R110
counts.R110


title: O837

description: Sample 55

value: Unoperated


title: Brescia Ovarian Tumour - 105

description:
Library name: R109
counts.R109


title: ENSXETG00000023721

description:
raw data file:
A262_2.D.txt
channel:
2
RNCMPT00828


title: PUF60

description:
raw data file:
A258_2.D.txt
channel:
2
RNCMPT00820


title: Brescia Ovarian Tumour - 104

description:
Library name: R108
counts.R108


title: 79BLA, Paired-encoding, rep 2, ATAC


title: O836

description: Sample 54

value: FxFAD


title: 29PC, Unpaired-encoding, rep 2, ATAC


title: Brescia Ovarian Tumour - 103

description:
Library name: R107
counts.R107


title: O927

description: Sample 72

value: Brain


title: FUBP1

description:
raw data file:
A259_2.D.txt
channel:
2
RNCMPT00822


title: RBFOX2

description:
raw data file:
A257_2.D.txt
channel:
2
RNCMPT00818


title: 29BLA, Unpaired-encoding, rep 2, ATAC


title: O835

description: Sample 53

value: Male


title: Brescia Ovarian Tumour - 102

description:
Library name: R106
counts.R106


title: 79PC, Paired-encoding, rep 2, ATAC

value: brain, piriform cortex


title: Brescia Ovarian Tumour - 101

description:
Library name: R105
counts.R105


title: 02PC, Paired-retrieval, rep 3, ATAC


title: O833

description: Sample 51

value: Female


title: O834

description: Sample 52


title: ELAVL2

description:
raw data file:
A255_2.D.txt
channel:
2
RNCMPT00814

value: GST-tagged RNA-binding protein pulldown


title: 02BLA, Paired-retrieval, rep 3, ATAC

value: Sprague-Dawley


title: TRNAU1AP

description:
raw data file:
A255_2.D.txt
channel:
1
RNCMPT00813


title: O832

description: Sample 50


title: ESRP1

description:
raw data file:
A252_2.D.txt
channel:
2
RNCMPT00808


title: Brescia Ovarian Tumour - 100

description:
Library name: R104
counts.R104


title: Brescia Ovarian Tumour - 99

description:
Library name: R103
counts.R103


title: O831

description: Sample 49


title: 95PC, Unpaired-retrieval, rep 2, GEX

molecule: nuclear RNA

value: GEX


title: Brescia Ovarian Tumour - 98

description:
Library name: R102
counts.R102


title: rsp-1

description:
raw data file:
A249_2.D.txt
channel:
1
RNCMPT00801


title: RBM45

description:
raw data file:
A251_2.D.txt
channel:
1
RNCMPT00805


title: PFE0865c

description:
raw data file:
A248_2.D.txt
channel:
2
RNCMPT00800


title: O830

description: Sample 48


title: 95BLA, Unpaired-retrieval, rep 2, GEX


title: Brescia Ovarian Tumour - 97

description:
Library name: R101
counts.R101


title: 94PC, Unpaired-encoding, rep 2, GEX


title: tdp-1

description:
raw data file:
A256_2.D.txt
channel:
2
RNCMPT00816


title: U2B''

description:
raw data file:
C40_2.txt
channel:
1
RNCMPT01660


title: O829

description: Sample 47


title: Brescia Ovarian Tumour - 96

description:
Library name: R100
counts.R100


title: O828

description: Sample 46


title: 94BLA, Unpaired-encoding, rep 2, GEX


title: Brescia Ovarian Tumour - 94

description:
Library name: R98
counts.R98


title: O826

description: Sample 44


title: Brescia Ovarian Tumour - 95

description:
Library name: R99
counts.R99


title: O827

description: Sample 45


title: 91PC, Paired-retrieval, rep 2, GEX

value: Paired-retrieval


title: O825

description: Sample 43


title: Brescia Ovarian Tumour - 93

description:
Library name: R97
counts.R97


title: RBM34

description:
raw data file:
A258_2.D.txt
channel:
1
RNCMPT00819


title: Brescia Ovarian Tumour - 92

description:
Library name: R96
counts.R96


title: 93PC, Unpaired-retrieval, rep 3, GEX


title: 90PC, Unpaired-retrieval, rep 1, GEX


title: O822

description: Sample 40


title: Brescia Ovarian Tumour - 90

description:
Library name: R94
counts.R94


title: Brescia Ovarian Tumour - 91

description:
Library name: R95
counts.R95


title: 93BLA, Unpaired-retrieval, rep 3, GEX

value: brain, basolateral amygdala


title: O821

description: Sample 39


title: 90BLA, Unpaired-retrieval, rep 1, GEX

value: Unpaired-retrieval


title: cpb-2

description:
raw data file:
A245_2.D.txt
channel:
2
RNCMPT00794


title: PK21582.1

description:
raw data file:
A244_2.D.txt
channel:
2
RNCMPT00792


title: PFI0820c

description:
raw data file:
A245_2.D.txt
channel:
1
RNCMPT00793


title: Imp

description:
raw data file:
A242_2.D.txt
channel:
1
RNCMPT00787

value: Imp


title: PK20656.1

description:
raw data file:
A244_2.D.txt
channel:
1
RNCMPT00791


title: heph

description:
raw data file:
A242_2.D.txt
channel:
2
RNCMPT00788

value: heph


title: O820

description: Sample 38

value: CLP


title: PK07890.1

description:
raw data file:
A243_2.D.txt
channel:
2
RNCMPT00790


title: O824

description: Sample 42

value: WT


title: Brescia Ovarian Tumour - 88

description:
Library name: R92
counts.R92

value: Ovarian Tumour


title: PK00353.1

description:
raw data file:
A243_2.D.txt
channel:
1
RNCMPT00789


title: O819

description: Sample 37


title: Brescia Ovarian Tumour - 86

description:
Library name: R90
counts.R90


title: Brescia Ovarian Tumour - 87

description:
Library name: R91
counts.R91


title: 89PC, Paired-retrieval, rep 2, GEX


title: O818

description: Sample 36


title: Brescia Ovarian Tumour - 89

description:
Library name: R93
counts.R93


title: 85PC, Unpaired-encoding, rep 3, GEX

value: Unpaired-encoding


title: 82PC, Paired-retrieval, rep 1, GEX


title: O817

description: Sample 35


title: O816

description: Sample 34

value: FxFAD


title: 85BLA, Unpaired-encoding, rep 3, GEX


title: Brescia Ovarian Tumour - 85

description:
Library name: R89
counts.R89


title: Brescia Ovarian Tumour - 84

description:
Library name: R88
counts.R88


title: O815

description: Sample 33

value: Brain


title: 81PC, Paired-encoding, rep 1, GEX

value: Paired-encoding


title: 82BLA, Paired-encoding, rep 3, GEX


title: Brescia Ovarian Tumour - 83

description:
Library name: R87
counts.R87


title: O814

description: Sample 32

value: Male


title: 81BLA, Paired-encoding, rep 1, GEX


title: Brescia Ovarian Tumour - 82

description:
Library name: R86
counts.R86


title: O813

description: Sample 31

value: Female


title: 79PC, Paired-encoding, rep 2, GEX

value: brain, piriform cortex


title: Brescia Ovarian Tumour - 81

description:
Library name: R85
counts.R85


title: 89BLA, Paired-retrieval, rep 2, GEX

value: Sprague-Dawley


title: O812

description: Sample 30


title: CG4806

description:
raw data file:
A240_2.D.txt
channel:
2
RNCMPT00784

value: GST-tagged RNA-binding protein pulldown


title: TBPH

description:
raw data file:
A236_2.D.txt
channel:
2
RNCMPT00776

value: TBPH


title: Tb11.01.5690

description:
raw data file:
A235_2.D.txt
channel:
1
RNCMPT00773


title: sart3

description:
raw data file:
A235_2.D.txt
channel:
2
RNCMPT00774


title: 79BLA, Paired-encoding, rep 2, GEX

value: brain, basolateral amygdala

value: GEX


title: LmjF.30.1110

description:
raw data file:
A230_2.D.txt
channel:
1
RNCMPT00763


title: O810

description: Sample 28


title: O811

description: Sample 29


title: Brescia Ovarian Tumour - 80

description:
Library name: R84
counts.R84


title: 29PC, Unpaired-encoding, rep 2, GEX


title: Brescia Ovarian Tumour - 78

description:
Library name: R82
counts.R82


title: ENSGALG00000014089

description:
raw data file:
A228_2.D.txt
channel:
2
RNCMPT00760


title: 29BLA, Unpaired-encoding, rep 2, GEX


title: ENSMODG00000011903

description:
raw data file:
A227_2.D.txt
channel:
2
RNCMPT00758


title: O809

description: Sample 27


title: Brescia Ovarian Tumour - 77

description:
Library name: R81
counts.R81


title: 91BLA, Paired-retrieval, rep 2, GEX

value: Paired-retrieval


title: 02PC, Paired-retrieval, rep 3, GEX


title: O808

description: Sample 26


title: Brescia Ovarian Tumour - 79

description:
Library name: R83
counts.R83


title: Brescia Ovarian Tumour - 76

description:
Library name: R80
counts.R80


title: T07F10.3

description:
raw data file:
A259_2.D.txt
channel:
1
RNCMPT00821


title: RBPMS2

description:
raw data file:
A227_2.D.txt
channel:
1
RNCMPT00757


title: LmjF.29.1370

description:
raw data file:
A229_2.D.txt
channel:
2
RNCMPT00762


title: Tb927.7.320

description:
raw data file:
A224_2.D.txt
channel:
1
RNCMPT00751


title: LmjF.24.1570

description:
raw data file:
A229_2.D.txt
channel:
1
RNCMPT00761


title: NCU00556

description:
raw data file:
A225_2.D.txt
channel:
2
RNCMPT00754


title: O807

description: Sample 25


title: Brescia Ovarian Tumour - 75

description:
Library name: R79
counts.R79


title: O806

description: Sample 24


title: EVs biol rep2

city: Chongqing

first: Jie

last: Li

state: Chongqing

address: 426# Songshibei Road, Yubei District

department: College of Stomatology

institute: Chongqing Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp
The clean reads were mapped to the reference genome using HISAT2
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

growth_protocol: Rat bone marrow-derived dendritic cells were maintained in 1640 supplemented with 10% FBS, 20ng/mL GM-CSF and 20ng/mL IL-4 in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: 1μg/mL LPS，50ng/mL treated 24h

value: bone marrow

value: primary cell

value: Immune cells

value: LPS and  EVs


title: NCU00707

description:
raw data file:
A232_2.D.txt
channel:
2
RNCMPT00768


title: 02BLA, Paired-retrieval, rep 3, GEX


title: Brescia Ovarian Tumour - 74

description:
Library name: R78
counts.R78

value: Ovarian Tumour


title: DDX53

description:
raw data file:
A220_2.D.txt
channel:
1
RNCMPT00743


title: O805

description: Sample 23

value: CLP

value: WT


title: EVs biol rep3


title: Tb11.03.0550

description:
raw data file:
A223_2.D.txt
channel:
1
RNCMPT00749


title: Brescia Ovarian Tumour - 72

description:
Library name: R76
counts.R76


title: PK10695.1

description:
raw data file:
A219_2.D.txt
channel:
1
RNCMPT00741


title: LPS biol rep3

value: LPS


title: Brescia Ovarian Tumour - 71

description:
Library name: R75
counts.R75


title: O803

description: Sample 21

value: Brain

value: Male


title: LPS biol rep2


title: Brescia Ovarian Tumour - 70

description:
Library name: R74
counts.R74


title: O804

description: Sample 22


title: O802

description: Sample 20


title: Tb927.3.3960

description:
raw data file:
A216_2.D.txt
channel:
1
RNCMPT00735


title: mex3c

description:
raw data file:
A212_2.D.txt
channel:
1
RNCMPT00727


title: Brescia Ovarian Tumour - 69

description:
Library name: R73
counts.R73


title: LPS biol rep1


title: Control biol rep3


title: Brescia Ovarian Tumour - 68

description:
Library name: R72
counts.R72


title: Tb10.389.1650

description:
raw data file:
A214_2.D.txt
channel:
2
RNCMPT00732


title: BATDEDRAFT_13807

description:
raw data file:
A218_2.D.txt
channel:
1
RNCMPT00739


title: O800

description: Sample 18

value: Female


title: Brescia Ovarian Tumour - 66

description:
Library name: R70
counts.R70


title: Control biol rep1


title: Brescia Ovarian Tumour - 67

description:
Library name: R71
counts.R71


title: O801

description: Sample 19


title: O799

description: Sample 17


title: Brescia Ovarian Tumour - 65

description:
Library name: R69
counts.R69


title: O797

description: Sample 15


title: SCHCODRAFT_35516

description:
raw data file:
A211_2.D.txt
channel:
1
RNCMPT00725


title: SWT_6h_2

city: Vienna

first: Dorota

last: Szwarc-Hofbauer

state: Vienna

address: Höchstädtplatz 5

department: Life Science Engineering

country: Austria

institute: UAS Technikum Wien

description:
Library name: 70508
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)

data_processing:
Samples were multiplexed and sequenced using Illumina HiSeqV4 SR50.
Raw reads were quality checked (FastQC), pre-processed (Trimmomatic) and mapped (Bowtie2) to the reference genome (genome version: mus musculus genome assembly GRCm38 (mm10))
Mapped reads were counted and aligned to genome features, such as genes (htseq-count). Only uniquely mapped and uniquely assigned reads were counted.
Mapped reads were normalised to gene lengths (cufflinks) and differentially expressed genes were determined (DESeq2).
Assembly: mus musculus genome assembly GRCm38 (mm10)
Supplementary files format and content: tabular files include FPKM values for each sample

growth_protocol: The C3H/10T1/2 mesenchymal cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FCS, 100 units/ml penicillin G sodium, 0.1 mg/ml streptomycin sulfate, and 2 mM L-glutamine in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using the peqGold Total RNA Kit.
mRNA sequencing library was prepared using NEB, poly-A Kit and NEBNext Dual 701-710 adaptors were annealed to individual samples

treatment_protocol: Cells were subjected to in vitro shock wave treatment (300 pulses, 0.18 mJ/mm2, 3 Hz; MTS Dermagold 100 device with an OP155 applicator) and samples were collected 30 minutes or 6 hours after stimulation.

value: mesenchymal cells

value: SWT (300 pulses, 0.18 mJ/mm2, 3 Hz)

tag: time

value: 6 h


title: SWT_6h_3

description:
Library name: 70509
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)


title: O798

description: Sample 16


title: Brescia Ovarian Tumour - 64

description:
Library name: R68
counts.R68


title: SWT_6h_1

description:
Library name: 70507
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)


title: O795

description: Sample 13


title: Brescia Ovarian Tumour - 63

description:
Library name: R67
counts.R67


title: SWT_0.5h_3

description:
Library name: 70506
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)


title: O796

description: Sample 14


title: P237

description: Sample 78

value: Wt

value: WtCLP


title: SCHCODRAFT_72118

description:
raw data file:
A210_2.D.txt
channel:
1
RNCMPT00723

value: GST-tagged RNA-binding protein pulldown


title: Brescia Ovarian Tumour - 62

description:
Library name: R66
counts.R66


title: SWT_0.5h_2

description:
Library name: 70505
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)


title: P235

description: Sample 76


title: P236

description: Sample 77


title: Brescia Ovarian Tumour - 60

description:
Library name: R64
counts.R64


title: Brescia Ovarian Tumour - 61

description:
Library name: R65
counts.R65


title: control_3

description:
Library name: 70503
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)

value: control, no treatment


title: SWT_0.5h_1

description:
Library name: 70504
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)


title: Brescia Ovarian Tumour - 73

description:
Library name: R77
counts.R77


title: P233

description: Sample 74


title: EVs biol rep1

value: bone marrow

value: primary cell


title: NEMVEDRAFT_v1g141408

description:
raw data file:
A207_2.D.txt
channel:
2
RNCMPT00718


title: LmjF.32.2810

description:
raw data file:
A206_2.D.txt
channel:
2
RNCMPT00716


title: LmjF.33.1450

description:
raw data file:
A207_2.D.txt
channel:
1
RNCMPT00717


title: LmjF.29.1360

description:
raw data file:
A205_2.D.txt
channel:
2
RNCMPT00714


title: Lung fibroblasts, DKK1-treated, replicate 3

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
RNA-seq data was processed using Nextflow rnaseq pipeline (v.3.14) which performs QC, adapter trimming, alignment to reference genome GRCm38 using STAR and transcript quantification using RSEM. Differential gene expression analysis was conducted using Bioconductor package edgeR v4.2.1, based on normalized and filtered gene counts. Genes exhibiting statistically significant changes (adjusted p-value < 0.05) were further analyzed using downstream bioinformatics approaches.
Assembly: GRCm38/mm10
Supplementary files format and content: text, tab-separated

source_name: Lung

growth_protocol: Lungs were perfused, then chopped into small pieces and digested in a collagenase solution (Collagenase type IV (1200 U/ml), 2% FBS and 2% Pen/Strep in sterile PBS). After a 30-minute incubation at 37 °C, the homogenates were centrifuged at 1000 x g for 5 minutes at room temperature, then washed in a washing solution (2% FBS and 2% Pen/Strep in sterile PBS). The homogenates were subsequently resuspended in 0.05% Trypsin-EDTA and incubated at 37 °C for 20 minutes. After centrifugation, cells were suspended in fibroblast culture medium (DMEM supplemented with 10% FBS, 2% Pen/Strep and 1% GlutaMax) and seeded into 6-well plates. After seven days, the cells were detached and purified.

extract_protocol:
Total RNA was extracted from lung fibroblasts using TRIzol (15596026, Thermo Fisher Scientific), followed by purification with the Rneasy Plus Mini Kit (74136, QIAGEN), according to the manufacturer’s instructions.
Total RNA

treatment_protocol: Recombinant mouse DKK1 (30 ng/ml) was treated for 24 hours.

value: Lung

value: fibroblasts


title: LmjF.30.2180

description:
raw data file:
A206_2.D.txt
channel:
1
RNCMPT00715


title: LmjF.29.0680

description:
raw data file:
A208_2.D.txt
channel:
2
RNCMPT00720


title: P234

description: Sample 75

value: CLP


title: Control biol rep2

value: Immune cells

value: WT


title: CG1316

description:
raw data file:
A197_2.D.txt
channel:
2
RNCMPT00698


title: Brescia Ovarian Tumour - 58

description:
Library name: R62
counts.R62

value: Ovarian Tumour


title: Brescia Ovarian Tumour - 57

description:
Library name: R61
counts.R61


title: LmjF.29.1340

description:
raw data file:
A204_2.D.txt
channel:
2
RNCMPT00712


title: LmjF.29.1350

description:
raw data file:
A205_2.D.txt
channel:
1
RNCMPT00713


title: P231

description: Sample 72

value: Brain


title: Lung fibroblasts, DKK1-treated, replicate 2


title: Brescia Ovarian Tumour - 56

description:
Library name: R60
counts.R60


title: P232

description: Sample 73

value: Female


title: Lung fibroblasts, DKK1-treated, replicate 1


title: Tb11.01.3940

description:
raw data file:
A196_2.D.txt
channel:
1
RNCMPT00695


title: P230

description: Sample 71


title: ENSMODG00000011916

description:
raw data file:
A202_2.D.txt
channel:
1
RNCMPT00707


title: Brescia Ovarian Tumour - 55

description:
Library name: R59
counts.R59


title: P229

description: Sample 70

value: Male


title: Lung fibroblasts, control, replicate 3

value: control


title: Brescia Ovarian Tumour - 53

description:
Library name: R57
counts.R57


title: P228

description: Sample 69


title: P227

description: Sample 68


title: Lung fibroblasts, control, replicate 2


title: Brescia Ovarian Tumour - 54

description:
Library name: R58
counts.R58


title: P226

description: Sample 67


title: Brescia Ovarian Tumour - 51

description:
Library name: R55
counts.R55


title: Brescia Ovarian Tumour - 52

description:
Library name: R56
counts.R56


title: WT HC 9mo_5

city: strasbourg

first: Charles

last: DECRAENE

address: 12 rue Goethe

department: UMR 7364 CNRS

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 95 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: whole hippocampal

extract_protocol:
Astrcytes were isolated from dissected whole hippocampus using the Anti-ACSA-2 MicroBead Kit mouse (Miltenyi Biotec) according to manufacturer's instructions.
Full length cDNA were generated from 800 pg of total RNAusing Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: whole hippocampal

value: isolated astrocyte


title: Lung fibroblasts, control, replicate 1


title: LmjF.36.5420

description:
raw data file:
A194_2.D.txt
channel:
2
RNCMPT00692


title: P225

description: Sample 66

value: Wt

value: WtCLP


title: estExt_fgenesh1_pg.C_Chr_03.00010087

description:
raw data file:
A195_2.D.txt
channel:
2
RNCMPT00694

value: GST-tagged RNA-binding protein pulldown


title: P224

description: Sample 65


title: LmjF.34.4560

description:
raw data file:
A194_2.D.txt
channel:
1
RNCMPT00691


title: LmjF.25.0500

description:
raw data file:
A193_2.D.txt
channel:
1
RNCMPT00689


title: Tau HC 9mo_2


title: P223

description: Sample 64


title: Brescia Ovarian Tumour - 49

description:
Library name: R53
counts.R53

data_processing:
Raw sequencing data from Brescia ovarian tumour samples was subjected to adapter trimming using Trim Galore v0.6.5, clipping 12bp from the 5' end of reads and discarding reads that were shorter than 60bp.
Transcript expression was quantified in transcripts per million (TPM) using Kallisto v0.46.2 with cDNA annotations from Ensembl release 75.
Transcript-level abundance from Brescia Ovarian Tumour sequences was imported and summarised at the gene level using tximport v1.14.2. Whole transcriptome data from ovarian tumour epithelial cells were aligned to hg19 using STAR and then counted using FeatureCount tool.
Assembly: GRCh37
Supplementary files format and content: TPM_BresciaSamples contains Transcripts Per Million data for all Brescia ovarian tumour samples. FeatureCounts_TumourEpithelialCells.csv contains Feature counts data for all Ovarian Tumour epithelial cells.

extract_protocol:
RNA from Brescia Ovarian tumour samples was extracted using Trizol reagent (ThermoFisher Scientific, CA, USA) followed by clean-up with RNeasy MinElute Cleanup Kit (Qiagen, CA, USA) according to manufacturer’s instructions. Single cell RNA purification kit (Norgen Biotek Corp., Canada) was used for extracting RNA from ovarian tumour epithelial cells.
Libraries from total RNA samples from Brescia samples were prepared using NEB Next® Ultra RNA Library Prep Kit for Illumina (NEB, UK) using manufacturer’s recommendations. . SMARTer Stranded total RNA-Seq kit v2 Pico input (Takara Bio USA) was used for ovarian tumour epithelial cells according to manufacturer’s protocol.


title: Brescia Ovarian Tumour - 48

description:
Library name: R52
counts.R52


title: P222

description: Sample 63


title: Brescia Ovarian Tumour - 47

description:
Library name: R51
counts.R51


title: LmjF.25.0080

description:
raw data file:
A192_2.D.txt
channel:
2
RNCMPT00688


title: Brescia Ovarian Tumour - 50

description:
Library name: R54
counts.R54


title: Brescia Ovarian Tumour - 46

description:
Library name: R50
counts.R50


title: Tau HC 9mo_4


title: P221

description: Sample 62


title: WT HC 9mo_2


title: LmjF.18.0190

description:
raw data file:
A192_2.D.txt
channel:
1
RNCMPT00687


title: Tau HC 9mo_3


title: WT HC 9mo_4


title: Tau HC 3mo_4


title: P220

description: Sample 61

value: Anesthesia


title: tardbpl

description:
raw data file:
A190_2.D.txt
channel:
1
RNCMPT00683

value: tardbpl


title: hnrnpa0

description:
raw data file:
A190_2.D.txt
channel:
2
RNCMPT00684


title: PK27183.1

description:
raw data file:
A191_2.D.txt
channel:
1
RNCMPT00685


title: P219

description: Sample 60


title: Tau HC 3mo_2


title: SCHCODRAFT_80278

description:
raw data file:
A187_2.D.txt
channel:
2
RNCMPT00678


title: WT HC 3mo_4


title: Brescia Ovarian Tumour - 44

description:
Library name: R48
counts.R48


title: P218

description: Sample 59


title: WT HC 3mo_2


title: hnrnpa0a

description:
raw data file:
A187_2.D.txt
channel:
1
RNCMPT00677


title: Brescia Ovarian Tumour - 41

description:
Library name: R45
counts.R45


title: NCU09742

description:
raw data file:
A186_2.D.txt
channel:
2
RNCMPT00676


title: P216

description: Sample 57

value: WtAnesthesia


title: P217

description: Sample 58


title: Brescia Ovarian Tumour - 43

description:
Library name: R47
counts.R47


title: P215

description: Sample 56


title: Brescia Ovarian Tumour - 40

description:
Library name: R44
counts.R44


title: Brescia Ovarian Tumour - 39

description:
Library name: R43
counts.R43


title: WT HC 3mo_3


title: Brescia Ovarian Tumour - 59

description:
Library name: R63
counts.R63


title: P214

description: Sample 55


title: Brescia Ovarian Tumour - 42

description:
Library name: R46
counts.R46


title: control_2

description:
Library name: 70502
Instrument model used: Illumina HiSeqV4 SR50 (not available in dropdown list)

value: mesenchymal cells

value: control, no treatment


title: Brescia Ovarian Tumour - 45

description:
Library name: R49
counts.R49


title: Old_4

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: mm10

source_name: dorsal hippocampal tissue from mice

extract_protocol: Full length cDNA were generated from 4 ng of total RNAusing Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

value: brain


title: LmjF.27.2100

description:
raw data file:
A182_2.D.txt
channel:
1
RNCMPT00667


title: Brescia Ovarian Tumour - 37

description:
Library name: R41
counts.R41


title: Old_1


title: P212

description: Sample 53


title: Brescia Ovarian Tumour - 38

description:
Library name: R42
counts.R42


title: Old_3


title: PRR3

description:
raw data file:
A162_2.D.txt
channel:
2
RNCMPT00628


title: e_gw1.13.00.297.1

description:
raw data file:
A189_2.D.txt
channel:
1
RNCMPT00681


title: Young_4


title: TVAG_371220

description:
raw data file:
A160_2.D.txt
channel:
1
RNCMPT00623


title: Brescia Ovarian Tumour - 36

description:
Library name: R40
counts.R40


title: Young_3


title: P210

description: Sample 51


title: Old_2


title: RNPC3

description:
raw data file:
A163_2.D.txt
channel:
2
RNCMPT00630


title: Young_2


title: P213

description: Sample 54


title: P209

description: Sample 50


title: LmjF.17.0550

description:
raw data file:
A156_2.D.txt
channel:
1
RNCMPT00615


title: P208

description: Sample 49


title: P211

description: Sample 52


title: Young_1


title: Brescia Ovarian Tumour - 35

description:
Library name: R39
counts.R39


title: Brescia Ovarian Tumour - 33

description:
Library name: R37
counts.R37


title: Tau_TTK 4

extract_protocol: Full length cDNA were generated from 1 ng of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.


title: Brescia Ovarian Tumour - 32

description:
Library name: R36
counts.R36


title: Tau_TTK 3


title: Brescia Ovarian Tumour - 31

description:
Library name: R35
counts.R35


title: pabpc4

description:
raw data file:
A103_2.D.txt
channel:
1
RNCMPT00511


title: rbm14

description:
raw data file:
A104_2.D.txt
channel:
2
RNCMPT00514


title: qkr58E-2

description:
raw data file:
A167_2.D.txt
channel:
1
RNCMPT00637


title: Brescia Ovarian Tumour - 34

description:
Library name: R38
counts.R38


title: rnp-3

description:
raw data file:
A102_2.D.txt
channel:
2
RNCMPT00510


title: CG15440

description:
raw data file:
A104_2.D.txt
channel:
1
RNCMPT00513


title: P205

description: Sample 46

value: CLP


title: Tau_CSP 4


title: Brescia Ovarian Tumour - 30

description:
Library name: R34
counts.R34

value: Ovarian Tumour


title: P207

description: Sample 48

value: Brain


title: snrpB2_Cy3_2

description:
raw data file:
A101_2.D.txt
channel:
1
RNCMPT00507


title: pabpc1A

description:
raw data file:
A101_2.D.txt
channel:
2
RNCMPT00508


title: P204

description: Sample 45

value: Female


title: PF14_0151

description:
raw data file:
A100_2.D.txt
channel:
1
RNCMPT00505


title: Brescia Ovarian Tumour - 29

description:
Library name: R33
counts.R33


title: P203

description: Sample 44


title: Tau_CSP 2


title: grld-1

description:
raw data file:
A102_2.D.txt
channel:
1
RNCMPT00509


title: Tau_CSP 3


title: Brescia Ovarian Tumour - 27

description:
Library name: R31
counts.R31


title: Tau_TTK 2


title: Brescia Ovarian Tumour - 28

description:
Library name: R32
counts.R32


title: P201

description: Sample 42


title: Brescia Ovarian Tumour - 26

description:
Library name: R28
counts.R28


title: P200

description: Sample 41

value: Male


title: P202

description: Sample 43


title: P199

description: Sample 40


title: Wt_CSP 3


title: rsp-3

description:
raw data file:
A99_2.D.txt
channel:
1
RNCMPT00503


title: Brescia Ovarian Tumour - 25

description:
Library name: R27
counts.R27


title: Tau_CSP 1


title: Wt_CSP 4


title: P198

description: Sample 39


title: Brescia Ovarian Tumour - 23

description:
Library name: R25
counts.R25


title: Smp_024140

description:
raw data file:
A98_2.D.txt
channel:
1
RNCMPT00501


title: Wt_CSP 2


title: Brescia Ovarian Tumour - 24

description:
Library name: R26
counts.R26


title: Wt_CSP 1


title: Brescia Ovarian Tumour - 21

description:
Library name: R23
counts.R23


title: Brescia Ovarian Tumour - 22

description:
Library name: R24
counts.R24


title: Smp_006320

description:
raw data file:
A97_2.D.txt
channel:
2
RNCMPT00500


title: Wtcsp 12mo2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: mm10
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: ChIPed DNA obtained from whole tissue (mouse hippocampus)

extract_protocol: ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 3 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.


title: INPcsp TTK 12mo1


title: INPcsp TAU 12mo1


title: Brescia Ovarian Tumour - 20

description:
Library name: R22
counts.R22


title: PGTG_00837

description:
raw data file:
A85_2.D.txt
channel:
2
RNCMPT00476


title: PK01594.1

description:
raw data file:
A86_2.D.txt
channel:
2
RNCMPT00478


title: Brescia Ovarian Tumour - 19

description:
Library name: R21
counts.R21


title: Brescia Ovarian Tumour - 18

description:
Library name: R20
counts.R20


title: INPcsp WT12mo1


title: TTKcsp 12mo2


title: TAUcsp 12mo2


title: Brescia Ovarian Tumour - 17

description:
Library name: R19
counts.R19


title: fmr1

description:
raw data file:
A84_2.D.txt
channel:
2
RNCMPT00474


title: PGTG_09691

description:
raw data file:
A88_2.D.txt
channel:
2
RNCMPT00482


title: TTKcsp 12mo1


title: Brescia Ovarian Tumour - 16

description:
Library name: R18
counts.R18


title: bladder_cancer_TURBT_100

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

value: male

tag: age at randomization

tag: clinical stage


title: bladder_cancer_TURBT_102

value: female


title: Brescia Ovarian Tumour - 15

description:
Library name: R17
counts.R17


title: UBA2B

description:
raw data file:
A85_2.D.txt
channel:
1
RNCMPT00475


title: TAUcsp 12mo1


title: rbm-28

description:
raw data file:
A82_2.D.txt
channel:
2
RNCMPT00470


title: pab-1

description:
raw data file:
A83_2.D.txt
channel:
1
RNCMPT00471


title: bladder_cancer_TURBT_96


title: C44B7.2

description:
raw data file:
A81_2.D.txt
channel:
2
RNCMPT00468


title: bladder_cancer_TURBT_101


title: bladder_cancer_TURBT_98


title: bladder_cancer_TURBT_99


title: Wtcsp 12mo1


title: Brescia Ovarian Tumour - 14

description:
Library name: R16
counts.R16


title: INPUT 12mo WT NEUN+

source_name: ChIPed DNA obtained from FACS sorted cells from the brain (NeuN+ and NeuN-) of mouse

extract_protocol: ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: tisuue


title: K07H8.9

description:
raw data file:
A82_2.D.txt
channel:
1
RNCMPT00469


title: P206

description: Sample 47

source_name: Brain


title: Brescia Ovarian Tumour - 12

description:
Library name: R14
counts.R14


title: PK20770.1

description:
raw data file:
A79_2.D.txt
channel:
2
RNCMPT00464


title: PK00513.1

description:
raw data file:
A78_2.D.txt
channel:
2
RNCMPT00462


title: PK23097.1

description:
raw data file:
A80_2.D.txt
channel:
1
RNCMPT00465


title: B0280.17

description:
raw data file:
A81_2.D.txt
channel:
1
RNCMPT00467


title: bladder_cancer_TURBT_94


title: WT 12mo H3k27ac NEUN+


title: bladder_cancer_TURBT_95


title: bladder_cancer_TURBT_97


title: Brescia Ovarian Tumour - 11

description:
Library name: R13
counts.R13


title: PK00840.1

description:
raw data file:
A78_2.D.txt
channel:
1
RNCMPT00461


title: bladder_cancer_TURBT_92


title: Brescia Ovarian Tumour - 10

description:
Library name: R12
counts.R12


title: WT 12mo H3K27ac NEUN-


title: PK05405.1

description:
raw data file:
A80_2.D.txt
channel:
2
RNCMPT00466


title: PK16782.1

description:
raw data file:
A77_2.D.txt
channel:
2
RNCMPT00460


title: Brescia Ovarian Tumour - 8

description:
Library name: R10
counts.R10


title: INPUT 5mo WT NEUN-

source_name: ChIPed DNA obtained from FACS sorted NeuN- nulei from brain of mouse hippocampus


title: bladder_cancer_TURBT_93


title: Brescia Ovarian Tumour - 9

description:
Library name: R11
counts.R11


title: WT 5mo H3K27me3 NEUN+

source_name: ChIPed DNA obtained from purified nuclei of mouse total hippocampus


title: INPUT 5mo WT NEUN+

source_name: ChIPed DNA obtained from FACS sorted NeuN+ cells from brain of mouse total hippocampus


title: Brescia Ovarian Tumour - 7

description:
Library name: R8
counts.R8


title: Brescia Ovarian Tumour - 6

description:
Library name: R7
counts.R7


title: WT 5mo H3K27me3 NEUN-


title: bladder_cancer_TURBT_91


title: WT 5mo H3k27ac NEUN+


title: CPEB1

description:
raw data file:
A64_2.D.txt
channel:
2
RNCMPT00434

source_name: Pulldown RNA labeled with Cy5


title: bladder_cancer_TURBT_88


title: CBG03563

description:
raw data file:
A64_2.D.txt
channel:
1
RNCMPT00433

source_name: Pulldown RNA labeled with Cy3


title: cwf2

description:
raw data file:
A63_2.D.txt
channel:
2
RNCMPT00432


title: bladder_cancer_TURBT_83


title: bladder_cancer_TURBT_87


title: bladder_cancer_TURBT_85


title: Brescia Ovarian Tumour - 13

description:
Library name: R15
counts.R15

source_name: Ovarian Tumour


title: bladder_cancer_TURBT_86


title: bladder_cancer_TURBT_89


title: INPUT 12mo WT NEUN-


title: PK27602.1

description:
raw data file:
A63_2.D.txt
channel:
1
RNCMPT00431


title: SNRPB2_Cy3

description:
raw data file:
A60_2.D.txt
channel:
1
RNCMPT00425


title: Brescia Ovarian Tumour - 5

description:
Library name: R6
counts.R6


title: bladder_cancer_TURBT_90


title: PK25912.1

description:
raw data file:
A62_2.D.txt
channel:
2
RNCMPT00430