title: TNBC006|ROI-013|PanCK+

description:
Library name: DSP-1001660016069-E-G06
TNBC006 - 013 - PanCK+
TNBC006-slide.png
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TNBC006 - 013 - Segments.png


title: LB922695

status: Public on Dec 19 2025

type: SRA

city: Beijing

first: Dingding

last: Wang

state: None Selected

address: 56 Nanlishi Road

country: China

institute: Beijing Children Hospital, Capital Medical University

description: Library name: sample13

library_source: transcriptomic

data_processing:
The paired-end reads were gene-annotated by STAR[2] 2.7.9a and quantified gene expression using Stringtie[3] v2.1.4 with Ensembl gene annotation (GRCh38/hg38 assembly).
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: A combined file include FPKM value for each sample

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Total RNA was extracted from liver tissues. RNA libraries were constructed using a poly(A) protocol. cDNA libraries were constructed using a random hexamer primer, M-MuLV Reverse Transcriptase (RNase H Minus), DNA polymerase I, and RNase H.
The Illumina NovaSeq 6000 system was used to sequence the cDNA libraries with paired-end 150 bp reads.

tag: tissue

value: liver

tag: genotype

value: BA


title: LB916880

description: Library name: sample12


title: TNBC006|ROI-012|PanCK-

city: Pasadena

first: David

middle: Eugene

last: Frankhouser

state: CA

address: 1500 E Duarte Rd

department: Population Sciences

country: USA

institute: City of Hope

description:
Library name: DSP-1001660016069-E-G05
TNBC006 - 012 - PanCK-
TNBC006-slide.png
TNBC006 - 012.png
TNBC006 - 012 - Segments.png

data_processing:
The "GeomxTools" library in R was used to read in the DCC files using the .pkc file, and the raw counts were output into the "raw_counts.tsv" file
Assembly: Hg38
Supplementary files format and content: "Hs_R_NGS_WTA_v1.0.pkc" is the GeoMx probe code file used to map probes to gene names when producing the "raw_counts.tsv" file
Supplementary files format and content: "raw_counts.tsv" is a gene by sample expression matrix of raw counts where each sample is the "library name" and corresponds to ether a PanCK+/- segmented ROI (AOI); NTC control samples and samples that failed QC are not included

source_name: Breast

extract_protocol:
Tissue sections were prepared following the instruction of GeoMx slide preparation, and the slides were processed using the protocol of RNA slide preparation  for  formalin-fixed paraffin-embedded (FFPE) samples as described in the GeoMx DSP Manual Slide Preparation User Manual (NanoString Technologies, GeoMx-DSP-Manual-Slide-Preparation, MAN-10150). Briefly, deparaffinization and rehydration, antigen retrieval (Invitrogen, IHC Antigen Retrieval Solution, Cat#00-4956-58), and proteinase K digestion (1ug/ml, at 37°C) were performed. Human whole transcriptome atlas (WTA) probes (GeoMx WTA, Mouse RNA Probe for NGS, catalog #121401103) were hybridized in Buffer R (GeoMx RNA Slide Prep Kit PCLN catalog #121300313) and incubated in a hybridization humidity chamber (UVP, HB-1000 Hybridizer) overnight at 37°C. To remove nonspecifically bound probes, slides were washed in 50% Formamide/2x SSC (Thermo Fisher, catalog AM9763, USA) at 37°C (2 washes/25 min each), then slides were blocked and incubated with antibodies diluted with 200 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313). Then, immunostaining was performed for detection of the region of interest (ROI) . Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22 μL SYTO (GeoMx Nuclear Stain Morphology Kit, catalog 121300303), 5.5 μL Pan-CK, 5.5 μL CD45 (GeoMx Solid Tumor TME Morphology, Human FFPE RNA Compatible, catalog 121300315), and 181.5 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313) for a total volume of 220 μL/slide. Slides were incubated in this solution at room temperature for 1 hour followed by 2 consecutive SSC washes, then, slides were loaded into the for ROI selection following GeoMxTM Digital Spatial Profiler Instrument User Manual.
After ROI selection, the WTA probe tags were selectively isolated (UV-cleaved) and collected from each of these ROIs, then transferred to individual wells of a collection plate on the DSP. The collections were processed for library preparation following the manual of MANUAL GeoMx® DSP NGS Readout (MAN-10153-06). The quality of library was assessed by the Bioanalyzer DNA 1000 assay (Agilent, catalog 5067-1504). The library was then sequenced on Illumina NextSeq2000. The fastq files were converted to .DCC files using the software of GeoMx-NGS Pipeline; the DCC files were loaded on GeoMx DSP for QC, normalization.  Q3 data was generated and used for all the analysis.

value: Breast

tag: prognosis

value: PPx


title: JM964

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description: Library name: JMme964_BT

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.7
WES reads were aligned to the GRCm38 genome assembly using BWA with the default configurations
GATK pipeline was used to detect the somatic mutations
Control-FREEC was used to generate segment data and to detect copy number alterations
Assembly: GRCm38
Supplementary files format and content: tab-delimited text (tsv) file includes copy number segment data for each tumor sample

molecule: genomic DNA

organism: Mus musculus

source_name: Mammary Tumor

extract_protocol:
mice with germline p53 alterations were sacrificed and tumors collected at end point
Genomic DNA libraries were constructed following standard Illumina protocols for DNA sequencing in a sequencing and microarray core facility. Indexed DNA libraries were minimally PCR amplified, pooled and sequenced.

value: Mammary Tumor


title: LB916519

description: Library name: sample11


title: GroupD, mouse 4, RNA, replicate 1

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Library name: D-4-RNA-rep1

data_processing:
Read trimming was performed using default settings by Trim Galore!
The trimmed reads were mapped to GRCm38 genome by hisat2.
Mapped bam files were imported into SeqMonk v1.47.1 (Babraham Institute).
Datasets with poor quality (percentage of reads aligned to exons < 40%) were discarded.
FeatureCounts was used to count reads and DEGs were determined by pairwise comparison using DESeq2 (FDR < 0.05).
Assembly: mm10
Supplementary files format and content: featureCounts txt file

source_name: Frontal cortex

extract_protocol:
Adult mice were euthanized by cervical dislocation, and bilateral samples of the frontal cortex (spanning bregma 1.90 to 1.40) were rapidly dissected and flash-frozen at –80°C for later processing. For transcriptomic analysis via RNA-seq, frozen frontal cortex tissue was processed to isolate neuronal nuclei. Fluorescence-activated cell sorting (FACS) was used to enrich for NeuN-positive (NeuN⁺) neuronal populations. Each RNA-seq replicate was prepared from approximately 6,000 sorted neuronal nuclei.
For transcriptomic analysis via RNA-seq, frozen frontal cortex tissue (bregma 1.90–1.40) was processed to isolate neuronal nuclei. Fluorescence-activated cell sorting (FACS) was used to enrich for NeuN-positive (NeuN⁺) populations. A total of 100 μL of sorted neuronal nuclei suspension (~12,000 nuclei) was used for RNA extraction using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Set, following the manufacturer’s instructions. RNA from ~6,000 nuclei (in 30 μL) was concentrated by ethanol precipitation and resuspended in 4.6 μL of RNase-free water. Libraries were prepared using the SMART-seq v4 Ultra Low Input RNA kit (Clontech) and the Nextera XT DNA Library Preparation kit (Illumina), with ~600 pg of purified cDNA used per replicate. Library quality was assessed using the Agilent High Sensitivity DNA kit on a TapeStation system. Libraries were pooled with ChIP-seq samples (18–22 total per run), quantified with a KAPA Library Quantification Kit, and sequenced on an Illumina HiSeq 4000 (single-end, 50 bp), yielding ~11 million reads per RNA-seq sample.

treatment_protocol: Pregnant CD1 mice were exposed to maternal immune activation (MIA) via intranasal administration of 5 × 10³ plaque-forming units (pfu) of influenza A/WSN/33 (H1N1) on embryonic day 9.5 (E9.5), or received PBS as a control. At birth, approximately half of the offspring were cross-fostered to surrogate dams—either MIA-exposed or control—to dissociate prenatal from postnatal influences. Offspring were weaned at postnatal day 21 (P21) and housed in same-sex groups of 3–5 per cage. Litters were organized based on their prenatal and postnatal exposure conditions and distributed across multiple cages. Adult mice were sacrificed for tissue collection.

value: Frontal cortex

tag: cell type

value: Neuron

tag: treatment

value: MIA-MIA


title: TNBC006|ROI-012|PanCK+

description:
Library name: DSP-1001660016069-E-G04
TNBC006 - 012 - PanCK+
TNBC006-slide.png
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TNBC006 - 012 - Segments.png


title: GroupD, mouse 3, RNA, replicate 2

description: Library name: D-3-RNA-rep2


title: LB916506

description: Library name: sample10


title: TNBC006|ROI-011|PanCK-

description:
Library name: DSP-1001660016069-E-G03
TNBC006 - 011 - PanCK-
TNBC006-slide.png
TNBC006 - 011.png
TNBC006 - 011 - Segments.png


title: JM884

description: Library name: JMme884_Breast_Tumor

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: GroupD, mouse 3, RNA, replicate 1

description: Library name: D-3-RNA-rep1


title: TNBC006|ROI-011|PanCK+

description:
Library name: DSP-1001660016069-E-G02
TNBC006 - 011 - PanCK+
TNBC006-slide.png
TNBC006 - 011.png
TNBC006 - 011 - Segments.png


title: JM747

description: Library name: JMme747_BT


title: LB913158

description: Library name: sample8


title: TNBC006|ROI-010|PanCK-

description:
Library name: DSP-1001660016069-E-G01
TNBC006 - 010 - PanCK-
TNBC006-slide.png
TNBC006 - 010.png
TNBC006 - 010 - Segments.png


title: GroupD, mouse 2, RNA, replicate 1

description: Library name: D-2-RNA-rep1


title: GroupD, mouse 2, RNA, replicate 2

description: Library name: D-2-RNA-rep2


title: JM596

description: Library name: JMme596_Breast_Tumor


title: LB912502

description: Library name: sample7


title: TNBC006|ROI-010|PanCK+

description:
Library name: DSP-1001660016069-E-F12
TNBC006 - 010 - PanCK+
TNBC006-slide.png
TNBC006 - 010.png
TNBC006 - 010 - Segments.png


title: GroupD, mouse 1, RNA, replicate 2

description: Library name: D-1-RNA-rep2


title: LB912225

description: Library name: sample6


title: TNBC006|ROI-009|PanCK-

description:
Library name: DSP-1001660016069-E-F11
TNBC006 - 009 - PanCK-
TNBC006-slide.png
TNBC006 - 009.png
TNBC006 - 009 - Segments.png


title: JM594

description: Library name: JMme594_BT


title: JM1561

description: Library name: JMme1561_BT


title: TNBC006|ROI-009|PanCK+

description:
Library name: DSP-1001660016069-E-F10
TNBC006 - 009 - PanCK+
TNBC006-slide.png
TNBC006 - 009.png
TNBC006 - 009 - Segments.png


title: GroupC, mouse 6, RNA, replicate 2

description: Library name: C-6-RNA-rep2

value: Mock-MIA


title: LB911784

description: Library name: sample5


title: TNBC006|ROI-008|PanCK-

description:
Library name: DSP-1001660016069-E-F09
TNBC006 - 008 - PanCK-
TNBC006-slide.png
TNBC006 - 008.png
TNBC006 - 008 - Segments.png


title: GroupC, mouse 6, RNA, replicate 1

description: Library name: C-6-RNA-rep1


title: JM1262

description: Library name: JMme1262_Breast_Tumor


title: LB908812

description: Library name: sample4


title: TNBC006|ROI-008|PanCK+

description:
Library name: DSP-1001660016069-E-F08
TNBC006 - 008 - PanCK+
TNBC006-slide.png
TNBC006 - 008.png
TNBC006 - 008 - Segments.png


title: LB888240

description: Library name: sample3


title: JM756

description: Library name: JMme756_Breast_Tumor


title: GroupC, mouse 5, RNA, replicate 2

description: Library name: C-5-RNA-rep2


title: TNBC006|ROI-007|PanCK-

description:
Library name: DSP-1001660016069-E-F07
TNBC006 - 007 - PanCK-
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TNBC006 - 007.png
TNBC006 - 007 - Segments.png


title: LB886229

description: Library name: sample2


title: JM1491-T2

description: Library name: JMme1491_T2_BT


title: GroupC, mouse 5, RNA, replicate 1

description: Library name: C-5-RNA-rep1


title: TNBC006|ROI-007|PanCK+

description:
Library name: DSP-1001660016069-E-F06
TNBC006 - 007 - PanCK+
TNBC006-slide.png
TNBC006 - 007.png
TNBC006 - 007 - Segments.png


title: JM1491-T1

description: Library name: JMme1491_T1_BT


title: GroupC, mouse 4, RNA, replicate 2

description: Library name: C-4-RNA-rep2


title: GroupD, mouse 1, RNA, replicate 1

description: Library name: D-1-RNA-rep1


title: JM714

description: Library name: JMme714_BT


title: GroupC, mouse 4, RNA, replicate 1

description: Library name: C-4-RNA-rep1


title: K562 CTCF bulk D&D-seq

city: New York

first: Dan

last: Landau

state: NY

address: 413 East 69th Street

institute: Weill Cornell Medicine

description:
Library name: Bulk D_D-seq CTCF
D&D deamination targeting CTCF binding loci

data_processing:
Data quality of raw fastq data was analyzed using FastQC (v0.12.1).
Nextera transposaes adapter sequences and homo polymer G were trimmed using CutAdapt (4.0) with minimum read length 20bp.
Trimmed reads were aligned to the human reference genome (GRCh38) using bwa-mem2 (2.1).
Duplicated reads, non-primary and low quality alignments were filtered using picard MarkDuplicates (3.3.0).
Peaks were called using MACS2 (2.2.9.1) with -f BAM --nomodel and peaks found in the blacklist annotation were filtered out using bedtools (v2.31.1).
Motif enrichment analysis was performed using MEME SEA (v5.5.5) with the HOCOMOCO v11 core human motif database. Target peaks with motif sequence were resized to 200bp (+/-100bp from the motif center).
C>T variants were collected using bcftools mpileup and highly frequent variants (>10%) and germlines (gnomAD) were filtered out.
C>T variants were overlapped with target peaks and annotated as D&D edits using bedtools intersect.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, vcf (D&D edits)

source_name: Bone marrow

growth_protocol: Human K562 (ATCC, CCL-243) and CA46 (ATCC, CRL-1648) cell lines were maintained according to standard procedures in RPMI-1640 (Thermo Fisher Scientific, 11-875-119) with 10% FBS (Thermo Fisher Scientific, 10-437-028) at 37 °C with 5% CO2. Cell lines in culture were screened biweekly for mycoplasma contamination using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, LT07-703).

extract_protocol:
For all the following centrifugations, cells were centrifuged in a swing-bucket centrifuge at 300g for 5 minutes before fixation and 600g for 5 minutes after fixation. About 200K to 1 million cells were collected and resuspended in 400 µl PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration 0.1%) at room temperature for 5 minutes. Glycine (final concentration 125 mM) was added to stop the cross-linking, followed by a wash with 1 ml of PBS. Fixed cells were permeabilized in 200 µl permeabilization buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice (7 minutes for cell lines, 5 minutes for primary cells), followed by a wash with 200 µl cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors). After cell counting, 100K-400K cells were transferred to PCR tubes and resuspended in 100 µl antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors), with 1 µl (1:100 dilution) of the antibodies. The cells were incubated at 4 °C with slow rotation overnight. The cells were washed once with 200 ul wash buffer, and another time with 200 ul D&D binding buffer. The cells were resuspended in 50 ul D&D activation buffer with 100 uM DddA_NT, and incubated at room temperature on a rotator for 1 hour. The cells were then washed with 200 ul D&D binding buffer, resuspended in 50 ul DnD activation buffer, and incubated at 37 °C for 1 hour for deamination.
After D&D activation, the cells were washed once with 200 ul 1x Tris-TD buffer and resuspended in 50 ul 1x Tris-TD buffer with loaded TnY or Tn5 (volume depends on its  concentration and needs to be titrated to get the optimal tagmentation). To initiate tagmentation, the reaction was incubated at 37°C for 1 hour. To extract DNA, 1 ul 10% SDS, 2 ul proteinase K (NEB, P8107S), and 3 ul 0.5M EDTA were added to the reactions, which were then incubated at 55°C for 1 hour, followed by column-based DNA purification per the manufacturer’s instruction (Zymo, D5205). For library preparation PCR, we used uracil-tolerant DNA polymerase (NEBNext Q5U Master Mix, NEB M0597S) and Nextera-compatible indexing primers to amplify the purified DNA. To increase the efficiency of the initial gap fill-in step, we spiked in 1 ul of non-hot-start polymerase Bst 3.0 (NEB, M0374). The PCR steps are: 72°C for 5 min; 98°C for 30 s; 12 cycles of 98°C for 10 s, 55°C for 30 s and 72 °C for 30 s; followed by 72 °C for 5 min. Bulk samples are sequenced PE150 or PE100 for about 40M reads per sample.

value: Bone marrow

tag: cell line

value: Erythroleukemia

value: WT

value: CTCF D&D


title: TNBC006|ROI-006|PanCK-

description:
Library name: DSP-1001660016069-E-F05
TNBC006 - 006 - PanCK-
TNBC006-slide.png
TNBC006 - 006.png
TNBC006 - 006 - Segments.png


title: TNBC006|ROI-006|PanCK+

description:
Library name: DSP-1001660016069-E-F04
TNBC006 - 006 - PanCK+
TNBC006-slide.png
TNBC006 - 006.png
TNBC006 - 006 - Segments.png


title: JM1039

description: Library name: JMme1039_Breast_Tumor


title: JM885

description: Library name: JMme885_BT


title: JM1384

description: Library name: JMme1384_BT


title: HC_3

city: Rotterdam

first: Yifan

last: van Hasselt

state: Zuid holland

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

description:
Library name: Sample 3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed using the Cell Ranger software v7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCh38-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated according to manufacturer’s protocol and stored in liquid nitrogen. For single-cell RNA sequencing (scRNA-seq) analyses, PBMCs from healthy donors (n = 3) were stained by fluorescence-activated cell sorting (FACS) using fluorochrome-labeled monoclonal anti-human antibodies (Table S8). Viable CD19+ B cells were sorted using the FACSAriaTM Fusion cell sorter (BD Biosciences) in 5 ml pure fetal calf serum (FCS). Cells were washed and resuspended in RPMI with 10% FCS, to continue single-cell processing. Single-cell samples were loaded on a 10xGenomics Next GEM K chip to aim for a final recovery of 10000 cells.
Final 5’ gene expression (5’ GEX) libraries, were generated according to the Chromium Next GEM Single cell 5’ kit (v2 chemistry, dual index) User Guide (CG000330, 10x Genomics). Libraries were sequenced on a NovaSeq 6000 platform (Illumina), paired-end mode with a 28-10-10-90 cycle setting, with a sequencing depth of around 25000 reads/cell.

value: PBMC

value: CD19+ B cells

tag: gender

value: female

tag: age at_sampling

value: healthy donoor


title: HC_2

description:
Library name: Sample 2
10x Genomics


title: HC_1

description:
Library name: Sample 1
10x Genomics


title: TNBC006|ROI-005|PanCK-

description:
Library name: DSP-1001660016069-E-F03
TNBC006 - 005 - PanCK-
TNBC006-slide.png
TNBC006 - 005.png
TNBC006 - 005 - Segments.png


title: TNBC006|ROI-004|PanCK-

description:
Library name: DSP-1001660016069-E-F01
TNBC006 - 004 - PanCK-
TNBC006-slide.png
TNBC006 - 004.png
TNBC006 - 004 - Segments.png


title: GroupC, mouse 2, RNA, replicate 1

description: Library name: C-2-RNA-rep1


title: JM1275

description: Library name: JMme1275_BT


title: TNBC006|ROI-005|PanCK+

description:
Library name: DSP-1001660016069-E-F02
TNBC006 - 005 - PanCK+
TNBC006-slide.png
TNBC006 - 005.png
TNBC006 - 005 - Segments.png


title: GroupC, mouse 3, RNA, replicate 1

description: Library name: C-3-RNA-rep1


title: GroupC, mouse 2, RNA, replicate 2

description: Library name: C-2-RNA-rep2


title: JM590 T1

description: Library name: JMme590_L45_BT


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #3 Open Chromatin

city: Suita

first: Yosuke

last: Kugo

state: Osaka

address: 2-2 Yamadaoka

department: Cardiovascular Surgery

country: Japan

institute: Graduate School of Medicine Faculty of Medicine, Osaka University

description: Library name: E3_ATAC

data_processing:
The resulting FASTQ data were processed using the cell-ranger-arc count command in the Cell Ranger ARC (10X Genomics, version 2.0.0), which performs alignment, counting, and peak calling to generate a feature-barcode matrix. The GRCh38 reference genome was used for the alignment.
Assembly: GRCh38
Supplementary files format and content: raw matrix data(.h5)

source_name: left ventricular apex

extract_protocol:
The myocardial tissues from the LV apex were extracted at LVAD implantation, being divided into several blocks. One block was immediately sealed in a polypropylene tube and stored at -80°C for preservation.
Nuclei were isolated and extracted from frozen myocardial tissue samples from selected cases using the Miltenyi Gentle MACS Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). This kit has been validated for nuclear isolation from frozen mouse myocardial tissues and subsequent single-nucleus RNA sequencing following the same protocol. 14,15 Lysis buffer was prepared using nuclei extraction buffer and RNase inhibitor, whereas resuspension buffer was prepared using phosphate-buffered saline, bovine serum albumin, and RNase inhibitor. Tissue fragments were incubated with lysis buffer, and the nuclei were isolated using the gentleMACS Dissociator (Miltenyi Biotec). The protocol included filtering the lysate through strainers and centrifuging, after which the nuclei were extracted. DAPI staining was used to assess the nuclear morphology and count. The isolated nuclei were preserved in a resuspension buffer and promptly processed for library preparation. The library preparation was performed using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression Kit (10X Genomics, CA, USA).

value: left ventricular apex

value: cardiomyocytes and other cells


title: YZ-21

description: Library name: JMme_Yun21_BT


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #1 Open Chromatin

description: Library name: E1_ATAC


title: GroupC, mouse 3, RNA, replicate 2

description: Library name: C-3-RNA-rep2


title: LB885618

description: Library name: sample1

value: liver

value: BA


title: GroupC, mouse 1, RNA, replicate 1

description: Library name: C-1-RNA-rep1

value: Frontal cortex


title: TNBC006|ROI-003|PanCK+

description:
Library name: DSP-1001660016069-E-E10
TNBC006 - 003 - PanCK+
TNBC006-slide.png
TNBC006 - 003.png
TNBC006 - 003 - Segments.png

value: Breast

value: PPx


title: GroupB, mouse 6, RNA, replicate 2

description: Library name: B-6-RNA-rep2

value: Neuron

value: MIA-Mock


title: YZ-5

description: Library name: JMme_Yun_5_BT

value: Mammary Tumor


title: TNBC006|ROI-002|PanCK-

description:
Library name: DSP-1001660016069-E-E09
TNBC006 - 002 - PanCK-
TNBC006-slide.png
TNBC006 - 002.png
TNBC006 - 002 - Segments.png


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #2 Open Chromatin

description: Library name: C2_ATAC


title: RM0087

description: Library name: RMme0087_BT

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: TNBC006|ROI-002|PanCK+

description:
Library name: DSP-1001660016069-E-E08
TNBC006 - 002 - PanCK+
TNBC006-slide.png
TNBC006 - 002.png
TNBC006 - 002 - Segments.png


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #2 Open Chromatin

description: Library name: E2_ATAC


title: YZ-1

description: Library name: JMme_Yun1_BT


title: GroupB, mouse 6, RNA, replicate 1

description: Library name: B-6-RNA-rep1


title: JM733

description: Library name: JMme733_BT


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #3 Open Chromatin

description: Library name: C3_ATAC


title: TNBC006|ROI-004|PanCK+

description:
Library name: DSP-1001660016069-E-E12
TNBC006 - 004 - PanCK+
TNBC006-slide.png
TNBC006 - 004.png
TNBC006 - 004 - Segments.png


title: GroupB, mouse 5, RNA, replicate 2

description: Library name: B-5-RNA-rep2


title: RM249

description: Library name: RMme249_BT


title: TNBC006|ROI-003|PanCK-

description:
Library name: DSP-1001660016069-E-E11
TNBC006 - 003 - PanCK-
TNBC006-slide.png
TNBC006 - 003.png
TNBC006 - 003 - Segments.png


title: GroupB, mouse 5, RNA, replicate 1

description: Library name: B-5-RNA-rep1


title: TNBC006|ROI-001|PanCK+

description:
Library name: DSP-1001660016069-E-E06
TNBC006 - 001 - PanCK+
TNBC006-slide.png
TNBC006 - 001.png
TNBC006 - 001 - Segments.png


title: RM0058

description: Library name: RMme0058_Breast


title: TNBC005|ROI-016|PanCK-

description:
Library name: DSP-1001660016069-E-E05
TNBC005 - 016 - PanCK-
TNBC005-slide.png
TNBC005 - 016.png
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value: GPx


title: RM247

description: Library name: RMme247_Breast_Tumor


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #1 Open Chromatin

description: Library name: C1_ATAC


title: GroupC, mouse 1, RNA, replicate 2

description: Library name: C-1-RNA-rep2

value: Mock-MIA


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #3 Gene Expression

description: Library name: E3_GEX

molecule: polyA RNA


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #2 Gene Expression

description: Library name: E2_GEX


title: GroupB, mouse 4, RNA, replicate 2

description: Library name: B-4-RNA-rep2


title: RM0008-T1-Cut2

description: Library name: RMme0008_BT_cut2


title: GroupB, mouse 4, RNA, replicate 1

description: Library name: B-4-RNA-rep1


title: Pediatric dilated cardiomyopathy with left ventricular functional recovery, #1 Gene Expression

description: Library name: E1_GEX


title: TNBC006|ROI-001|PanCK-

description:
Library name: DSP-1001660016069-E-E07
TNBC006 - 001 - PanCK-
TNBC006-slide.png
TNBC006 - 001.png
TNBC006 - 001 - Segments.png


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #3 Gene Expression

description: Library name: C3_GEX


title: GroupB, mouse 3, RNA, replicate 2

description: Library name: B-3-RNA-rep2


title: RM0008-T1-Cut1

description: Library name: RMme0008_cut1_BT


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #2 Gene Expression

description: Library name: C2_GEX


title: TNBC005|ROI-015|PanCK-

description:
Library name: DSP-1001660016069-E-E03
TNBC005 - 015 - PanCK-
TNBC005-slide.png
TNBC005 - 015.png
TNBC005 - 015 - Segments.png


title: TNBC005|ROI-016|PanCK+

description:
Library name: DSP-1001660016069-E-E04
TNBC005 - 016 - PanCK+
TNBC005-slide.png
TNBC005 - 016.png
TNBC005 - 016 - Segments.png


title: JM583

description: Library name: JMme583_Breast_Tumor


title: GroupB, mouse 3, RNA, replicate 1

description: Library name: B-3-RNA-rep1


title: TNBC005|ROI-015|PanCK+

description:
Library name: DSP-1001660016069-E-E02
TNBC005 - 015 - PanCK+
TNBC005-slide.png
TNBC005 - 015.png
TNBC005 - 015 - Segments.png


title: Pediatric dilated cardiomyopathy without left ventricular functional recovery, #1 Gene Expression

description: Library name: C1_GEX


title: GroupB, mouse 2, RNA, replicate 2

description: Library name: B-2-RNA-rep2


title: JM1566 T2

description: Library name: JMme1566_Breast_Tumor_2


title: TNBC005|ROI-014|PanCK-

description:
Library name: DSP-1001660016069-E-E01
TNBC005 - 014 - PanCK-
TNBC005-slide.png
TNBC005 - 014.png
TNBC005 - 014 - Segments.png


title: GroupB, mouse 2, RNA, replicate 1

description: Library name: B-2-RNA-rep1


title: JM1566 T1

description: Library name: JMme1566_Breast_Tumor_1


title: Human_Rep3

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

data_processing:
Demultiplexing, quality control, and preprocessing of the scRNA data was conducted with the BD Rhapsody Sequence Analysis Pipeline v.1.11 from SevenBridges.
Sequences were aligned against a targeted genome panel based on the human reference hg38 with the BD Rhapsody. Sequence Analysis Pipeline v1.11
Assembly: GRCh38
Supplementary files format and content: Comma-separated values files and matrix files

source_name: Kidney

extract_protocol:
Renal biopsies were minced into small pieces and were digested in 1 mL HBSS (Ca/Mg) including DNAse I (10mg/mL) and Collagenase I (100 U/µL) at 37°C and 350 rpm for 30 min. Addition of 2ml PBS to all organs was followed by filtering suspensions trough a 70 µm cell strainer. Samples were then centrifuged at 400 xg for 5 min and cell pellets were resuspended in PBS with 1% FCS.
Approximately 2,000-3,500 vital cells of each sample were processed for scRNA-seq using using BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (BD Biosciences, Cat. No. 633774) according to the manufacturer's instructions. Quality, purity, average size and concentration of copy DNAs and libraries were determined by measurements on a Qubit FLuorometer (Thermo Fisher Scientific) and a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced using a NovaSeq 6000 sequencing platform with PE150. flow cell and reagents (Illumina).

treatment_protocol: We included patients hospitalized for kidney transplant injury at the University Hospital Muenster (Muenster, Germany). The indication for a graft biopsy was unexplained graft injury as assessed by creatinine or proteinuria. The standard immunosuppressive regimen comprised tacrolimus, mycophenolate, and prednisolone. Exclusion criteria were coinfections (hepatitis, HIV, CMV, BK virus).

value: Kidney

tag: diagnosis

value: kidney transplant injury


title: TNBC005|ROI-014|PanCK+

description:
Library name: DSP-1001660016069-E-D12
TNBC005 - 014 - PanCK+
TNBC005-slide.png
TNBC005 - 014.png
TNBC005 - 014 - Segments.png


title: GroupB, mouse 1, RNA, replicate 2

description: Library name: B-1-RNA-rep2


title: Human_Rep2


title: JM1558

description: Library name: JMme1558_BT


title: Human_Rep1


title: GroupB, mouse 1, RNA, replicate 1

description: Library name: B-1-RNA-rep1


title: JM1173 T2

description: Library name: JMme1173_R45_BT


title: TNBC005|ROI-013|PanCK+

description:
Library name: DSP-1001660016069-E-D10
TNBC005 - 013 - PanCK+
TNBC005-slide.png
TNBC005 - 013.png
TNBC005 - 013 - Segments.png


title: TNBC005|ROI-013|PanCK-

description:
Library name: DSP-1001660016069-E-D11
TNBC005 - 013 - PanCK-
TNBC005-slide.png
TNBC005 - 013.png
TNBC005 - 013 - Segments.png


title: GroupA, mouse 6, RNA, replicate 2

description: Library name: A-6-RNA-rep2

value: Mock-Mock


title: YZ-4 T1

description: Library name: JMme_Yun4_BT


title: TNBC005|ROI-012|PanCK+

description:
Library name: DSP-1001660016069-E-D08
TNBC005 - 012 - PanCK+
TNBC005-slide.png
TNBC005 - 012.png
TNBC005 - 012 - Segments.png


title: GroupA, mouse 5, RNA, replicate 1

description: Library name: A-5-RNA-rep1


title: JM1173 T1

description: Library name: JMme1173_L45_BT


title: TNBC005|ROI-012|PanCK-

description:
Library name: DSP-1001660016069-E-D09
TNBC005 - 012 - PanCK-
TNBC005-slide.png
TNBC005 - 012.png
TNBC005 - 012 - Segments.png


title: GroupA, mouse 6, RNA, replicate 1

description: Library name: A-6-RNA-rep1


title: TNBC005|ROI-010|PanCK+

description:
Library name: DSP-1001660016069-E-D04
TNBC005 - 010 - PanCK+
TNBC005-slide.png
TNBC005 - 010.png
TNBC005 - 010 - Segments.png


title: GroupA, mouse 3, RNA, replicate 2

description: Library name: A-3-RNA-rep2


title: GroupA, mouse 4, RNA, replicate 1

description: Library name: A-4-RNA-rep1


title: TNBC005|ROI-009|PanCK-

description:
Library name: DSP-1001660016069-E-D03
TNBC005 - 009 - PanCK-
TNBC005-slide.png
TNBC005 - 009.png
TNBC005 - 009 - Segments.png


title: Donor-7_UVJ-Nuc, snRNA-Seq

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: snRNA-Seq of Homo sapiens: Donor 7 Bladder UVJ

data_processing:
Raw sequencing data were demultiplrxrd and aligned using cellranger v7.1.0 with genome GRCh38-2020A (pre-built GRCh38 genome reference provided by 10X Genomics).
Transcriptome filtering, sample integration, batch correction, and clustering were performed using Seurat v4.3.0.1.
Assembly: GRCh38-2020A  (pre-built GRCh38 genome reference provided by 10X Genomics).
Supplementary files format and content: We provide normalized RNA expression, barcodes, and features for each sample. Cell types with matched barcodes are provided as a part of the supplemental data. We also provide APA and DEG tables for each donor sample for each of the twenty cell types identified in this study.

source_name: Bladder

extract_protocol:
10x Chromium Next GEM Single Cell 3ʹ Kit v3.1. Barcoded single cell RNA seq libraries were prepared for each sample and subjected to 150 base paired-end sequencing on Illumina NovaSeq.
Each sample library was loaded on 4 lanes of flowcell generating 4 sets of fastq files.
snRNA-seq

value: Bladder


title: Donor-7_Neck-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 7 Bladder Neck


title: GroupA, mouse 5, RNA, replicate 2

description: Library name: A-5-RNA-rep2


title: RM0053 RNA-seq

description:
Library name: RMmr_0053_BT
RM0053

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: mammary tumor

growth_protocol: MaPR245W/+_ mice were intraductally injected with adenovirus containing Cre recombinase to induce expression of p53R245W in the mammary ducts of mice; mammary tumors were collected at endpoint for genomic profiling.

extract_protocol:
Total RNA was isolated with the  Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit . The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in the University of Texas MD Anderson Cancer Center Advanced Technology Genomics Core (ATGC). Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

value: mammary tumor


title: YZ-24

description: Library name: JMme_Yun24_BT


title: TNBC005|ROI-011|PanCK-

description:
Library name: DSP-1001660016069-E-D07
TNBC005 - 011 - PanCK-
TNBC005-slide.png
TNBC005 - 011.png
TNBC005 - 011 - Segments.png


title: YZ-20

description: Library name: JMme_Yun20_BT


title: TNBC005|ROI-009|PanCK+

description:
Library name: DSP-1001660016069-E-D02
TNBC005 - 009 - PanCK+
TNBC005-slide.png
TNBC005 - 009.png
TNBC005 - 009 - Segments.png


title: GroupA, mouse 4, RNA, replicate 2

description: Library name: A-4-RNA-rep2


title: TNBC005|ROI-011|PanCK+

description:
Library name: DSP-1001660016069-E-D06
TNBC005 - 011 - PanCK+
TNBC005-slide.png
TNBC005 - 011.png
TNBC005 - 011 - Segments.png


title: YZ-14

description: Library name: JMme_Yun14_BT


title: TNBC005|ROI-010|PanCK-

description:
Library name: DSP-1001660016069-E-D05
TNBC005 - 010 - PanCK-
TNBC005-slide.png
TNBC005 - 010.png
TNBC005 - 010 - Segments.png


title: Donor-5_Dome-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 5 Bladder Dome


title: JM825 RNA-seq

description:
Library name: JMmr_825_BT
JM825


title: JM731 RNA-seq

description:
Library name: JMmr_731_BT
JM731


title: RM221 RNA-seq

description:
Library name: RMmr_221_BT
RM221


title: Donor-4_Dome-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 4 Bladder Dome


title: GroupA, mouse 3, RNA, replicate 1

description: Library name: A-3-RNA-rep1


title: TNBC005|ROI-008|PanCK-

description:
Library name: DSP-1001660016069-E-D01
TNBC005 - 008 - PanCK-
TNBC005-slide.png
TNBC005 - 008.png
TNBC005 - 008 - Segments.png


title: Donor_6-UVJ-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 6 Bladder UVJ


title: JM1582-Cut 2 RNA-seq

description:
Library name: JMmr_1582_BT1_C1
JM1582-Cut 2


title: GroupA, mouse 2, RNA, replicate 2

description: Library name: A-2-RNA-rep2


title: Donor-7_Dome-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 7 Bladder Dome


title: TNBC005|ROI-008|PanCK+

description:
Library name: DSP-1001660016069-E-C12
TNBC005 - 008 - PanCK+
TNBC005-slide.png
TNBC005 - 008.png
TNBC005 - 008 - Segments.png


title: GroupA, mouse 2, RNA, replicate 1

description: Library name: A-2-RNA-rep1


title: GroupA, mouse 1, RNA, replicate 2

description: Library name: A-1-RNA-rep2


title: Day7, bio rep 2

city: Suzhou

first: Jinming

last: Liu

address: 199 Ren-ai Road

institute: Soochow University

data_processing:
Sequence reads were trimmed for adapters sequence/low-quality sequence using fastp (version 0.18.0)
Trimmed sequence reads were mapped to Ensembl_release106 using HISAT2. 2.4
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Read count extraction and normalization were performed using RSEM software.
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: umbilical cord

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, NEB). The purified double-stranded cDNA fragments were end-repaired, and A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads, and amplified by PCR. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: umbilical cord

value: mesenchymal stem cells

tag: time

value: neural differentiation


title: TNBC005|ROI-007|PanCK-

description:
Library name: DSP-1001660016069-E-C11
TNBC005 - 007 - PanCK-
TNBC005-slide.png
TNBC005 - 007.png
TNBC005 - 007 - Segments.png


title: Donor_6-Neck-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 6 Bladder Neck


title: GroupA, mouse 1, RNA, replicate 1

description: Library name: A-1-RNA-rep1

value: Frontal cortex


title: Day7, bio rep 1


title: JM1581 RNA-seq

description:
Library name: JMmr_1581_BT
JM1581


title: Day3, bio rep 2


title: JM1261 RNA-seq

description:
Library name: JMmr_1261_BT
JM1261


title: HEK293T-ACE2_SARS-CoV-2_3

city: Edmonton

first: Alberto

last: Felix-Lopez

state: Alberta

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

description: Library name: CoV2_3

data_processing:
MAGeCK (https://doi.org/10.1186/s13059-014-0554-4)
Assembly: MAGeCK (https://doi.org/10.1186/s13059-014-0554-4)
Supplementary files format and content: SARS-CoV-2_KO_screen_results.xlsx
Library strategy: CRISPR Screen

extract_protocol: Following Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening (https://doi.org/10.1038/nprot.2017.016)


title: TNBC005|ROI-006|PanCK-

description:
Library name: DSP-1001660016069-E-C09
TNBC005 - 006 - PanCK-
TNBC005-slide.png
TNBC005 - 006.png
TNBC005 - 006 - Segments.png

value: Breast


title: Day3, bio rep 1


title: JM590-T2 RNA-seq

description:
Library name: JMmr_590_R45_BT
JM590-T2


title: Donor-2_Dome-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 2 Bladder Dome


title: TNBC005|ROI-006|PanCK+

description:
Library name: DSP-1001660016069-E-C08
TNBC005 - 006 - PanCK+
TNBC005-slide.png
TNBC005 - 006.png
TNBC005 - 006 - Segments.png


title: HEK293T-ACE2_SARS-CoV_2_1

description: Library name: CoV2_1


title: Day0, bio rep 2


title: JM1419 RNA-seq

description:
Library name: JMmr_1419_BT
JM1419


title: Day0, bio rep 1


title: TNBC005|ROI-005|PanCK-

description:
Library name: DSP-1001660016069-E-C07
TNBC005 - 005 - PanCK-
TNBC005-slide.png
TNBC005 - 005.png
TNBC005 - 005 - Segments.png


title: RM0057 RNA-seq

description:
Library name: RMmr_0057_BT
RM0057


title: HEK293T-ACE2_Mock_3

description: Library name: Mock_3


title: Donor_6-UO-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 6 Bladder UO


title: JM1582-Cut 1 RNA-seq

description:
Library name: JMmr_1582_BT1_C2
JM1582-Cut 1


title: mouse2_BMDM_unstimulated

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23, and fastq files were mapped to the mm9 assembly mouse genome using Bowtie2 with the "--very-sensitive" option.
The reads were excluded from downstream analysis if they were unmapped to the index genome, had multiple alignments, or were aligned to the mitochondrial genome.
Peaks were called using MACS2, and peaks from all samples were merged to generate a single combined probe list using HOMER.
The sorted bam files were imported into SeqMonk for quantification. Exact duplicate reads were removed before the raw reads export spreadsheet was generated.
Reads per kilobase per million (RPKM) were then calculated using the raw reads aligned to each peak, the peak length in kilobases, and the per million reads of total read counts within probes.
Assembly: mm9
Supplementary files format and content: Tab-delimited .txt file containing calculated RPKM values for each peak in each sample. Genomic coordinates of the called peaks are described.

source_name: bone marrow

growth_protocol: Bone-marrow derived macrophages were grown in CMG media containing FBS prior to stimulation.

extract_protocol:
Library prep was performed according to Buenrostro et al., 2015 (Curr Protoc Mol Biol. 109:21.29.1-21.29.9). Fifty thousand BMDM were centrifuged and washed with cold PBS. The cell pellet was resuspended with cold hypotonic lysis buffer. The lysate was centrifuged and the supernatant was discarded.
The crude nuclei were treated with the transposition reaction mix containing Tn5 transposase (Nextera) and incubated at 37ºC for 30 minutes. DNA clean up was performed with the Qiagen Minelute PCR Purification Kit. The transposed DNA was PCR with primer 1 and barcode primer 2 at non-saturating conditions. The amplified DNA was size selected after agarose gel electrophoresis and only fragments ranging from 100bp to 1000bp were recovered. DNA purification from the gel was performed with the Qiagen QIAquick Gel Extraction Kit.

treatment_protocol: Bone marrow-derived macrophages (BMDM) were treated with 1 µM of the β2 adrenergic receptor (β2AR) agonist Fenoterol for 15 min. The cells were then activated with 100ng/mL LPS for 1 hour prior to  crude nuclear extraction for ATAC-Seq library prep. Controls included unstimulated cells and cells that received either Fenoterol or LPS alone.

value: bone marrow

value: bone marrow derived macrophages (BMDM)

tag: strain

value: WT

value: unstimulated


title: TNBC005|ROI-007|PanCK+

description:
Library name: DSP-1001660016069-E-C10
TNBC005 - 007 - PanCK+
TNBC005-slide.png
TNBC005 - 007.png
TNBC005 - 007 - Segments.png


title: JM967 RNA-seq

description:
Library name: JMmr_967_BT
JM967

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: TNBC005|ROI-004|PanCK-

description:
Library name: DSP-1001660016069-E-C05
TNBC005 - 004 - PanCK-
TNBC005-slide.png
TNBC005 - 004.png
TNBC005 - 004 - Segments.png

value: GPx


title: HEK293T-ACE2_Mock_1

description: Library name: Mock_1


title: HEK293T-ACE2_Mock_2

description: Library name: Mock_2


title: Donor_6-Dome-Nuc, snRNA-Seq

description: snRNA-Seq of Homo sapiens: Donor 6 Bladder Dome


title: TNBC005|ROI-004|PanCK+

description:
Library name: DSP-1001660016069-E-C04
TNBC005 - 004 - PanCK+
TNBC005-slide.png
TNBC005 - 004.png
TNBC005 - 004 - Segments.png


title: mouse2_BMDM_β2AGO

value: 1µM β2AR agonist (Fenoterol) for 15 min


title: mouse2_BMDM_LPS

value: 100ng/mL LPS for 1 hour


title: JM884 RNA-seq

description:
Library name: JMmr_884_BT
JM884


title: mouse2_BMDM_β2AGO_LPS

value: 1µM β2AR agonist (Fenoterol) for 15 min, than 100ng/mL LPS for 1 hour


title: HEK293T-ACE2_SARS-CoV-2_2

description: Library name: CoV2_2


title: L-SFMA

city: Nantong

first: Xiaoxuan

last: Tang

address: 19 Qixiu road

institute: Nantong university

description: Library name: Sample 3

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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (https://ftp.ensembl.org/pub/release-112/fasta/rattus_norvegicus/dna/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-112/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.112.gtf.gz.
Assembly: mRatBN7.2
Supplementary files format and content: Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: primary cells from cerebral cortex

growth_protocol: Primary cells from cerebral cortex of E16 SD pups were seeded at a density of 100000 cells/well on hydrogels and cultured for 24 hours in Neurobasal with 2% B27 and 1% PS, at 37 oC in 5% CO2.

extract_protocol:
After 24 hours, remove the medium and directly add 1000μL Trizol into the each hydrogel group to harvest samples. Total RNA was extracted using Trizol reagent (Sigma-Aldrich, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Primary cells were grown on 4 kinds of hydrogels as usual in 6-well plates for 24h. Each kind of hydrogel is provided with 5 parallel holes.

value: primary cells from cerebral cortex

value: cultured on L@SFMA hydrogels


title: NL-SFMA

description: Library name: Sample 4

value: cultured on NL@SFMA hydrogels


title: JM756 RNA-seq

description:
Library name: JMmr_756_BT
JM756

value: mammary tumor


title: N-SFMA

description: Library name: Sample 2

value: cultured on N-SFMA hydrogels


title: mouse1_BMDM_unstimulated


title: JM747 RNA-seq

description:
Library name: JMmr_747_BT
JM747


title: TNBC005|ROI-005|PanCK+

description:
Library name: DSP-1001660016069-E-C06
TNBC005 - 005 - PanCK+
TNBC005-slide.png
TNBC005 - 005.png
TNBC005 - 005 - Segments.png


title: JM596 RNA-seq

description:
Library name: JMmr_596_BT
JM596


title: TNBC005|ROI-002|PanCK-

description:
Library name: DSP-1001660016069-E-C01
TNBC005 - 002 - PanCK-
TNBC005-slide.png
TNBC005 - 002.png
TNBC005 - 002 - Segments.png


title: mouse1_BMDM_β2AGO


title: mouse1_BMDM_LPS


title: JM964 RNA-seq

description:
Library name: JMmr_964_BT
JM964


title: TNBC005|ROI-002|PanCK+

description:
Library name: DSP-1001660016069-E-B12
TNBC005 - 002 - PanCK+
TNBC005-slide.png
TNBC005 - 002.png
TNBC005 - 002 - Segments.png


title: TNBC005|ROI-001|PanCK-

description:
Library name: DSP-1001660016069-E-B11
TNBC005 - 001 - PanCK-
TNBC005-slide.png
TNBC005 - 001.png
TNBC005 - 001 - Segments.png


title: mouse1_BMDM_β2AGO_LPS


title: TNBC005|ROI-001|PanCK+

description:
Library name: DSP-1001660016069-E-B10
TNBC005 - 001 - PanCK+
TNBC005-slide.png
TNBC005 - 001.png
TNBC005 - 001 - Segments.png


title: total RNAs from control KD in OSCs with polyA selection replicate1

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were grown in M3 medium supplemented with 10% fetal bovine serum, insulin, glutathion and fly extract in hunidified incubator with 2.5% CO2 at 27º C

extract_protocol:
RNA was extracted using NucleoSpin® RNA Kit from Macherey-Nagel
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)

value: OSCs


title: JM1561 RNA-seq

description:
Library name: JMmr_1561_BT
JM1561


title: JM594 RNA-seq

description:
Library name: JMmr_594_BT
JM594


title: TNBC005|ROI-003|PanCK-

description:
Library name: DSP-1001660016069-E-C03
TNBC005 - 003 - PanCK-
TNBC005-slide.png
TNBC005 - 003.png
TNBC005 - 003 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG7065 KD OSCs, replicate2

description: Library name: input_H3K9me3_siCG7065_rep2

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
with NEBNext Ultra DNA Library Prep Kit Illumina (NEB)


title: TNBC004|ROI-010|PanCK-

description:
Library name: DSP-1001660016069-E-B09
TNBC004 - 010 - PanCK-
TNBC004-slide.png
TNBC004 - 010.png
TNBC004 - 010 - Segments.png

value: PPx


title: total RNAs from CG7065 KD in OSCs with polyA selection replicate3


title: JM1384 RNA-seq

description:
Library name: JMmr_1384_BT
JM1384


title: TNBC005|ROI-003|PanCK+

description:
Library name: DSP-1001660016069-E-C02
TNBC005 - 003 - PanCK+
TNBC005-slide.png
TNBC005 - 003.png
TNBC005 - 003 - Segments.png

value: Breast


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG31510 KD OSCs, replicate2

description: Library name: input_H3K9me3_siCG31510_rep2


title: JM1262 RNA-seq

description:
Library name: JMmr_1262_R45_BT
JM1262


title: total RNAs from CG7065 KD in OSCs with polyA selection replicate2


title: SFMA

description: Library name: Sample 1

value: cultured on SFMA hydrogels


title: JM1491-T2 RNA-seq

description:
Library name: JMmr_1491_BT2
JM1491-T2


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG31510 KD OSCs, replicate1

description: Library name: input_H3K9me3_siCG31510_rep1


title: total RNAs from control KD in OSCs with polyA selection replicate3


title: JM1491-T1 RNA-seq

description:
Library name: JMmr_1491_BT1
JM1491-T1


title: total RNAs from control KD in OSCs with polyA selection replicate2


title: total RNAs from CG7065 KD in OSCs with polyA selection replicate1


title: TNBC004|ROI-009|PanCK+

description:
Library name: DSP-1001660016069-E-B06
TNBC004 - 009 - PanCK+
TNBC004-slide.png
TNBC004 - 009.png
TNBC004 - 009 - Segments.png


title: ChIP with anti-H3K9me3 antibody from CG7065 KD OSCs, replicate2

description: Library name: H3K9me3_siCG7065_rep2


title: JM714 RNA-seq

description:
Library name: JMmr_714_BT
JM714


title: total RNAs from CG31510 and CG7065 KD in OSCs with polyA selection replicate3


title: ChIP with anti-H3K9me3 antibody from CG7065 KD OSCs, replicate1

description: Library name: H3K9me3_siCG7065_rep1


title: input DNA used for ChIP with anti-H3K9me3 antibody from CG7065 KD OSCs, replicate1

description: Library name: input_H3K9me3_siCG7065_rep1


title: JM1193 RNA-seq

description:
Library name: JMmr_1193_BT
JM1193


title: TNBC004|ROI-008|PanCK+

description:
Library name: DSP-1001660016069-E-B04
TNBC004 - 008 - PanCK+
TNBC004-slide.png
TNBC004 - 008.png
TNBC004 - 008 - Segments.png


title: ChIP with anti-H3K9me3 antibody from CG31510 KD OSCs, replicate2

description: Library name: H3K9me3_siCG31510_rep2


title: TNBC004|ROI-010|PanCK+

description:
Library name: DSP-1001660016069-E-B08
TNBC004 - 010 - PanCK+
TNBC004-slide.png
TNBC004 - 010.png
TNBC004 - 010 - Segments.png


title: total RNAs from CG31510 and CG7065 KD in OSCs with polyA selection replicate1


title: total RNAs from CG31510 KD in OSCs with polyA selection replicate3


title: JM1039 RNA-seq

description:
Library name: JMmr_1039_BT
JM1039


title: ChIP with anti-H3K9me3 antibody in control reporter OSCs, replicate2

tag: antibody

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: ChIP with anti-H3K9me3 antibody from CG31510 KD OSCs, replicate1

description: Library name: H3K9me3_siCG31510_rep1


title: TNBC004|ROI-007|PanCK-

description:
Library name: DSP-1001660016069-E-B03
TNBC004 - 007 - PanCK-
TNBC004-slide.png
TNBC004 - 007.png
TNBC004 - 007 - Segments.png


title: JM885 RNA-seq

description:
Library name: JMmr_885_BT
JM885


title: LB913619

description: Library name: sample9

value: liver

value: BA


title: TNBC004|ROI-007|PanCK+

description:
Library name: DSP-1001660016069-E-B02
TNBC004 - 007 - PanCK+
TNBC004-slide.png
TNBC004 - 007.png
TNBC004 - 007 - Segments.png


title: JM733 RNA-seq

description:
Library name: JMmr_733_BT
JM733


title: total RNAs from CG31510 KD in OSCs with polyA selection replicate2


title: ChIP with anti-H3K9me3 antibody in control reporter OSCs, replicate1


title: total RNAs from CG31510 KD in OSCs with polyA selection replicate1


title: TNBC004|ROI-006|PanCK-

description:
Library name: DSP-1001660016069-E-B01
TNBC004 - 006 - PanCK-
TNBC004-slide.png
TNBC004 - 006.png
TNBC004 - 006 - Segments.png


title: JM590-T1 RNA-seq

description:
Library name: JMmr_590_L45_BT
JM590-T1

value: MaPR245W/+; Rosa26LSL-TdTomato/+


title: TNBC004|ROI-008|PanCK-

description:
Library name: DSP-1001660016069-E-B05
TNBC004 - 008 - PanCK-
TNBC004-slide.png
TNBC004 - 008.png
TNBC004 - 008 - Segments.png


title: TNBC004|ROI-006|PanCK+

description:
Library name: DSP-1001660016069-E-A12
TNBC004 - 006 - PanCK+
TNBC004-slide.png
TNBC004 - 006.png
TNBC004 - 006 - Segments.png


title: JM1275 RNA-seq

description:
Library name: JMmr_1275_BT
JM1275


title: TNBC004|ROI-005|PanCK-

description:
Library name: DSP-1001660016069-E-A11
TNBC004 - 005 - PanCK-
TNBC004-slide.png
TNBC004 - 005.png
TNBC004 - 005 - Segments.png


title: Blood, PD378m, Healthy control

city: Busan

first: Jungho

last: Kim

address: 57, Oryundae-ro, Geumjeong-gu, Busan, Republic of Korea

department: Department of Clinical Laboratory Science, College of Health Sciences

country: South Korea

institute: Catholic University of Pusan

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Blood

extract_protocol:
RNA was harvested using PAXgene Blood miRNA kit (QIAGEN). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruseqStranded Total RNA Ribo-Zero Globin Prep Kit standard protocols.

value: Blood

value: Blood cell

value: Healthy control


title: ChIP with anti-H3K9me3 antibody in LN-Panx tagged reporter OSCs, replicate2


title: Blood, PD326m, Healthy control


title: total RNAs from CG31510 and CG7065 KD in OSCs with polyA selection replicate2


title: ChIP with anti-H3K9me3 antibody in LN-Panx tagged reporter OSCs, replicate1


title: YZ-21 RNA-seq

description:
Library name: Gigi_R597_245_T21
YZ-21


title: TNBC004|ROI-005|PanCK+

description:
Library name: DSP-1001660016069-E-A10
TNBC004 - 005 - PanCK+
TNBC004-slide.png
TNBC004 - 005.png
TNBC004 - 005 - Segments.png


title: Blood, PD371m, Healthy control


title: YZ-1 RNA-seq

description:
Library name: Gigi_R597_245_T1
YZ-1


title: ChIP with anti-H3K9me3 antibody in LN-CG7065 tagged reporter OSCs, replicate2


title: ChIP with anti-H3K9me3 antibody in LN-CG7065 tagged reporter OSCs, replicate1


title: Blood, PD362m, Healthy control


title: TNBC004|ROI-004|PanCK-

description:
Library name: DSP-1001660016069-E-A09
TNBC004 - 004 - PanCK-
TNBC004-slide.png
TNBC004 - 004.png
TNBC004 - 004 - Segments.png


title: TNBC004|ROI-004|PanCK+

description:
Library name: DSP-1001660016069-E-A08
TNBC004 - 004 - PanCK+
TNBC004-slide.png
TNBC004 - 004.png
TNBC004 - 004 - Segments.png


title: ChIP with anti-H3K9me3 antibody in LN-CG31510 tagged reporter OSCs, replicate2


title: Blood, PD353m, Healthy control


title: YZ-5 RNA-seq

description:
Library name: Gigi_R597_245_T5
YZ-5


title: RM0087 RNA-seq

description:
Library name: RMmr_0087_BT
RM0087


title: Blood, PD352m, Healthy control


title: ChIP with anti-H3K9me3 antibody in LN-CG31510 tagged reporter OSCs, replicate1


title: TNBC004|ROI-009|PanCK-

description:
Library name: DSP-1001660016069-E-B07
TNBC004 - 009 - PanCK-
TNBC004-slide.png
TNBC004 - 009.png
TNBC004 - 009 - Segments.png


title: RM249 RNA-seq

description:
Library name: RMmr_249_BT
RM249


title: Blood, PD350m, Healthy control


title: RM247 RNA-seq

description:
Library name: RMmr_247_BT
RM247


title: TNBC004|ROI-003|PanCK+

description:
Library name: DSP-1001660016069-E-A06
TNBC004 - 003 - PanCK+
TNBC004-slide.png
TNBC004 - 003.png
TNBC004 - 003 - Segments.png


title: TNBC004|ROI-002|PanCK-

description:
Library name: DSP-1001660016069-E-A05
TNBC004 - 002 - PanCK-
TNBC004-slide.png
TNBC004 - 002.png
TNBC004 - 002 - Segments.png


title: Blood, PD348m, Healthy control


title: input DNA used for ChIP with anti-H3K9me3 antibody from Rrp41 KD OSCs, replicate1


title: RM0058 RNA-seq

description:
Library name: RMmr_0058_BT
RM0058


title: TNBC004|ROI-002|PanCK+

description:
Library name: DSP-1001660016069-E-A04
TNBC004 - 002 - PanCK+
TNBC004-slide.png
TNBC004 - 002.png
TNBC004 - 002 - Segments.png


title: Blood, PD344m, Healthy control


title: input DNA used for ChIP with anti-H3K9me3 antibody from Rrp40 KD OSCs, replicate2


title: RM0008-T1-Cut 2 RNA-seq

description:
Library name: RMmr_0008_BT1_C2
RM0008-T1-Cut 2


title: TNBC004|ROI-001|PanCK-

description:
Library name: DSP-1001660016069-E-A03
TNBC004 - 001 - PanCK-
TNBC004-slide.png
TNBC004 - 001.png
TNBC004 - 001 - Segments.png


title: RM0008-T1-Cut 1 RNA-seq

description:
Library name: RMmr_0008_BT1_C1
RM0008-T1-Cut 1


title: Blood, PD339m, Healthy control


title: input DNA used for ChIP with anti-H3K9me3 antibody from Rrp40 KD OSCs, replicate1


title: JM583 RNA-seq

description:
Library name: JMmr_583_BT
JM583


title: Blood, PD337m, Healthy control


title: input DNA used for ChIP with anti-H3K9me3 antibody from Mtr4 KD OSCs, replicate2


title: TNBC004|ROI-003|PanCK-

description:
Library name: DSP-1001660016069-E-A07
TNBC004 - 003 - PanCK-
TNBC004-slide.png
TNBC004 - 003.png
TNBC004 - 003 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody from Mtr4 KD OSCs, replicate1


title: Blood, PD332m, Healthy control


title: JM566-T2 RNA-seq

description:
Library name: JMmr_1566_BT2
JM566-T2


title: TNBC003|ROI-017|PanCK-

description:
Library name: DSP-1001660016068-D-H04
TNBC003 - 017 - PanCK-
TNBC003-slide.png
TNBC003 - 017.png
TNBC003 - 017 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody from dZfc3h1 and dZcchc8 KD OSCs, replicate2


title: input DNA used for ChIP with anti-H3K9me3 antibody from Rrp41 KD OSCs, replicate2


title: TNBC003|ROI-017|PanCK+

description:
Library name: DSP-1001660016068-D-H03
TNBC003 - 017 - PanCK+
TNBC003-slide.png
TNBC003 - 017.png
TNBC003 - 017 - Segments.png


title: Blood, PD331m, Healthy control


title: JM1566-T1 RNA-seq

description:
Library name: JMmr_1566_BT1
JM1566-T1


title: input DNA used for ChIP with anti-H3K9me3 antibody from dZfc3h1 and dZcchc8 KD OSCs, replicate1


title: TNBC003|ROI-016|PanCK-

description:
Library name: DSP-1001660016068-D-H02
TNBC003 - 016 - PanCK-
TNBC003-slide.png
TNBC003 - 016.png
TNBC003 - 016 - Segments.png


title: JM1558 RNA-seq

description:
Library name: JMmr_1558_BT
JM1558


title: Blood, PD311m, Healthy control


title: JM1381 RNA-seq

description:
Library name: JMmr_1381_BT
JM1381


title: Blood, PD284m, latent tuberculosis infection

value: subjects with latent tuberculosis infection


title: TNBC003|ROI-016|PanCK+

description:
Library name: DSP-1001660016068-D-H01
TNBC003 - 016 - PanCK+
TNBC003-slide.png
TNBC003 - 016.png
TNBC003 - 016 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody from Dis3 KD OSCs, replicate2


title: input DNA used for ChIP with anti-H3K9me3 antibody from Dis3 KD OSCs, replicate1


title: JM1173-T2 RNA-seq

description:
Library name: JMmr_1173_R45_BT
JM1173-T2


title: TNBC003|ROI-015|PanCK-

description:
Library name: DSP-1001660016068-D-G12
TNBC003 - 015 - PanCK-
TNBC003-slide.png
TNBC003 - 015.png
TNBC003 - 015 - Segments.png


title: TNBC004|ROI-001|PanCK+

description:
Library name: DSP-1001660016069-E-A02
TNBC004 - 001 - PanCK+
TNBC004-slide.png
TNBC004 - 001.png
TNBC004 - 001 - Segments.png


title: TNBC003|ROI-015|PanCK+

description:
Library name: DSP-1001660016068-D-G11
TNBC003 - 015 - PanCK+
TNBC003-slide.png
TNBC003 - 015.png
TNBC003 - 015 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody from control KD OSCs, replicate2


title: JM1173-T1 RNA-seq

description:
Library name: JMmr_1173_L45_BT
JM1173-T1


title: Blood, PD281m, latent tuberculosis infection


title: TNBC003|ROI-014|PanCK-

description:
Library name: DSP-1001660016068-D-G10
TNBC003 - 014 - PanCK-
TNBC003-slide.png
TNBC003 - 014.png
TNBC003 - 014 - Segments.png


title: Blood, PD279m, latent tuberculosis infection


title: input DNA used for ChIP with anti-H3K9me3 antibody from control KD OSCs, replicate1


title: YZ-4 RNA-seq

description:
Library name: Gigi_R597_245_T4
YZ-4


title: TNBC003|ROI-014|PanCK+

description:
Library name: DSP-1001660016068-D-G09
TNBC003 - 014 - PanCK+
TNBC003-slide.png
TNBC003 - 014.png
TNBC003 - 014 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody in control reporter OSCs, replicate2

value: input


title: input DNA used for ChIP with anti-H3K9me3 antibody in control reporter OSCs, replicate1


title: YZ-24 RNA-seq

description:
Library name: Gigi_R597_245_T24
YZ-24


title: YZ-20 RNA-seq

description:
Library name: Gigi_R597_245_T20
YZ-20


title: Blood, PD276m, latent tuberculosis infection


title: TNBC003|ROI-013|PanCK+

description:
Library name: DSP-1001660016068-D-G07
TNBC003 - 013 - PanCK+
TNBC003-slide.png
TNBC003 - 013.png
TNBC003 - 013 - Segments.png


title: TNBC003|ROI-012|PanCK+

description:
Library name: DSP-1001660016068-D-G05
TNBC003 - 012 - PanCK+
TNBC003-slide.png
TNBC003 - 012.png
TNBC003 - 012 - Segments.png


title: TNBC003|ROI-012|PanCK-

description:
Library name: DSP-1001660016068-D-G06
TNBC003 - 012 - PanCK-
TNBC003-slide.png
TNBC003 - 012.png
TNBC003 - 012 - Segments.png


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-CG7065 tagged reporter OSCs, replicate2


title: YZ-14 RNA-seq

description:
Library name: JMmr_WM245_14
YZ-14


title: Blood, PD282m, latent tuberculosis infection


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-Panx tagged reporter OSCs, replicate1


title: YZ-17 RNA-seq

description:
Library name: Gigi_R597_245_T17
YZ-17


title: Blood, PD271m, latent tuberculosis infection


title: TNBC003|ROI-011|PanCK-

description:
Library name: DSP-1001660016068-D-G04
TNBC003 - 011 - PanCK-
TNBC003-slide.png
TNBC003 - 011.png
TNBC003 - 011 - Segments.png


title: Blood, PD275m, latent tuberculosis infection


title: Blood, PD274m, latent tuberculosis infection


title: NPs@GEM/DLV+NIR3

city: Nanjing

first: Zichun

last: Hua

state: Jiangsu

address: Xianlin Road No.163

department: School of Life Sciences

institute: Nanjing University

description: Library name: Sample9

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. 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-count4
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The transcriptome library was constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit according to the instructions.

value: Tumor

value: Tumor cell

value: BALB/c

value: 1.0×10^5 M-BLAST cells followed by NIR treatment


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-CG7065 tagged reporter OSCs, replicate1

value: OSCs


title: Blood, PD270m, latent tuberculosis infection


title: Blood, PD277m, latent tuberculosis infection


title: Blood, PD246m, latent tuberculosis infection


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-CG31510 tagged reporter OSCs, replicate1


title: TNBC003|ROI-010|PanCK+

description:
Library name: DSP-1001660016068-D-G01
TNBC003 - 010 - PanCK+
TNBC003-slide.png
TNBC003 - 010.png
TNBC003 - 010 - Segments.png

data_processing:
The "GeomxTools" library in R was used to read in the DCC files using the .pkc file, and the raw counts were output into the "raw_counts.tsv" file
Assembly: Hg38
Supplementary files format and content: "Hs_R_NGS_WTA_v1.0.pkc" is the GeoMx probe code file used to map probes to gene names when producing the "raw_counts.tsv" file
Supplementary files format and content: "raw_counts.tsv" is a gene by sample expression matrix of raw counts where each sample is the "library name" and corresponds to ether a PanCK+/- segmented ROI (AOI); NTC control samples and samples that failed QC are not included

extract_protocol:
Tissue sections were prepared following the instruction of GeoMx slide preparation, and the slides were processed using the protocol of RNA slide preparation  for  formalin-fixed paraffin-embedded (FFPE) samples as described in the GeoMx DSP Manual Slide Preparation User Manual (NanoString Technologies, GeoMx-DSP-Manual-Slide-Preparation, MAN-10150). Briefly, deparaffinization and rehydration, antigen retrieval (Invitrogen, IHC Antigen Retrieval Solution, Cat#00-4956-58), and proteinase K digestion (1ug/ml, at 37°C) were performed. Human whole transcriptome atlas (WTA) probes (GeoMx WTA, Mouse RNA Probe for NGS, catalog #121401103) were hybridized in Buffer R (GeoMx RNA Slide Prep Kit PCLN catalog #121300313) and incubated in a hybridization humidity chamber (UVP, HB-1000 Hybridizer) overnight at 37°C. To remove nonspecifically bound probes, slides were washed in 50% Formamide/2x SSC (Thermo Fisher, catalog AM9763, USA) at 37°C (2 washes/25 min each), then slides were blocked and incubated with antibodies diluted with 200 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313). Then, immunostaining was performed for detection of the region of interest (ROI) . Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22 μL SYTO (GeoMx Nuclear Stain Morphology Kit, catalog 121300303), 5.5 μL Pan-CK, 5.5 μL CD45 (GeoMx Solid Tumor TME Morphology, Human FFPE RNA Compatible, catalog 121300315), and 181.5 μL Buffer W (GeoMx RNA Slide Prep Kit PCLN catalog 121300313) for a total volume of 220 μL/slide. Slides were incubated in this solution at room temperature for 1 hour followed by 2 consecutive SSC washes, then, slides were loaded into the for ROI selection following GeoMxTM Digital Spatial Profiler Instrument User Manual.
After ROI selection, the WTA probe tags were selectively isolated (UV-cleaved) and collected from each of these ROIs, then transferred to individual wells of a collection plate on the DSP. The collections were processed for library preparation following the manual of MANUAL GeoMx® DSP NGS Readout (MAN-10153-06). The quality of library was assessed by the Bioanalyzer DNA 1000 assay (Agilent, catalog 5067-1504). The library was then sequenced on Illumina NextSeq2000. The fastq files were converted to .DCC files using the software of GeoMx-NGS Pipeline; the DCC files were loaded on GeoMx DSP for QC, normalization.  Q3 data was generated and used for all the analysis.

value: PPx


title: NPs@GEM/DLV3

description: Library name: Sample6

value: 1.0×10^5 M-BLAST cells


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-CG31510 tagged reporter OSCs, replicate2


title: TNBC003|ROI-013|PanCK-

description:
Library name: DSP-1001660016068-D-G08
TNBC003 - 013 - PanCK-
TNBC003-slide.png
TNBC003 - 013.png
TNBC003 - 013 - Segments.png

value: Breast


title: NPs@GEM/DLV+NIR1

description: Library name: Sample7


title: TNBC003|ROI-011|PanCK+

description:
Library name: DSP-1001660016068-D-G03
TNBC003 - 011 - PanCK+
TNBC003-slide.png
TNBC003 - 011.png
TNBC003 - 011 - Segments.png


title: Blood, PD244m, latent tuberculosis infection


title: NPs@GEM/DLV+NIR2

description: Library name: Sample8


title: input DNA used for ChIP with anti-H3K9me3 antibody in LN-Panx tagged reporter OSCs, replicate2


title: NPs@GEM/DLV2

description: Library name: Sample5


title: TNBC003|ROI-010|PanCK-

description:
Library name: DSP-1001660016068-D-G02
TNBC003 - 010 - PanCK-
TNBC003-slide.png
TNBC003 - 010.png
TNBC003 - 010 - Segments.png


title: ChIP with anti-H3K9me3 antibody from Rrp41 KD OSCs, replicate2

value: anti-H3K9me3 antibody produced in rabbit (Active Motif Cat# 39161)


title: Blood, PD237m, latent tuberculosis infection


title: NPs@GEM/DLV1

description: Library name: Sample4


title: TNBC003|ROI-009|PanCK+

description:
Library name: DSP-1001660016068-D-F11
TNBC003 - 009 - PanCK+
TNBC003-slide.png
TNBC003 - 009.png
TNBC003 - 009 - Segments.png


title: Blood, PD231m, latent tuberculosis infection


title: Saline3

description: Library name: Sample3

value: Saline


title: ChIP with anti-H3K9me3 antibody from Rrp40 KD OSCs, replicate2


title: TNBC003|ROI-009|PanCK-

description:
Library name: DSP-1001660016068-D-F12
TNBC003 - 009 - PanCK-
TNBC003-slide.png
TNBC003 - 009.png
TNBC003 - 009 - Segments.png


title: Blood, PD137m, patient after completion of treatment

value: patient

value: anti-tuberculosis treamtent


title: TNBC003|ROI-008|PanCK-

description:
Library name: DSP-1001660016068-D-F10
TNBC003 - 008 - PanCK-
TNBC003-slide.png
TNBC003 - 008.png
TNBC003 - 008 - Segments.png


title: Blood, PD236m, latent tuberculosis infection

value: Blood


title: ChIP with anti-H3K9me3 antibody from Rrp41 KD OSCs, replicate1


title: ChIP with anti-H3K9me3 antibody from Rrp40 KD OSCs, replicate1


title: TNBC003|ROI-008|PanCK+

description:
Library name: DSP-1001660016068-D-F09
TNBC003 - 008 - PanCK+
TNBC003-slide.png
TNBC003 - 008.png
TNBC003 - 008 - Segments.png


title: Blood, PD137m, patient during treatment

value: Blood cell


title: Blood, PD137m, patient at diagnossis


title: ChIP with anti-H3K9me3 antibody from Mtr4 KD OSCs, replicate1


title: ChIP with anti-H3K9me3 antibody from Mtr4 KD OSCs, replicate2


title: ChIP with anti-H3K9me3 antibody from dZfc3h1 and dZcchc8 KD OSCs, replicate2


title: Tumor, M-BLAST+NIR-3

description: Library name: Sample9

value: 3.0×10^5 M-BLAST cells followed by NIR treatment


title: Blood, PD129m, patient after completion of treatment


title: Tumor, M-BLAST+NIR-2

description: Library name: Sample8


title: TNBC003|ROI-007|PanCK+

description:
Library name: DSP-1001660016068-D-F07
TNBC003 - 007 - PanCK+
TNBC003-slide.png
TNBC003 - 007.png
TNBC003 - 007 - Segments.png


title: Tumor, M-BLAST+NIR-1

description: Library name: Sample7


title: ChIP with anti-H3K9me3 antibody from Dis3 KD OSCs, replicate2


title: Blood, PD129m, patient during treatment


title: Blood, PD129m, patient at diagnossis


title: Blood, PD127m, patient after completion of treatment


title: ChIP with anti-H3K9me3 antibody from dZfc3h1 and dZcchc8 KD OSCs, replicate1


title: Tumor, M-BLAST-3

description: Library name: Sample6

value: 3.0×10^5 M-BLAST cells


title: ChIP with anti-H3K9me3 antibody from Dis3 KD OSCs, replicate1


title: ChIP with anti-H3K9me3 antibody from control KD OSCs, replicate2


title: Tumor, M-BLAST-1

description: Library name: Sample4


title: Blood, PD127m, patient during treatment


title: TNBC003|ROI-006|PanCK+

description:
Library name: DSP-1001660016068-D-F05
TNBC003 - 006 - PanCK+
TNBC003-slide.png
TNBC003 - 006.png
TNBC003 - 006 - Segments.png


title: TNBC003|ROI-004|PanCK-

description:
Library name: DSP-1001660016068-D-F02
TNBC003 - 004 - PanCK-
TNBC003-slide.png
TNBC003 - 004.png
TNBC003 - 004 - Segments.png


title: TNBC003|ROI-005|PanCK-

description:
Library name: DSP-1001660016068-D-F04
TNBC003 - 005 - PanCK-
TNBC003-slide.png
TNBC003 - 005.png
TNBC003 - 005 - Segments.png


title: Saline1

description: Library name: Sample1


title: ChIP with anti-H3K9me3 antibody from control KD OSCs, replicate1


title: TNBC003|ROI-007|PanCK-

description:
Library name: DSP-1001660016068-D-F08
TNBC003 - 007 - PanCK-
TNBC003-slide.png
TNBC003 - 007.png
TNBC003 - 007 - Segments.png


title: Tumor, M-BLAST-2

description: Library name: Sample5


title: TNBC003|ROI-006|PanCK-

description:
Library name: DSP-1001660016068-D-F06
TNBC003 - 006 - PanCK-
TNBC003-slide.png
TNBC003 - 006.png
TNBC003 - 006 - Segments.png


title: Blood, PD127m, patient at diagnossis


title: Tumor, Saline-3

description: Library name: Sample3


title: TNBC003|ROI-004|PanCK+

description:
Library name: DSP-1001660016068-D-F01
TNBC003 - 004 - PanCK+
TNBC003-slide.png
TNBC003 - 004.png
TNBC003 - 004 - Segments.png


title: Tumor, Saline-2

description: Library name: Sample2


title: Saline2

description: Library name: Sample2


title: TNBC003|ROI-003|PanCK-

description:
Library name: DSP-1001660016068-D-E12
TNBC003 - 003 - PanCK-
TNBC003-slide.png
TNBC003 - 003.png
TNBC003 - 003 - Segments.png


title: Blood, PD120m, patient after completion of treatment


title: Blood, PD120m, patient during treatment


title: TNBC003|ROI-003|PanCK+

description:
Library name: DSP-1001660016068-D-E11
TNBC003 - 003 - PanCK+
TNBC003-slide.png
TNBC003 - 003.png
TNBC003 - 003 - Segments.png


title: total RNAs from Rrp6 (dExosc10) KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: total RNAs from Rrp6 (dExosc10) KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: Tumor, Saline-1

description: Library name: Sample1


title: Blood, PD120m, patient at diagnossis


title: TNBC003|ROI-002|PanCK-

description:
Library name: DSP-1001660016068-D-E10
TNBC003 - 002 - PanCK-
TNBC003-slide.png
TNBC003 - 002.png
TNBC003 - 002 - Segments.png


title: total RNAs from Rrp6 (dExosc10) KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: TNBC003|ROI-005|PanCK+

description:
Library name: DSP-1001660016068-D-F03
TNBC003 - 005 - PanCK+
TNBC003-slide.png
TNBC003 - 005.png
TNBC003 - 005 - Segments.png


title: HFDHS DAS, rep 3 short term

city: Seville

first: Alejandro

last: Martin-Montalvo

address: Av/ Américo Vespucio 24

country: Spain

institute: CABIMER

description:
Library name: GEN52_21_69
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx

data_processing:
Quality control analyses, FASTQ generation files, adapters trimming and filtering of sequencing were performed using FASTQ toolkit v1.0.0 and basespace.
Differeintal analysis was performed using DESeq2 from Illumina.
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: Files include raw counts for each sample

source_name: Liver

growth_protocol: Male mice were purchased and fed with different diets (standard healthy diet, high fat diet, high sucrose diet or high fot diet with high sucrose). Treatments in each diet were of 1 week for short term and 18 weeks for long term. Liver were frozen in liquid nitrogen and stored at -80 ºC.

extract_protocol:
RNA extraction was performed using RNAeasy mini Kit (Qiagen).
RNA-seq libreries were made using the Illumina Stranded mRNA prep ligation kit

treatment_protocol: Mice were treated with DAD or DAT at 150 mg/kg of food for long term studies. DAS were provided by oral gavage (200 mg/Kg) 3 hours before euthanization.

value: Liver

value: Wild type

value: HFDHS DAS


title: Blood, PD118m, patient after completion of treatment


title: total RNAs from Rrp41 (dExosc4) KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: HFDHS DAS, rep 2 short term

description:
Library name: GEN52_21_68
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD118m, patient during treatment


title: TNBC003|ROI-002|PanCK+

description:
Library name: DSP-1001660016068-D-E09
TNBC003 - 002 - PanCK+
TNBC003-slide.png
TNBC003 - 002.png
TNBC003 - 002 - Segments.png


title: TNBC003|ROI-001|PanCK-

description:
Library name: DSP-1001660016068-D-E08
TNBC003 - 001 - PanCK-
TNBC003-slide.png
TNBC003 - 001.png
TNBC003 - 001 - Segments.png


title: total RNAs from Rrp41 (dExosc4) KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: HFDHS DAS, rep 1 short term

description:
Library name: GEN52_21_67
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD118m, patient at diagnossis


title: HFDHS, rep 3 short term

description:
Library name: GEN52_21_66
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx

value: HFDHS


title: TNBC003|ROI-001|PanCK+

description:
Library name: DSP-1001660016068-D-E07
TNBC003 - 001 - PanCK+
TNBC003-slide.png
TNBC003 - 001.png
TNBC003 - 001 - Segments.png


title: total RNAs from Rrp41 (dExosc4) KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: HFDHS, rep 2 short term

description:
Library name: GEN52_21_65
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from Rrp40 (dExosc3) KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: Blood, PD117m, patient after completion of treatment


title: total RNAs from Rrp40 (dExosc3) KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: Blood, PD117m, patient during treatment


title: TNBC002|ROI-020|PanCK-

description:
Library name: DSP-1001660016068-D-E06
TNBC002 - 020 - PanCK-
TNBC002-slide.png
TNBC002 - 020.png
TNBC002 - 020 - Segments.png

value: GPx


title: HFDHS, rep 1 short term

description:
Library name: GEN52_21_64
LiverSHOT_HFDHS.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD117m, patient at diagnossis


title: HS DAS, rep 3 short term

description:
Library name: GEN52_21_63
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv

value: HS DAS


title: total RNAs from Rrp40 (dExosc3) KD in OSCs with rRNA depletion (ribo-zero) replicate1

value: OSCs


title: total RNAs from Piwi KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: Blood, PD116m, patient after completion of treatment


title: TNBC002|ROI-019|PanCK-

description:
Library name: DSP-1001660016068-D-E04
TNBC002 - 019 - PanCK-
TNBC002-slide.png
TNBC002 - 019.png
TNBC002 - 019 - Segments.png


title: HS DAS, rep 2 short term

description:
Library name: GEN52_21_62
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv


title: TNBC002|ROI-019|PanCK+

description:
Library name: DSP-1001660016068-D-E03
TNBC002 - 019 - PanCK+
TNBC002-slide.png
TNBC002 - 019.png
TNBC002 - 019 - Segments.png


title: Blood, PD116m, patient at diagnossis


title: total RNAs from Piwi KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: Blood, PD116m, patient during treatment


title: total RNAs from Piwi KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: TNBC002|ROI-018|PanCK-

description:
Library name: DSP-1001660016068-D-E02
TNBC002 - 018 - PanCK-
TNBC002-slide.png
TNBC002 - 018.png
TNBC002 - 018 - Segments.png


title: TNBC002|ROI-018|PanCK+

description:
Library name: DSP-1001660016068-D-E01
TNBC002 - 018 - PanCK+
TNBC002-slide.png
TNBC002 - 018.png
TNBC002 - 018 - Segments.png


title: total RNAs from Mtr4 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: HS, rep 3 short term

description:
Library name: GEN52_21_60
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv

value: HS


title: HS DAS, rep 1 short term

description:
Library name: GEN52_21_61
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv


title: TNBC002|ROI-017|PanCK-

description:
Library name: DSP-1001660016068-D-D12
TNBC002 - 017 - PanCK-
TNBC002-slide.png
TNBC002 - 017.png
TNBC002 - 017 - Segments.png

value: Breast


title: Blood, PD112m, patient after completion of treatment


title: HS, rep 2 short term

description:
Library name: GEN52_21_59
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv


title: total RNAs from Mtr4 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: Blood, PD112m, patient during treatment


title: TNBC002|ROI-020|PanCK+

description:
Library name: DSP-1001660016068-D-E05
TNBC002 - 020 - PanCK+
TNBC002-slide.png
TNBC002 - 020.png
TNBC002 - 020 - Segments.png


title: HS, rep 1 short term

description:
Library name: GEN52_21_58
LiverSHOT_HS.genes.deseq.counts_EXCEL.csv


title: total RNAs from Mtr4 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: HFD DAS, rep 3 short term

description:
Library name: GEN52_21_57
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD DAS


title: Blood, PD112m, patient at diagnossis


title: TNBC002|ROI-017|PanCK+

description:
Library name: DSP-1001660016068-D-D11
TNBC002 - 017 - PanCK+
TNBC002-slide.png
TNBC002 - 017.png
TNBC002 - 017 - Segments.png


title: TNBC002|ROI-016|PanCK-

description:
Library name: DSP-1001660016068-D-D10
TNBC002 - 016 - PanCK-
TNBC002-slide.png
TNBC002 - 016.png
TNBC002 - 016 - Segments.png


title: Blood, PD111m, patient after completion of treatment


title: HFD DAS, rep 2 short term

description:
Library name: GEN52_21_56
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-016|PanCK+

description:
Library name: DSP-1001660016068-D-D09
TNBC002 - 016 - PanCK+
TNBC002-slide.png
TNBC002 - 016.png
TNBC002 - 016 - Segments.png


title: total RNAs from control KD for 4 days in OSCs with rRNA depletion (ribo-zero) replicate3


title: HFD DAS, rep 1 short term

description:
Library name: GEN52_21_55
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from control KD for 4 days in OSCs with rRNA depletion (ribo-zero) replicate2


title: Blood, PD111m, patient during treatment


title: TNBC002|ROI-015|PanCK-

description:
Library name: DSP-1001660016068-D-D08
TNBC002 - 015 - PanCK-
TNBC002-slide.png
TNBC002 - 015.png
TNBC002 - 015 - Segments.png


title: total RNAs from control KD for 4 days in OSCs with rRNA depletion (ribo-zero) replicate1


title: HFD, rep 3 short term

description:
Library name: GEN52_21_54
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD


title: Blood, PD111m, patient at diagnossis

value: patient


title: Blood, PD108m, patient after completion of treatment

value: anti-tuberculosis treamtent


title: HFD, rep 2 short term

description:
Library name: GEN52_21_53
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from control KD (3 days) in OSCs with rRNA depletion (ribo-zero) replicate3


title: TNBC002|ROI-014|PanCK-

description:
Library name: DSP-1001660016068-D-D06
TNBC002 - 014 - PanCK-
TNBC002-slide.png
TNBC002 - 014.png
TNBC002 - 014 - Segments.png


title: total RNAs from control KD (3 days) in OSCs with rRNA depletion (ribo-zero) replicate2


title: HFD, rep 1 short term

description:
Library name: GEN52_21_52
LiverSHOT_HFD.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD108m, patient during treatment

value: Blood


title: TNBC002|ROI-014|PanCK+

description:
Library name: DSP-1001660016068-D-D05
TNBC002 - 014 - PanCK+
TNBC002-slide.png
TNBC002 - 014.png
TNBC002 - 014 - Segments.png


title: total RNAs from control KD (3 days) in OSCs with rRNA depletion (ribo-zero) replicate1


title: TNBC002|ROI-013|PanCK-

description:
Library name: DSP-1001660016068-D-D04
TNBC002 - 013 - PanCK-
TNBC002-slide.png
TNBC002 - 013.png
TNBC002 - 013 - Segments.png


title: STD DAS, rep 3 short term

description:
Library name: GEN52_21_51
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx

value: STD DAS


title: total RNAs from control KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: TNBC002|ROI-013|PanCK+

description:
Library name: DSP-1001660016068-D-D03
TNBC002 - 013 - PanCK+
TNBC002-slide.png
TNBC002 - 013.png
TNBC002 - 013 - Segments.png


title: total RNAs from control KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: STD DAS, rep 1 short term

description:
Library name: GEN52_21_49
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-012|PanCK-

description:
Library name: DSP-1001660016068-D-D02
TNBC002 - 012 - PanCK-
TNBC002-slide.png
TNBC002 - 012.png
TNBC002 - 012 - Segments.png


title: total RNAs from control KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: STD, rep 3 short term

description:
Library name: GEN52_21_48
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx

value: STD


title: TNBC002|ROI-012|PanCK+

description:
Library name: DSP-1001660016068-D-D01
TNBC002 - 012 - PanCK+
TNBC002-slide.png
TNBC002 - 012.png
TNBC002 - 012 - Segments.png


title: total RNAs from control KD for 3 days in OSCs with rRNA depletion (ribo-zero) replicate3


title: Blood, PD101m, patient after completion of treatment

value: Blood cell


title: TNBC002|ROI-015|PanCK+

description:
Library name: DSP-1001660016068-D-D07
TNBC002 - 015 - PanCK+
TNBC002-slide.png
TNBC002 - 015.png
TNBC002 - 015 - Segments.png


title: STD, rep 2 short term

description:
Library name: GEN52_21_47
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx

value: Liver


title: Blood, PD101m, patient during treatment


title: STD, rep 1 short term

description:
Library name: GEN52_21_46
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx

value: Wild type


title: total RNAs from control KD for 3 days in OSCs with rRNA depletion (ribo-zero) replicate1


title: Blood, PD107m, patient after completion of treatment


title: TNBC002|ROI-011|PanCK+

description:
Library name: DSP-1001660016068-D-C11
TNBC002 - 011 - PanCK+
TNBC002-slide.png
TNBC002 - 011.png
TNBC002 - 011 - Segments.png


title: STD DAS, rep 2 short term

description:
Library name: GEN52_21_50
LiverSHOT_STD.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD101m, patient at diagnossis


title: Blood, PD108m, patient at diagnossis


title: HFD DAD, rep 5 long term

description:
Library name: GEN52_21_35
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD DAD


title: PBMC, pdm09 protein, 6347, Day 42

city: Lincoln

first: Hiep

last: Vu

state: Nebraska

address: 4240 Fair St

department: Animal Science and Nebraska Center for Virology

institute: University of Nebraska-Lincoln

description:
Library name: pdm09 protein 6
Column name in raw_counts_All_Sample.txt: PDM09PRO_6347

data_processing:
Raw read datasets were utilized as input for the nf-core/rnaseq pipeline (version 3.14), employing STAR (version 2.7.9a) as the alignment tool with default settings. The reference genome and transcript annotation in Gene Transfer Format (GTF) for pigs were retrieved from the Sus scrofa genome (Sscrofa11.1; GenBank assembly number GCF_000003025.6) and Ensembl (https://ftp.ensembl.org/pub/release-112/fasta/sus_scrofa/dna/). The data matrix containing gene counts and gene lengths obtained from this pipeline served as input for nf-core/differentialabundance (version 1.5.0), where DESeq2 (version 1.34.0) was used for differential gene expression analysis, following the default parameters of the pipeline
Assembly: Sscrofa11.1 (GCF_000003025.6)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Sus scrofa

extract_protocol:
One million PBMC cells were shipped to GENEWIZ (Azenta Life Sciences) for Standard RNA-Seq service, where total RNA and polyA+ transcripts were isolated and prepared per their in-house protocols.
RNA-seq library was prepared per their in-house protocols.

value: PBMC

tag: group

value: Protein vaccine


title: HFD DAD, rep 4 long term

description:
Library name: GEN52_21_34
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: Blood, PD107m, patient during treatment


title: TNBC002|ROI-011|PanCK-

first: David

last: Frankhouser

description:
Library name: DSP-1001660016068-D-C12
TNBC002 - 011 - PanCK-
TNBC002-slide.png
TNBC002 - 011.png
TNBC002 - 011 - Segments.png

value: GPx


title: total RNAs from control KD for 3 days in OSCs with rRNA depletion (ribo-zero) replicate2

value: OSCs


title: TNBC002|ROI-009|PanCK-

description:
Library name: DSP-1001660016068-D-C08
TNBC002 - 009 - PanCK-
TNBC002-slide.png
TNBC002 - 009.png
TNBC002 - 009 - Segments.png


title: TNBC002|ROI-010|PanCK+

description:
Library name: DSP-1001660016068-D-C09
TNBC002 - 010 - PanCK+
TNBC002-slide.png
TNBC002 - 010.png
TNBC002 - 010 - Segments.png


title: total RNAs from control KD for 2 days in OSCs with rRNA depletion (ribo-zero) replicate1


title: HFD DAD, rep 3 long term

description:
Library name: GEN52_21_33
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from control KD for 2 days in OSCs with rRNA depletion (ribo-zero) replicate2


title: PBMC, pdm09 protein, 6331, Day 42

description:
Library name: pdm09 protein 3
Column name in raw_counts_All_Sample.txt: PDM09PRO_6331


title: Blood, PD107m, patient at diagnossis


title: HFD DAD, rep 1 long term

description:
Library name: GEN52_21_31
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: HFD DAT, rep 5 long term

description:
Library name: GEN52_21_30
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD DAT


title: total RNAs from control KD for 2 days in OSCs with rRNA depletion (ribo-zero) replicate3


title: PBMC, pdm09 protein, 6338, Day 42

description:
Library name: pdm09 protein 4
Column name in raw_counts_All_Sample.txt: PDM09PRO_6338


title: TNBC002|ROI-008|PanCK+

description:
Library name: DSP-1001660016068-D-C05
TNBC002 - 008 - PanCK+
TNBC002-slide.png
TNBC002 - 008.png
TNBC002 - 008 - Segments.png

value: Breast


title: TNBC002|ROI-010|PanCK-

description:
Library name: DSP-1001660016068-D-C10
TNBC002 - 010 - PanCK-
TNBC002-slide.png
TNBC002 - 010.png
TNBC002 - 010 - Segments.png


title: TNBC002|ROI-009|PanCK+

description:
Library name: DSP-1001660016068-D-C07
TNBC002 - 009 - PanCK+
TNBC002-slide.png
TNBC002 - 009.png
TNBC002 - 009 - Segments.png


title: HFD DAT, rep 4 long term

description:
Library name: GEN52_21_29
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-008|PanCK-

description:
Library name: DSP-1001660016068-D-C06
TNBC002 - 008 - PanCK-
TNBC002-slide.png
TNBC002 - 008.png
TNBC002 - 008 - Segments.png


title: PBMC, pdm09 protein, 6355, Day 42

description:
Library name: pdm09 protein 1
Column name in raw_counts_All_Sample.txt: PDM09PRO_6355


title: TNBC002|ROI-007|PanCK-

description:
Library name: DSP-1001660016068-D-C04
TNBC002 - 007 - PanCK-
TNBC002-slide.png
TNBC002 - 007.png
TNBC002 - 007 - Segments.png


title: total RNAs from dZfc3h1 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: total RNAs from dZfc3h1 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: TNBC002|ROI-007|PanCK+

description:
Library name: DSP-1001660016068-D-C03
TNBC002 - 007 - PanCK+
TNBC002-slide.png
TNBC002 - 007.png
TNBC002 - 007 - Segments.png


title: total RNAs from dZfc3h1 and dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: PBMC, pdm09 protein, 6357, Day 42

description:
Library name: pdm09 protein 5
Column name in raw_counts_All_Sample.txt: PDM09PRO_6357


title: HFD DAT, rep 3 long term

description:
Library name: GEN52_21_28
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: HFD DAD, rep 2 long term

description:
Library name: GEN52_21_32
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from dZfc3h1 and dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: total RNAs from dZfc3h1 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: TNBC002|ROI-006|PanCK-

description:
Library name: DSP-1001660016068-D-C02
TNBC002 - 006 - PanCK-
TNBC002-slide.png
TNBC002 - 006.png
TNBC002 - 006 - Segments.png


title: PBMC, pdm09 protein, 6328, Day 42

description:
Library name: pdm09 protein 2
Column name in raw_counts_All_Sample.txt: PDM09PRO_6328


title: PBMC, pdm09 LNP, 6336, Day 42

description:
Library name: pdm09 LNP 4
Column name in raw_counts_All_Sample.txt: PDM09LNP_6336

value: LNP vaccine


title: HFD DAT, rep 1 long term

description:
Library name: GEN52_21_26
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-006|PanCK+

description:
Library name: DSP-1001660016068-D-C01
TNBC002 - 006 - PanCK+
TNBC002-slide.png
TNBC002 - 006.png
TNBC002 - 006 - Segments.png


title: total RNAs from dZfc3h1 and dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: PBMC, pdm09 LNP, 6332, Day 42

description:
Library name: pdm09 LNP 3
Column name in raw_counts_All_Sample.txt: PDM09LNP_6332


title: TNBC002|ROI-005|PanCK-

description:
Library name: DSP-1001660016068-D-B12
TNBC002 - 005 - PanCK-
TNBC002-slide.png
TNBC002 - 005.png
TNBC002 - 005 - Segments.png


title: PBMC, pdm09 LNP, 6326, Day 42

description:
Library name: pdm09 LNP 2
Column name in raw_counts_All_Sample.txt: PDM09LNP_6326


title: PBMC, pdm09 LNP, 6352, Day 42

description:
Library name: pdm09 LNP 6
Column name in raw_counts_All_Sample.txt: PDM09LNP_6352


title: HFD, rep 4 long term

description:
Library name: GEN52_21_24
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: HFD control


title: total RNAs from dZfc3h1 and dZcchc7 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: HFD, rep 3 long term

description:
Library name: GEN52_21_23
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: PBMC, No vaccine, 6354, Day 42

description:
Library name: No vaccine 6
Column name in raw_counts_All_Sample.txt: NV_6354

value: No vaccine


title: PBMC, pdm09 LNP, 6346, Day 42

description:
Library name: pdm09 LNP 1
Column name in raw_counts_All_Sample.txt: PDM09LNP_6346


title: total RNAs from dZfc3h1 and dZcchc7 and dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: TNBC002|ROI-005|PanCK+

description:
Library name: DSP-1001660016068-D-B11
TNBC002 - 005 - PanCK+
TNBC002-slide.png
TNBC002 - 005.png
TNBC002 - 005 - Segments.png


title: TNBC002|ROI-003|PanCK-

description:
Library name: DSP-1001660016068-D-B08
TNBC002 - 003 - PanCK-
TNBC002-slide.png
TNBC002 - 003.png
TNBC002 - 003 - Segments.png


title: TNBC002|ROI-004|PanCK-

description:
Library name: DSP-1001660016068-D-B10
TNBC002 - 004 - PanCK-
TNBC002-slide.png
TNBC002 - 004.png
TNBC002 - 004 - Segments.png


title: total RNAs from dZfc3h1 KD in OSCs with rRNA depletion (ribo-zero) replicate2


title: PBMC, pdm09 LNP, 6341, Day 42

description:
Library name: pdm09 LNP 5
Column name in raw_counts_All_Sample.txt: PDM09LNP_6341


title: STD DAD, rep 5 long term

description:
Library name: GEN52_21_20
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx

value: STD DAD


title: total RNAs from dZfc3h1 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: HFD DAT, rep 2 long term

description:
Library name: GEN52_21_27
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: HFD, rep 2 long term

description:
Library name: GEN52_21_22
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: TNBC002|ROI-003|PanCK+

description:
Library name: DSP-1001660016068-D-B07
TNBC002 - 003 - PanCK+
TNBC002-slide.png
TNBC002 - 003.png
TNBC002 - 003 - Segments.png


title: TNBC002|ROI-004|PanCK+

description:
Library name: DSP-1001660016068-D-B09
TNBC002 - 004 - PanCK+
TNBC002-slide.png
TNBC002 - 004.png
TNBC002 - 004 - Segments.png


title: total RNAs from dZcchc8 KD in OSCs with rRNA depletion (ribo-zero) replicate3


title: STD DAD, rep 4 long term

description:
Library name: GEN52_21_19
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: PBMC, No vaccine, 6350, Day 42

description:
Library name: No vaccine 5
Column name in raw_counts_All_Sample.txt: NV_6350

value: Blood


title: PBMC, No vaccine, 6335, Day 42

description:
Library name: No vaccine 2
Column name in raw_counts_All_Sample.txt: NV_6335


title: HFD, rep 1 long term

description:
Library name: GEN52_21_21
STD_vs_HFD.genes.deseq.counts_EXCEL.xlsx


title: total RNAs from dZfc3h1 KD in OSCs with rRNA depletion (ribo-zero) replicate1


title: PBMC, No vaccine, 6356, Day 42

description:
Library name: No vaccine 1
Column name in raw_counts_All_Sample.txt: NV_6356


title: PBMC, No vaccine, 6340, Day 42

description:
Library name: No vaccine 3
Column name in raw_counts_All_Sample.txt: NV_6340