title: HCC_TMA_20210804_09_13084_ROI021_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P2_2

status: Public on Sep 23 2024

type: SRA

city: Los Angeles

first: Ting

last: Zhang

state: CA

address: 2506 Gonda Bldg, 695 Charles E.Young Dr. South

department: Pathology and laboratory medicine

country: USA

institute: University of California, Los Angeles

description: 6_Pons|2|Full ROI

library_source: transcriptomic

data_processing:
Following sequencing, the processing and normalization of data involves matching the raw probe counts to sequencing results to filter out unused probes and remove outliers, then subjected to third quartile Q3 normalization to the negative probes. The negative probes include probes for whole transcriptomic atlas and SARS-CoV2 (Neg-WTA and SARS-CoV2-Neg).
Processed data includes Q3 normalized counts
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: PATIENT

extract_protocol:
5-6 µm were mounted on glass slides and subjected to an overnight baking at 37°C, followed by a 3-hour baking at 65°C. The slides underwent processing on the Leica automation platform, including antigen retrieval for 20 minutes at 100°C and proteinase K treatment.
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.

tag: tissue

value: postmortem brain

tag: tissue type

value: FFPE

tag: area

value: Corticospinal Tract

tag: region

value: Pons

tag: grey/whitematter

value: White

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

value: Yes

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_13084_ROI022_Tumor

city: Boston

first: Joseph

last: Franses

state: Massachusetts

department: Cancer Center

institute: Massachusetts General Hospital

description: (v1.0) Cancer Transcriptome Atlas

data_processing:
Raw sequencing data were processed using the GeoMx NGS Pipeline to generate fastq files followed by dcc files
Sequences were aligned to the Cancer Transcriptome Atlas probe set using default settings
Assembly: hg38
Supplementary files format and content: rawCounts.tsv: gene count matrix file in tsv format
Supplementary files format and content: qnormCounts.tsv: Q3 normalized gene count matrix file in tsv format
Library strategy: GeoMx Spatial Transcriptomics

source_name: Liver cancer resection

extract_protocol:
We followed published experimental methods (NanoString) with modifications as noted below. Briefly, slides were baked at 60 °C for one hour, deparaffinized with CitriSolv (DECON), rehydrated, antigen-retrieved in 1x Tris-EDTA/pH 9 in a steamer for 15 min at 100 °C, proteinase K (Thermo Fisher Scientific, AM2548) digested at 0.1 ng/ml for 15 min at 37 °C, and postfixed in neutral-buffered formalin for 10 min, hybridized to UV-photocleavable barcode-conjugated RNA in situ hybridization probe set (CTA with 1,779 gene targets and 32 reference genes) overnight at 37 °C, washed to remove off-target probes and then counterstained with morphology markers for 2 h at room temperature. The morphology markers consisted of: 1:50 CD31 (Abcam, ab47063) and 1:50 Arginase-1 (Cell Signaling Technology, 93668S) in blocking buffer W (NanoString). The anti-CD31 antibody was conjugated using the Alexa Fluor 555 Lightning-Link kit (Abcam, ab269820) and the anti-Arginase-1 antibody with the Alexa Fluor 647 Lightning-Link kit (Abcam, ab269823). These two morphology markers allowed distinction between vessel areas of interest (AOIs) and tumor regions of interest (AOIs) within a microscopic region of interest (ROI). 22 Immunofluorescence images, ROI selection, segmentation into marker-specific AOIs and 23 spatially indexed barcode cleavage and collection were performed on a GeoMx DSP instrument 24 (NanoString). Typical exposure times were 400 ms for CD31 and 300 ms for Arg 1. Approximately 25 4 AOIs on average were collected per specimen (details in Table 1)
Library preparation was performed according to the manufacturer’s instructions and involved PCR amplification to add Illumina adapter sequences and unique dual sample indices. A minimum sequencing depth of 2 150–200 reads per square micron of illumination area was achieved by sequencing all CTA AOIs on a NovaSeq S2 (100 cycles, read 1: 27 nt, read 2: 27 nt, index 1: 8 nt, index 2: 8 nt).

tag: tissue

value: Liver cancer resection

tag: slide name

value: HCC TMA 04

tag: pool

tag: roi

tag: aoi type

value: Tumor

tag: area


title: Corticospinal Tract_P2_4

description: 6_Pons|4|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: HCC_TMA_20210804_09_12619_ROI019_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: HCC_TMA_20210804_09_12619_ROI020_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_13084_ROI021_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P5_1

description: Pons|7|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

value: Female

value: No

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_12619_ROI020_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_P2_3

description: 6_Pons|3|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: Corticospinal Tract_P2_1

description: 6_Pons|1|Full ROI

tag: tissue

tag: area

tag: roi

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Corticospinal Tract_P1_3

description: 5_Pons|3|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount


title: Corticospinal Tract_P1_2

description: 5_Pons|2|Full ROI

tag: tissue

tag: area

tag: roi

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: HCC_TMA_20210804_09_11242_ROI018_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210804_09_12619_ROI019_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P1_1

description: 5_Pons|1|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_11242_ROI018_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_11242_ROI017_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_C4_2

description: 7_Pons-Control|2|Full ROI

source_name: CONTROL

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Corticospinal Tract_C4_1

description: 7_Pons-Control|1|Full ROI

tag: tissue

tag: area

tag: roi

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_11242_ROI017_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: Corticospinal Tract_C3_2

description: 7_Pons|14|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: HCC_TMA_20210804_09_10440_ROI016_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_C2_2

description: 6_Pons|14|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Corticospinal Tract_C3_1

description: 7_Pons|13|Full ROI

tag: tissue

tag: area

tag: roi

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: Corticospinal Tract_C1_3

description: 5_Pons|15|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount


title: HCC_TMA_20210804_09_09752_ROI013_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_C2_3

description: 6_Pons|15|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_10440_ROI015_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_09752_ROI014_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_10440_ROI015_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_C2_1

description: 6_Pons|13|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: HCC_TMA_20210804_09_09752_ROI013_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_C1_2

description: 5_Pons|14|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_09752_ROI012_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_09752_ROI014_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_C4_3

description: 7_Pons-Control|3|Full ROI

tag: tissue type

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: HCC_TMA_20210804_09_09752_ROI011_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Control

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to a custom mm10 reference file that included tdTomato and GFP reference sequences. CellRanger Count estimated 17117 nuclei from the combined Control and Repair Drive samples, averaging 30K reads per nucleus with a median of 2000 unique genes per nucleus. Ambient background RNA was removed after alignment using CellBender. Single nuclear RNA-seq data was analyzed using the latest Seurat v4.0 package suite. Quality control filters were used to remove low quality nuclei. All genes that were not expressed in at least 10 nuclei were excluded, and nuclei with less than 200 genes were removed. 15979 nuclei and 18153 genes remained after filtration. Nuclei Doublets were determined both manually and through DoubletFinder. RNA count was normalized using SCT from Seurat V4 (SCTransform) regressing out any contaminating mitochondria mRNA. Principle components analysis (PCA) was determined by RunPCA and both samples were integrated using Harmony package. The number of PCA to be used for downstream analysis was determined using elbowplot and jackstraw for downstream analysis. We used Uniform Manifold Approximation and Projection (UMAP) for dimensional reduction and visualization of the single nuclear data. For determining hepatocyte zonation and ploidy prediction, we used a set of previously identified markers.
Assembly: custom mm10 reference file that included tdTomato and GFP reference sequences
Supplementary files format and content: CellRanger Output (Barcode, Features, Matrix)
Supplementary files format and content: Cellbender Filtered h5

molecule: nuclear RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
~ 100 mg of frozen liver were used for nuclei isolation and single nucleus RNA sequencing (snRNAseq) analysis. Nuclei were isolated from one Control and one CRISPR/Donor + siRNA (Repair Drive) mouse sacrificed at 12 weeks post-AAV injection. Liver samples were cut into tiny pieces in 250 µL of buffer HB (0.25 M Sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH, pH 7.8) supplemented with 1x DTT, spermine and spermidine, and 0.2 U/µL of Protector RNase inhibitor (Millipore Sigma) (referred as buffer HB++). Then, samples were centrifuge at 500 g for 5 minutes and resuspended in 500 µL of buffer HB++. Samples were homogenized in a Dounce homogenizer firstly with a loose pestle for 30 strokes, followed by a tight pestle for 10 strokes after adding 250 µL of 1% NP-40 (in buffer HB++). Homogenates were filtered through a pre-wet 40 µm cell strainer (Falcon) by adding 10 mL of nuclei wash buffer (NWB, 1% BSA in PBS supplemented with 0.2 U/µL of Protector RNase inhibitor). Samples were centrifuged at 500 g for 10 minutes at 4°C using a swinging bucket rotor and the pellets were resuspended in 500 µL of NWB buffer and filtered through a 40 µm cell strainer (Flowmi, Millipore Sigma). 900 µL of sucrose cushion buffer (SCB: 9 volumes of Nuclei PURE 2M sucrose cushion solution and 1 volume of Nuclei PURE sucrose cushion solution, Sigma-Aldrich, supplemented with 0.2 U/µL of Protector RNase inhibitor) were added to the resuspended pellet and the obtained mix was layered on top of 500 µL of SCB in a 2 mL Eppendorf tube. Nuclei were centrifuged at 13000 g for 45 minutes at 4°C. The obtained pellet was resuspended in 1 mL of NWB and filtered through a pre-wet 20 µm CellTrics filter (Fisher Scientific). Nuclei were finally centrifuged at 500 g for 5 minutes and resuspended in 200 µL of NWB buffer. Nuclei were stained with DAPI and nuclei purity and integrity were confirmed using a fluorescent microscope.
Samples were diluted to obtain 15000 - 18000 nuclei for single cell library construction according to the 10X single cell gene expression workflow (10X Genomics, Chromium Next GEM Single Cell 3’ Kit v3.1, 1000269). Quality of the cDNA and the libraries were analyzed using the high sensitivity NGS fragment analysis kit (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Mice were injected with adeno-associated viruses (AAVs) for targeted integration of a selectable marker and a therapeutic gene into the Apoa1 locus of hepatocytes. Targeted hepatocytes were expanded in vivo by transiently knockdown an essential gene with small interfering RNAs. This conditioning protocol induces depletion of untargeted hepatocytes. On the contrary, correctly targeted hepatocytes are resistant to liver conditioning through the selectable marker and expand over time, therefore boosting the expression of the therapeutic gene.

value: Liver

tag: cell type

value: Hepatocytes, endothelial cells, Kupffer cells, cholangiocytes, stellate cells

tag: genotype

tag: treatment

value: Control


title: dyW2 muscle fibers E17.5

city: Lisboa

first: Ana Rita

last: Carlos

address: FCUL, Campo Grande

country: Portugal

institute: Faculty of Sciences, University of Lisbon

data_processing:
Galaxy Europe platform
Quality of fastq.gz reads was analyzed fastq.gzC
Reads was trimmed and filtered using Cutadapt
Reads were aligned against the mouse reference genome using RNA STAR
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include normalized counts for each sample
Supplementary files format and content: tab-delimited text files include DeSeq2 analysis of wildtype versus dyW/dyW samples

source_name: skeletal muscle

extract_protocol:
Muscle fibers were directly incubated with RTL lysis buffer
Nextera library preparation protocol (Nextera XT DNA Library Preparation kit, Illumina) was used for library preparation, including cDNA ‘tagmentation’, PCR-mediated dT adaptor addition, and library amplification
The libraries were sequenced using the NextSeq 2000 P2 Reagents (100 cycles) (Illumina)

value: skeletal muscle

tag: developmental stage

value: muscle fibers

value: dyW/dyW


title: HCC_TMA_20210804_09_09752_ROI012_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_C3_3

description: 7_Pons|15|Full ROI

value: postmortem brain

tag: tissue type

value: FFPE

value: Corticospinal Tract

tag: region

tag: grey/whitematter

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: REPAIR_DRIVE

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: HCC_TMA_20210804_09_09752_ROI011_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Corticospinal Tract_C1_1

description: 5_Pons|13|Full ROI

tag: tissue type

tag: region

value: Pons

tag: grey/whitematter

value: White

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: Frontal_WhiteMatter_P6_4

description: Frontal|20|Full ROI

extract_protocol:
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.
5-6 µm were mounted on glass slides and subjected to an overnight baking at 37°C, followed by a 3-hour baking at 65°C. The slides underwent processing on the Leica automation platform, including antigen retrieval for 20 minutes at 100°C and proteinase K treatment.
The slides were incubated overnight with the GeoMx Human whole transcriptome atlas (WTA) assay probe cocktail, targeting 18,702 genes including 3 SARS-CoV2 targets. Immunofluorescent cell type/morphology markers, anti-NeuN antibody (Millipore) for neurons, anti-GFAP antibody (Invitrogen) for astrocyte, anti-IBA1 antibody (Millipore) for microglia, and Syto83 (Invitrogen) for nuclei were then applied to the slides.
The GeoMx Deep Spatial Platform (DSP) was used to scan the slides, followed by region-of-interest (ROI) selections performed by senior neuropathologists. Probe barcodes were UV cleaved, collected, and sequenced on the Illumina NovaSeq 6000 platform with paired end reads.

tag: tissue

tag: tissue type

tag: area

tag: region

value: Frontal lobe

value: Frontal

tag: roi

value: Yes

tag: lung pathology

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_10440_ROI016_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

value: HCC TMA 04

tag: pool

tag: aoi type

value: Tumor


title: Basal_Ganglia_C11

type: RNA

hyb_protocol: A master mix is created containing the hybrid buffer and the reporter probe. 8 ul of master mix is added  to each 12 tubes, and add 5 ul of 20ng/ul of RNA in each tube. Add 2 ul of Capture probeSet to each tube immediately before placing at 65°C.  Briefly spin down and immediately place the tubes in the pre-heated 65°C thermal cycler. Incubate reactions for at least 16 hours. After hybridization, excess probes are washed away using a two-step magnetic bead-based purification on an nCounter instrument. Finally, the purified target-probe complexes are eluted off the beads and are immobilized and aligned for data collection.

scan_protocol: Data collection is performed using epifluorescence microscopy and CCD capture technology on the nCounter analyzer to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument and the Reporter probe ounts are tabulated in comma separated value (CSV) format  for data analysis with Nanostring nSolver Analysis Software.

data_processing: The raw data were re-scaled to account for differences in hybridization efficiency using positive control ERCC spike-ins. Internal housekeeping genes were then used to normalize for different input amounts.

label_protocol: High-plex flourescently labelled DNA oligos annealed to target RNA

extract_protocol: 3-5 FFPE tissue section on the slides were scraped to be collected for RNA extraction. RNA extraction was performed using Qiagen RNeasy FFPE kit.

tag: tissue preparation

value: Basal Ganglia

tag: age

tag: gender

value: Female

tag: postmortem interval (day)

tag: immunocompromised status

value: YES


title: HCC_TMA_20210804_09_09690_ROI009_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: roi

value: Vessel

tag: area


title: HCC_TMA_20210804_09_09690_ROI009_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P6_3

description: Frontal|19|Full ROI

tag: tissue type

tag: region

tag: lotid

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: HCC_TMA_20210804_09_08455_ROI008_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_08455_ROI008_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_08455_ROI007_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Basal_Ganglia_C10

value: postmortem brain

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Basal_Ganglia_C9

value: FFPE


title: HCC_TMA_20210804_09_08455_ROI007_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P6_1

description: Frontal|13|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Basal_Ganglia_C8

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status

value: NO


title: HCC_TMA_20210804_09_08455_ROI006_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_08455_ROI006_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_09_08455_ROI005_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P5_5

description: Frontal|10|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_09_08236_ROI004_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_09_08455_ROI005_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Basal_Ganglia_C7

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_WhiteMatter_P5_6

description: Frontal|11|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_09690_ROI010_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_P6_2

description: Frontal|17|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_09_08236_ROI003_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: Frontal_WhiteMatter_P5_4

description: Frontal|8|Full ROI

tag: tissue type

tag: area

tag: region

tag: lotid

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_09_08236_ROI002_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi


title: Frontal_WhiteMatter_P5_3

description: Frontal|7|Full ROI

tag: tissue type

tag: area

tag: region

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_09_08236_ROI002_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: aoi type


title: Basal_Ganglia_C6

tag: tissue preparation

tag: age


title: HCC_TMA_20210804_09_08236_ROI001_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: pool

tag: roi

tag: area


title: Frontal_WhiteMatter_P5_2

description: Frontal|6|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Basal_Ganglia_P18

tag: tissue

tag: tissue preparation

tag: age


title: Basal_Ganglia_P19

tag: region


title: HCC_TMA_20210804_12_20507_ROI021_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

value: HCC TMA 02

tag: pool

tag: roi

tag: aoi type

tag: area


title: Basal_Ganglia_P17

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Basal_Ganglia_P16


title: HCC_TMA_20210804_12_20507_ROI021_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P5_1

description: Frontal|1|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_WhiteMatter_P4_6

description: 4_Frontal|24|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_20507_ROI020_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210804_12_15683_ROI019_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_15683_ROI019_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P4_5

description: 4_Frontal|23|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Frontal_WhiteMatter_P4_4

description: 4_Frontal|22|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_15683_ROI018_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: Basal_Ganglia_P14

tag: tissue preparation


title: HCC_TMA_20210804_09_08236_ROI001_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue


title: dyW3 muscle fibers E17.5

value: skeletal muscle

tag: developmental stage

tag: cell type

value: muscle fibers

tag: genotype

value: dyW/dyW


title: Pons_P9

extract_protocol: Total RNA was extracted from 3-4 10µm FFPE curls using the Qiagen RNeasy FFPE kit.

tag: region

value: Pons

tag: age

value: Male


title: Basal_Ganglia_P15

tag: gender

tag: postmortem interval (day)


title: Frontal_WhiteMatter_P4_3

description: 4_Frontal|21|Full ROI

tag: tissue type

tag: area

value: Frontal lobe

tag: lotid

tag: roi

tag: immunocompromised status

value: Yes

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_12_15683_ROI016_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

value: Liver cancer resection

tag: slide name

tag: pool

tag: aoi type

value: Tumor

tag: area


title: Frontal_WhiteMatter_P4_2

description: 4_Frontal|20|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_13896_ROI015_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: Pons_P7

tag: tissue preparation

tag: region


title: HCC_TMA_20210804_12_15683_ROI017_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: roi

tag: area


title: HCC_TMA_20210804_12_15683_ROI016_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_13896_ROI014_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P3_6

description: 3_Frontal|17|Full ROI

tag: tissue type

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_12_20507_ROI020_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_12_13896_ROI013_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_13896_ROI013_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_15683_ROI018_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P4_1

description: 4_Frontal|19|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_13896_ROI012_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: Pons_P6

tag: tissue preparation

tag: region

tag: age


title: Pons_P8

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210804_12_13896_ROI012_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: Pons_P5


title: Frontal_WhiteMatter_P3_5

description: 3_Frontal|16|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_12_13896_ROI011_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Pons_P4

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_WhiteMatter_P3_4

description: 3_Frontal|15|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_15683_ROI017_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_12_13896_ROI011_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_12069_ROI010_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_12069_ROI010_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_12069_ROI009_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Pons_P17

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_WhiteMatter_P3_2

description: 3_Frontal|13|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210804_12_12069_ROI009_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_12_5965_ROI008_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Pons_P16

tag: tissue preparation

tag: region

tag: age

tag: gender

value: Female

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_WhiteMatter_P3_1

description: 3_Frontal|12|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_5965_ROI006_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_12_5965_ROI007_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Pons_P15

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Pons_P14


title: HCC_TMA_20210804_12_5539_ROI005_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_5539_ROI004_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P2_5

description: 2_Frontal|23|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Pons_P13

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210804_12_5539_ROI004_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210804_12_5965_ROI006_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_5539_ROI003_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P3_3

description: 3_Frontal|14|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_5539_ROI003_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_P2_4

description: 2_Frontal|22|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Pons_P12

tag: tissue

tag: tissue preparation


title: Frontal_WhiteMatter_P2_3

description: 2_Frontal|21|Full ROI

tag: tissue type

tag: area

tag: roi

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pons_P3

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210804_12_5539_ROI002_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type

tag: area


title: Pons_P11

tag: tissue preparation


title: HCC_TMA_20210804_12_5539_ROI002_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: roi


title: HCC_TMA_20210804_12_5539_ROI001_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210804_12_5539_ROI001_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Corticospinal Tract_P4_1

description: 9_MidBrain_Pons-COVID|4|Full ROI

tag: tissue type

value: Corticospinal Tract

tag: grey/whitematter

value: White

tag: lotid

tag: duration

tag: ventilation

tag: lung disease

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_WhiteMatter_P2_6

description: 2_Frontal|24|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: lung pathology

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210804_12_5539_ROI005_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: Frontal_WhiteMatter_P2_1

description: 2_Frontal|19|Full ROI

tag: tissue

tag: lotid

tag: duration

tag: ventilation

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Pons_P10

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status

value: No


title: Pons_P1

tag: tissue

value: postmortem brain


title: HCC_TMA_20210804_09_20703_ROI024_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

value: HCC TMA 04

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: Frontal_WhiteMatter_P1_6

description: 1_Frontal|24|Full ROI

tag: tissue type

value: FFPE

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pons_C9

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210804_NA_ROINA_NA

description: (v1.0) Cancer Transcriptome Atlas

source_name: Control

value: Control

tag: slide name

value: No Template Control

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_P1_5

description: 1_Frontal|23|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_12_03757_ROI027_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_12_03757_ROI026_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_12_03757_ROI026_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P1_4

description: 1_Frontal|22|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_12_03757_ROI023_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: HCC_TMA_20210729_12_03757_ROI024_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: HCC_TMA_20210729_12_03757_ROI025_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_P1_3

description: 1_Frontal|21|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_12_06412_ROI021_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: Pons_C7

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: immunocompromised status


title: HCC_TMA_20210729_12_03757_ROI022_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: Pons_C6

tag: postmortem interval (day)


title: Frontal_WhiteMatter_P2_2

description: 2_Frontal|20|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pons_C5

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Pons_C8


title: Frontal_WhiteMatter_P1_2

description: 1_Frontal|20|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_12_06412_ROI020_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: Frontal_WhiteMatter_P1_1

description: 1_Frontal|19|Full ROI

tag: tissue type

tag: region

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_12_03757_ROI027_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: area


title: HCC_TMA_20210729_12_06412_ROI019_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: aoi type


title: Pons_C4

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)


title: HCC_TMA_20210729_12_06412_ROI020_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Pons_C3

tag: immunocompromised status


title: HCC_TMA_20210729_12_12809_ROI018_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_C4_6

description: 4_Frontal|12|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_WhiteMatter_C4_5

description: 4_Frontal|11|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_WhiteMatter_C5_1

description: Pons|1|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HCC_TMA_20210729_10_66938_ROI013_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_12_12809_ROI016_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_12_12809_ROI016_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_10_66938_ROI015_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Pons_C10

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Pons_C2


title: HCC_TMA_20210729_10_66938_ROI014_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_09_43470_ROI012_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_09_43470_ROI011_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_12_06412_ROI021_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_C5_2

description: Pons|4|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_WhiteMatter_C4_4

description: 4_Frontal|10|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HCC_TMA_20210729_09_43470_ROI010_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: Midbrain_P9

tag: tissue preparation

value: Midbrain


title: HCC_TMA_20210729_12_12809_ROI017_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Midbrain_P8


title: Frontal_WhiteMatter_C4_2

description: 4_Frontal|8|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_08_74393_ROI009_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_12_06412_ROI019_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_C4_1

description: 4_Frontal|7|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HCC_TMA_20210729_08_74393_ROI008_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: Midbrain_P7

tag: tissue preparation

tag: region

tag: age


title: HCC_TMA_20210729_10_66938_ROI013_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: Frontal_WhiteMatter_C4_3

description: 4_Frontal|9|Full ROI

tag: tissue type

tag: lotid

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: aoinucleicount

tag: roicoordinatex

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Pons_C1

tag: tissue

tag: tissue preparation

tag: region

value: Pons

tag: age


title: HCC_TMA_20210729_08_74393_ROI006_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Midbrain_P5

tag: gender

value: Male

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_08_74393_ROI007_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_C3_5

description: 3_Frontal|5|Full ROI

tag: tissue type

value: Frontal lobe

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_WhiteMatter_C3_4

description: 3_Frontal|4|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

value: Yes

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Midbrain_P3

tag: tissue preparation


title: HCC_TMA_20210729_08_74393_ROI005_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210729_08_74393_ROI004_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_08_74393_ROI003_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: Frontal_WhiteMatter_C3_2

description: 3_Frontal|2|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_09_43470_ROI010_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_C3_3

description: 3_Frontal|3|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_06_59463_ROI002_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: HCC_TMA_20210729_06_59463_ROI001_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: area


title: HCC_TMA_20210729_06_59463_ROI002_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_06_59463_ROI001_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Midbrain_P6

tag: tissue preparation

tag: region

tag: age

tag: postmortem interval (day)


title: Frontal_WhiteMatter_C3_1

description: 3_Frontal|1|Full ROI

tag: tissue type

tag: lotid

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_05_38613_ROI032_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Midbrain_P17

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Midbrain_P16

value: Female


title: Frontal_WhiteMatter_C2_6

description: 2_Frontal|12|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Midbrain_P15

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Midbrain_P14


title: HCC_TMA_20210729_05_38613_ROI032_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_C2_5

description: 2_Frontal|11|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_05_38613_ROI031_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_C2_4

description: 2_Frontal|10|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Midbrain_P13

tag: tissue

tag: tissue preparation


title: Frontal_WhiteMatter_C2_3

description: 2_Frontal|9|Full ROI

tag: tissue type

tag: area

tag: roi

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Midbrain_P12

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Midbrain_P2

tag: tissue

tag: tissue preparation


title: HCC_TMA_20210729_11_30808_ROI030_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: MSC_NSC_4_24 h (miRNA)

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

hyb_protocol: The labeled samples were hybridized to Human SurePrint G3 Unrestricted miRNA arrays (Release 21.0, G4872A) following the instructions from the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: The microarray slides were scanned with a resolution of 3 μm.

data_processing: Raw data was extracted using Feature Extraction software (Agilent Technologies, Santa Clara, CA, USA). Raw microarray data were extracted and concatenated into one matrix using python (v 3.7) with numpy (v 1.16.4).

source_name: human bone marrow-derived MSCs , 24h

label_protocol: Cyanine-3 (Cy3) labeling was performed following the instructions from miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Cells were seeded at a density of 100.000 per 25 cm2 flask (coated with fibronectin), grown with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1-2 passages before induction of the trans-differentiation.

extract_protocol: Total RNA was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: Time-course cell samples were collected at 0, 3, 6, 9, 12, 24 and 48 h after addition of a standard commercial neurogenic differentiation medium (C-28015, PromoCell).

tag: cell type

value: human bone marrow-derived MSCs

tag: timepoint

tag: replicate

tag: treatment

value: neurogenic differentiation medium


title: MSC_NSC_4_48 h (miRNA)

source_name: human bone marrow-derived MSCs , 48h


title: MSC_NSC_4_12 h (miRNA)

source_name: human bone marrow-derived MSCs , 12h


title: HCC_TMA_20210729_11_30808_ROI029_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_WhiteMatter_C2_2

description: 2_Frontal|8|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

value: No

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_WhiteMatter_C2_1

description: 2_Frontal|7|Full ROI

tag: tissue

value: postmortem brain

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: Midbrain_P10

tag: tissue preparation


title: Frontal_WhiteMatter_C1_6

description: 1_Frontal|12|Full ROI

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight


title: HCC_TMA_20210729_15_6552_ROI028_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Midbrain_P1

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_15_6552_ROI028_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_4_3 h (miRNA)

source_name: human bone marrow-derived MSCs , 3h

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Frontal_WhiteMatter_C1_5

description: 1_Frontal|11|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: MSC_NSC_4_6 h (miRNA)

source_name: human bone marrow-derived MSCs , 6h

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Midbrain_C9

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_15_6552_ROI027_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_WhiteMatter_C1_4

description: 1_Frontal|10|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_05_38613_ROI031_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: MSC_NSC_4_0 h (miRNA)

source_name: human bone marrow-derived MSCs , 0h

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Midbrain_C8

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: MSC_NSC_3_48 h (miRNA)


title: HCC_TMA_20210729_15_6552_ROI027_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Midbrain_C7


title: MSC_NSC_4_9 h (miRNA)

source_name: human bone marrow-derived MSCs , 9h


title: Frontal_WhiteMatter_C1_3

description: 1_Frontal|9|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_WhiteMatter_C1_2

description: 1_Frontal|8|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: MSC_NSC_3_24 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_12_80107_ROI026_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210729_12_80107_ROI026_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: area


title: MSC_NSC_3_12 h (miRNA)


title: Midbrain_C6

tag: tissue preparation

tag: region


title: Midbrain_C5

tag: age


title: MSC_NSC_3_9 h (miRNA)


title: HCC_TMA_20210729_12_80107_ROI025_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: roi


title: Midbrain_C4

tag: gender

tag: postmortem interval (day)


title: HCC_TMA_20210729_12_80107_ROI025_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: MSC_NSC_3_6 h (miRNA)


title: Midbrain_C3

tag: immunocompromised status


title: Frontal_GreyMatter_P6_5

description: Frontal|21|Full ROI

tag: tissue type

tag: lotid

value: Frontal

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_GreyMatter_P6_4

description: Frontal|18|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: HCC_TMA_20210729_NA_ROI024_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: aoi type

value: Vessel


title: MSC_NSC_3_3 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_NA_ROI024_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: area


title: Frontal_GreyMatter_P6_2

description: Frontal|15|Full ROI

tag: tissue type

value: FFPE

tag: region

tag: lotid

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_WhiteMatter_C1_1

description: 1_Frontal|7|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: Frontal_GreyMatter_P6_3

description: Frontal|16|Full ROI

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Midbrain_C2

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: postmortem interval (day)


title: Frontal_GreyMatter_P6_1

description: Frontal|14|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: MSC_NSC_3_0 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Midbrain_C12

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: postmortem interval (day)


title: HCC_TMA_20210729_NA_ROI023_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Midbrain_C11

tag: gender

tag: immunocompromised status


title: Midbrain_C10


title: MSC_NSC_2_24 h (miRNA)


title: MSC_NSC_2_48 h (miRNA)


title: HCC_TMA_20210729_12_61116_ROI022_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_P5_6

description: Frontal|12|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Midbrain_C1

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_GreyMatter_P5_5

description: Frontal|9|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: MSC_NSC_2_12 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Frontal_P9

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: MSC_NSC_2_9 h (miRNA)


title: MSC_NSC_2_6 h (miRNA)


title: Frontal_GreyMatter_P5_4

description: Frontal|5|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_NA_ROI023_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: HCC_TMA_20210729_12_61116_ROI021_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: roi

tag: area


title: Frontal_P8

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_GreyMatter_P5_3

description: Frontal|4|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: HCC_TMA_20210729_12_61116_ROI021_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_P5_2

description: Frontal|3|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_11_09661_ROI020_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type


title: Frontal_GreyMatter_P4_6

description: 4_Frontal|18|Full ROI

tag: tissue type

tag: area

tag: region

tag: lotid

tag: age

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: MSC_NSC_2_3 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_11_09661_ROI019_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_11_09661_ROI020_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_11_09661_ROI019_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: HCC_TMA_20210729_12_61116_ROI022_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_P4_5

description: 4_Frontal|17|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_P3

tag: tissue

tag: tissue preparation

tag: region


title: Frontal_P7

tag: age

tag: gender

tag: postmortem interval (day)


title: Frontal_P5

tag: immunocompromised status


title: Frontal_P4


title: HCC_TMA_20210729_05_42842_ROI018_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_P19


title: MSC_NSC_1_48 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: MSC_NSC_2_0 h (miRNA)


title: Frontal_GreyMatter_P5_1

description: Frontal|2|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_GreyMatter_P4_4

description: 4_Frontal|16|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: MSC_NSC_1_24 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: Frontal_GreyMatter_P4_2

description: 4_Frontal|14|Full ROI

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: MSC_NSC_1_12 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_05_42842_ROI018_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: MSC_NSC_1_9 h (miRNA)


title: Frontal_P17

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_05_42842_ROI017_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_P6


title: Frontal_P16


title: MSC_NSC_1_3 h (miRNA)


title: HCT116, HDAC6-KD, NLS-HDAC6 expressing, TET2-ChIP, rep1

city: Shanghai

first: Yu

last: Yuanyuan

address: No. 1239, Siping Road, Shanghai

country: China

institute: Tongji University

library_source: genomic

data_processing:
ChIP-seq data were checked with FASTQC (v0.11.8) and trimmed using TrimGalore (v0.6.4)
ChIP-seq reads were aligned to hg38 using Bowtie2 (v2.3.5.1) with parameters: --no-unal --no-mixed --no-discordant, and were further filtered with mapping quality of at least 20
PCR duplicates were removed using Sambamba (v0.7.0)
Peaks were called using  MACS2 (v2.1.2) to call peaks with parameter -p 0.001
bigWig files were generated by bamCoverage in deepTools (v3.3.0) with 25 bp bin size and normalized as FPKM
Assembly: hg38
Supplementary files format and content: narrowPeak

molecule: genomic DNA

extract_protocol:
HCT116 cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were precleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-TET2 antibodies. After reverse crosslinking, ChIPed and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adapter ligation with the NEBNext Ultra Ligation Module (E7445, NEB).
Sequencing libraries were generated by Genefund Biotech (Shanghai, China). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with 150 bp paired-end protocol.

tag: cell line

tag: genotype

value: 6XNLS-HDAC6 expressing HDAC6 knockdown


title: Frontal_GreyMatter_P4_1

description: 4_Frontal|13|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCT116, HDAC6-KD, NLS-HDAC6 expressing, TET2-ChIP, rep2

tag: cell line

tag: genotype


title: MSC_NSC_1_0 h (miRNA)

tag: cell type

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_05_42842_ROI017_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_07_73244_ROI016_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Frontal_GreyMatter_P3_5

description: 3_Frontal|22|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_GreyMatter_P3_4

description: 3_Frontal|21|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Transporter_OE_YM155_Dox_rep3

city: Vienna

first: Giulio

last: Superti-Furga

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: other

data_processing:
read trimming (transporter-focused KO libraries): tracrRNA sequences flanking the 3’ end of the sgRNA regions were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1)
read trimming (transporter-focused OE libraries): 5’ flanking primer sequences (ACCCAGCTTTCTTGTACAAAG) were removed from the reads using cutadapt (Galaxy Version 4.8+galaxy1) and the remaining sequence was trimmed after the first 10 bp to receive the cDNA barcodes.
read trimming (genome-wide KO libraries): 5' flanking primer sequences and 3' flanking tracrRNA sequences were trimmed from the reads using Cutadapt (Galaxy Version 4.8+galaxy1) to receive the sgRNA sequences.
read/barcode mapping: MAGeCK count (Galaxy Version 0.5.9.2.4).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited raw gRNA count tables
Library strategy: Amplicon-Seq

molecule: other

source_name: HAP1 (RRID:CVCL_Y019)

growth_protocol: HAP1 (RRID:CVCL_Y019) cells were cultivated in DMEM (D5796 Sigma) supplemented with 10% Fetal Bovine Serum (10270-106, Lot 42F8381K, Gibco) and Penicillin-Streptomycin (15140-122, Gibco).

extract_protocol:
Genomic DNA was purified using QIAamp DNA Mini columns (Qiagen)
For transporter-focused KO screen samples, gDNA was digested overnight with 20U PacI (NEB) and double size-selected to enrich the sgRNA containing fragments (620 bp). Briefly, 0.6 x vol AmpliClean magnetic beads (Nimagen) were added to the sample to bind large gDNA fragments; the cleared supernatant was added to fresh beads (0.6 x volume of the original gDNA sample) to bind the smaller fragments. After size selection, sgRNA sequences were amplified in  with Q5 Polymerase (NEB) using the program recommended by the manufacturer (28 cycles, 72°C annealing temperature). PCR products were further double size-selected to remove residual large gDNA fragments as described above. For transporter-focused overexpression (OE) screen samples, barcode sequences were amplified from 10-20 µg gDNA per sample using pooled staggered primer containing partial Illumina adapter sequences with Q5 Polymerase (NEB) using the program recommended by the manufacturer (30 cycles, 63°C annealing temperature, 30 seconds extension). PCR products were double size selected using 0.65 x (to bind and remove gDNA) and 0.55 x volumes (to bind PCR products) AmpliClean magnetic beads (Nimagen). 2 µl of the purified PCR products were used in a second PCR with indexing primer with Q5 polymerase (10 cycles, 72°C annealing, 30 seconds extension) to generate Illumina libraries. For genome-wide KO screen samples, libraries were prepared as described previously (doi: 10.1038/nprot.2017.016).

treatment_protocol: Cells were transduced with lentiviral particles containing KO or OE libraries and selected with antibiotics to remove non-transduced cells. After 7-10 days of selection, each replicate was seeded to separate culture dishes and drug treatment was started the next day.

tag: cell line

value: HAP1 (RRID:CVCL_Y019)

tag: cell type

value: Myeloid haploid karyotype cell line

tag: screening library

value: Human SLC overexpression library (Addgene #213694)

tag: treatment

value: 20 nM YM155 + 1 µg/ml doxycycline for 8 days


title: Frontal_GreyMatter_P4_3

description: 4_Frontal|15|Full ROI

value: Frontal lobe

tag: gender

value: Male

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_P15

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: postmortem interval (day)

value: Yes


title: HCC_TMA_20210729_07_73244_ROI015_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Transporter_OE_YM155_Dox_rep2

tag: cell line

tag: cell type

tag: screening library

tag: treatment


title: Frontal_P13

tag: gender

tag: immunocompromised status


title: Frontal_GreyMatter_P3_3

description: 3_Frontal|20|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_07_73244_ROI014_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Tumor

tag: area


title: MSC_NSC_1_6 h (miRNA)

tag: cell type

value: human bone marrow-derived MSCs

tag: timepoint

tag: replicate

tag: treatment


title: HCC_TMA_20210729_15_31708_ROI012_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Transporter_OE_YM155_Dox_rep1

tag: cell line

tag: screening library


title: Frontal_P12

tag: tissue preparation

tag: region

tag: age

tag: gender

value: Female

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_GreyMatter_P3_1

description: 3_Frontal|18|Full ROI

tag: tissue

tag: tissue type

tag: lotid

value: No

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_P10

tag: tissue

value: postmortem brain

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_P1

value: Frontal


title: HCC_TMA_20210729_07_73244_ROI013_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_P11


title: Transporter_OE_YM155_noDox_rep3

tag: cell line

tag: cell type

tag: screening library

tag: treatment

value: 20 nM YM155 for 8 days


title: Frontal_GreyMatter_P3_2

description: 3_Frontal|19|Full ROI

tag: tissue type

value: FFPE

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_P14

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Transporter_OE_YM155_noDox_rep2

tag: cell line

tag: cell type

tag: screening library

tag: treatment


title: HCC_TMA_20210729_15_31708_ROI012_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_GreyMatter_P3_6

description: 3_Frontal|23|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_GreyMatter_P2_6

description: 2_Frontal|18|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation


title: Transporter_OE_YM155_noDox_rep1

tag: cell line

tag: cell type

tag: screening library

tag: treatment


title: Frontal_GreyMatter_P2_5

description: 2_Frontal|17|Full ROI

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Transporter_OE_MZ1_Dox_rep3

tag: cell line

tag: cell type

tag: screening library

tag: treatment

value: 180 nM MZ1 + 1 µg/ml doxycycline for 8 days


title: HCC_TMA_20210729_15_31708_ROI011_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: Transporter_OE_MZ1_Dox_rep2

value: HAP1 (RRID:CVCL_Y019)

value: Myeloid haploid karyotype cell line


title: Frontal_GreyMatter_P2_4

description: 2_Frontal|16|Full ROI

tag: tissue type

tag: region

tag: lotid

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: HCC_TMA_20210729_12_80422_ROI010_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_C9

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Transporter_OE_MZ1_Dox_rep1

tag: cell line

tag: cell type

tag: screening library

value: Human SLC overexpression library (Addgene #213694)

tag: treatment


title: Frontal_GreyMatter_P2_3

description: 2_Frontal|15|Full ROI

tag: tissue type

value: Frontal lobe

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_15_31708_ROI011_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_C7

tag: tissue preparation

tag: region

tag: age

tag: gender

value: Male

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_C8


title: HCC_TMA_20210729_12_80422_ROI010_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Transporter_OE_MZ1_noDox_rep3

tag: cell line

tag: cell type

tag: screening library

tag: treatment

value: 180 nM MZ1 for 8 days


title: Frontal_C6

value: Yes


title: Transporter_OE_MZ1_noDox_rep2


title: HCC_TMA_20210729_12_80422_ROI009_Vessel

description: (v1.0) Cancer Transcriptome Atlas

value: Liver cancer resection


title: HCC_TMA_20210729_12_80422_ROI009_Tumor

description: (v1.0) Cancer Transcriptome Atlas

value: Tumor


title: Frontal_GreyMatter_P1_6

description: 1_Frontal|18|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_C5

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

value: Female

tag: postmortem interval (day)

tag: immunocompromised status


title: Transporter_OE_MZ1_noDox_rep1

tag: cell line

tag: cell type

tag: screening library

tag: treatment


title: Frontal_GreyMatter_P2_1

description: 2_Frontal|13|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: HCC_TMA_20210729_08_18867_ROI008_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: Transporter_OE_DMSO_Dox_rep3

tag: cell line

tag: cell type

tag: screening library


title: Frontal_C4

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status

value: No


title: Frontal_GreyMatter_P1_5

description: 1_Frontal|17|Full ROI

value: postmortem brain

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_C3

tag: tissue

tag: tissue preparation

tag: region

value: Frontal

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_08_18867_ROI008_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Frontal_C2


title: Frontal_GreyMatter_P1_4

description: 1_Frontal|16|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Frontal_GreyMatter_P2_2

description: 2_Frontal|14|Full ROI

tag: tissue

tag: area

tag: region

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Transporter_OE_DMSO_Dox_rep2

tag: cell line

tag: cell type

tag: screening library


title: Frontal_GreyMatter_P1_3

description: 1_Frontal|15|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Transporter_OE_DMSO_Dox_rep1

tag: cell line

tag: cell type


title: Frontal_C12

tag: tissue

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_08_18867_ROI007_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: Transporter_OE_DMSO_noDox_rep3

tag: screening library


title: Frontal_C11


title: Frontal_GreyMatter_P1_2

description: 1_Frontal|14|Full ROI

tag: tissue type

tag: lotid

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Transporter_OE_DMSO_noDox_rep2

tag: cell line

tag: cell type

tag: screening library


title: Frontal_GreyMatter_P1_1

description: 1_Frontal|13|Full ROI

tag: tissue

tag: tissue type

tag: area

tag: region

tag: lotid

tag: roi

tag: age

tag: postmortem interval (day)

tag: gender

tag: immunocompromised status

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: sequencingsaturation


title: Transporter_OE_DMSO_noDox_rep1

tag: cell line

tag: cell type


title: HCC_TMA_20210729_11_14903_ROI006_Tumor

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

tag: slide name

tag: pool

tag: aoi type


title: Frontal_GreyMatter_C5_2

description: Pons|3|Full ROI

tag: tissue type

tag: area

tag: region

tag: lotid

value: Pons

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: Frontal_C10

tag: tissue

tag: tissue preparation

value: FFPE

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Frontal_C1

tag: region


title: Transporter_KO_9days_YM155_rep3

description: Transporter_KO_9_days_selection_sgRNA_counts.txt

tag: cell line

tag: cell type

tag: transgene

value: Lentivirally delivered Cas9 gene (Addgene #52962)

tag: screening library

value: Human Transporter Knockout Library with UMIs (Addgene #221409)

tag: treatment

value: 18 nM YM155 for 9 days


title: Frontal_GreyMatter_C5_3

description: Pons|5|Full ROI

tag: tissue type

tag: area

tag: lotid

tag: roi

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: Basal Ganglia_P9

tag: tissue

tag: tissue preparation

tag: region

value: Basal Ganglia

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: HCC_TMA_20210729_11_14903_ROI005_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: slide name

tag: pool

tag: roi

tag: aoi type

value: Vessel

tag: area


title: HCC_TMA_20210729_11_14903_ROI005_Tumor

description: (v1.0) Cancer Transcriptome Atlas


title: Basal Ganglia_P8


title: Transporter_KO_9days_YM155_rep2

tag: cell line

value: HAP1 (RRID:CVCL_Y019)

tag: cell type

value: Myeloid haploid karyotype cell line

tag: transgene

tag: screening library

tag: treatment


title: Frontal_GreyMatter_C5_1

description: Pons|2|Full ROI

tag: tissue

tag: tissue type

value: Frontal lobe

tag: lotid

value: Male

tag: duration

tag: ventilation

tag: lung pathology

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

tag: loq


title: HCC_TMA_20210729_08_18867_ROI007_Vessel

description: (v1.0) Cancer Transcriptome Atlas

tag: tissue

value: Liver cancer resection

tag: slide name

tag: pool

tag: roi

tag: aoi type

tag: area


title: HCC_TMA_20210729_06_67338_ROI004_Vessel

description: (v1.0) Cancer Transcriptome Atlas


title: Basal Ganglia_P7

tag: tissue preparation

tag: region

tag: age

tag: gender

tag: postmortem interval (day)

tag: immunocompromised status


title: Basal Ganglia_P6


title: Transporter_KO_9days_YM155_rep1

tag: cell line

tag: cell type

tag: transgene

tag: screening library

tag: treatment