title: DSP-1001250001619-C01 (D20_HeartLV_ROI16_alphaSMA-)

city: Cambridge

first: Samouil

last: Farhi

state: Massachusetts

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description: sample isolation protocol: Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.

data_processing:
Library strategy: GeoMx Seq
FastQ files were compiled and demultiplexed with IlluminaBasecallsToFastq (samples indexed with DSP-100166004764) or bcl2fastq (all others)
Adapter trimming with trim galore, trmGaloreOpts = " --hardtrim5 26 --dont_gzip"
Merge overlapping R1 and R2 with flash2, flash2Opts = "-m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
The resulting DCC files were converted to an expression count matrix. AOIs (2 for CTA, 2 for WTA) were removed from the analysis if sequencing reads totaled less than 10,000. Target counts were generated by taking the geometric mean of all probe counts against the same gene target in each well. Individual CTA probes were dropped if they had counts less than 10% of the target counts (2 CTA) or if they were global Grubb’s outliers at alpha = 0.01 (6 for CTA). These probe screens were not performed on the WTA assay as each gene is sampled by one probe only. As a quality control step, sequencing saturation was calculated by dividing the number of non-unique sequencing reads by the total number of reads for each AOI. AOIs with sequence saturation below 50% were dropped from analysis (2 CTA, 0 WTA).
Normalization: The 75th percentile of the target counts of each probe pool in each AOI were calculated and normalized to the geometric mean of the 75th percentiles across all AOIs to give normalization factors. Target counts were divided by these normalization factors to give normalized expression counts.
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode). Values represented in the collapsed target counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.
Genome_Build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc files

source_name: HeartLV

extract_protocol:
Sample extraction was performed according to NanoString GeoMx manufacturer instructions. Slides were stained with CTA or WTA panels and a SARS-CoV-2 panel spike-ins, all consisting of RNA-ISH probes conjugated with a UV-photocleavable barcodes; along with Syto13, Anti-PanCK, and Anti-CD45 morphological markers. One heart sample was akso stained with anti-aSMA antibody and one LUL and one trachea slide were stained with Syto13 and RNAScope probe against the SARS-CoV-2 S gene instead. ROIs were selected based on pathologist annotation of morphology, PanCK signal, and S-gene RNAScope from sequential slides. ROIs were segmented into PanCK+ and PanCK- for LUL samples, aSMA+ and aSMA- for the heart slide, and COVID+ and COVID- for one LUL and one trachea slide. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio. Libraries were combined for target counts of 30 counts/um^2 for CTA samples or 150 counts/um^2 for WTA samples and were sequenced on a NovaSeq 6000 S4 flow cell or NextSeq500 HO 75 cycle kit, loading with 5% PhiX.

value: alphaSMA-

value: unannotated

value: not provided


title: DSP-1001250001619-B09 (D20_HeartLV_ROI13_alphaSMA-)

status: Public on Apr 11 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: segment

tag: morphology

tag: assay

value: WTA

tag: race

value: White

tag: ethnicity

tag: Sex

value: F

tag: age

tag: organ failure

value: Lung, heart

tag: s/s to death (days)

tag: donor


title: DSP-1001250001619-B11 (D20_HeartLV_ROI15_alphaSMA+)

value: alphaSMA+


title: DSP-1001250001619-B10 (D20_HeartLV_ROI14_alphaSMA-)


title: DSP-1001250001619-B12 (D20_HeartLV_ROI15_alphaSMA-)


title: DSP-1001250001619-B07 (D20_HeartLV_ROI12_alphaSMA+)


title: DSP-1001250001619-B08 (D20_HeartLV_ROI12_alphaSMA-)


title: DSP-1001250001619-B06 (D20_HeartLV_ROI11_alphaSMA-)


title: DSP-1001250001619-B04 (D20_HeartLV_ROI10_alphaSMA+)


title: D13_Parenchyma_ROI14_Geometric

city: Boston

first: Yered

middle: Hammurabi

last: Pita-Juarez

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

description: Autopsies at Beth Israel Deaconess Medical Center were performed on a cohort of 5 patients with positive SARS-CoV-2 nasopharyngeal swab on admission. Consent for autopsy and research was obtained from the healthcare proxy or the next of kin. Ultrasound-guided biopsies were performed within 3 hours of death on a gurney in the hospital morgue. The body was not removed from the bag until staff was wearing standard precautions and an N95 mask. Biopsies were obtained through 13G coaxial guide with 14 core biopsy and 20 mm sample length. Multiple core biopsies were acquired from each organ by tilting the coaxial needle a few degrees in different directions. Cores for snRNA-Seq were flash-frozen and stored at -80˚C until assayed.

data_processing:
Library strategy: NanoString GeoMx DSP RNA
FastQ files were compiled and demultiplexed with bcl2fastq
Adapter trimming with trim galore, trmGaloreOpts = " --hardtrim5 26 --dont_gzip"
Merge overlapping R1 and R2 with flash2, flash2Opts = "-m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
The resulting DCC files were converted to an expression count matrix. Target counts were generated by taking the geometric mean of all probe counts against the same gene target in each well.
Normalization: The 75th percentile of the target counts of each probe pool in each AOI were calculated and normalized to the geometric mean of the 75th percentiles across all AOIs to give normalization factors. Target counts were divided by these normalization factors to give normalized expression counts.
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx .pkc files
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts

source_name: Parenchyma

extract_protocol:
Autopsy FFPE tissues from COVID-19 infected patents were processed following the GeoMx DSP slide prep user manual (MAN-10087-04). Autopsy slides were baked in oven at 60°C for at least 1 hour, and then deparaffinized and hydrated by Leica Biosystems BOND RX. Proteinase K was added prior to the incubation of incubated with RNA probe mix (WTA and COVID-19 spike-in panel). After overnight incubation, slides were washed with buffer and stained with CD68-594 (Novus Bio, NBP2-34736AF647), CD45-647 (Novus Bio, NBP2-34527AF647), and PanCK-488 (eBioscience, 53-9003-82) and Syto83 (ThermoFisher, S11364) for 1 hour, and loaded to the GeoMx DSP machine to scan 20X fluorescent images. Regions of interest (ROIs) were placed by referencing COVID viral staining on serial section, in particular V-nCoV2019-S RNAscope (Cat: 848568-C3) staining and SARS-CoV-2 spike glycoprotein (AbCam ab272504) IHC staining. Oligos were then UV-cleaved and collected into 96-well plates. Oligos from each AOI was uniquely indexed using Illumina’s i5 x i7 dual-indexing system. 4 uL of a GeoMx DSP sample was used in the PCR reaction. PCR reactions were purified with two rounds of AMPure XP beads (Beckman Coulter) at 1.2x bead-to-sample ratio. Libraries were paired-end sequenced (2x75) on a NovaSeq up to 3 billion total aligned reads. Fastq files were processed by the NanoString DND pipeline to generate count files for each target probe, and saved as DCC files.
DSP collection sample plates were dried down by sealing the plates with aeroseal and placed at room temperature overnight. Following resuspension of the wells with 10 μL of DEPC-treated water the plates were incubated for 10 min at room temperature before briefly spun down. 96-well PCR plates were prepared by mixing 2 μL PCR mix (NanoString), 4 μL of index primer mix (NanoString) and 4 μL of DSP sample. The following PCR program was used to amplify the Illumina sequencing compatible libraries; 37°C for 30 min, 50°C for 10 min, 95°C for 3 min, followed by 18 cycles of (95°C for 15 sec, 65°C for 1 min, 68°C for 30 sec), 68°C for 5 min and a final hold at 4°C. The indexed libraries were pooled with a 8-channel pipette by combining 4 μL per well from the 12 columns into 8-well strip tubes. The combined 48 μl pools in the 8-well strip were incubated with 58 μL AMPure XP beads (Beckman Coulter) (1.2x bead to sample ratio) for 5 min. The 8-well strip was placed on a magnetic stand for 5 min before removal of the supernatant. The beads were then washed twice with 200 μl of 80% ethanol and dried for 1 min before being eluted with 10 μL elution buffer (10mM Tris-HCl pH 8, 0.05% Tween-20). The 8 samples were combined into two pools of 40 μL each and incubated with 48 μL AMPure buffer (2.5M NaCl, 20% PEG 8000) for 5 min. Following magnetic incubation for 5 min and removal of supernatants the beads were washed twice with 200 μL of 80% ethanol and dried for 1 min before eluted with 17 μL elution buffer. The two pools were combined to a final elute of 34 μL. Sequencing library size was assessed with a DNA high sensitivity bioanalyzer assay (Agilent Technologies) and the expected library size of 161 bp was observed. Library concentration was assessed with Qubit dsDNA high sensitivity assay (Thermo Fisher Scientific).

value: Geometric Segment

value: Artery

value: Black/ AA

value: Not Hispanic

value: M

value: Lung


title: DSP-1001250001619-B03 (D20_HeartLV_ROI9_alphaSMA-)


title: DSP-1001250001619-B02 (D20_HeartLV_ROI9_alphaSMA+)


title: D13_Parenchyma_ROI1_Geometric

value: Inflamed Alveoli


title: DSP-1001250001619-A12 (D20_HeartLV_ROI8_alphaSMA+)


title: D13_Parenchyma_ROI3_Geometric


title: DSP-1001250001619-A09 (D20_HeartLV_ROI6_alphaSMA-)


title: DSP-1001250001619-A03 (D20_HeartLV_ROI2_alphaSMA-)


title: DSP-1001250001619-A11 (D20_HeartLV_ROI7_alphaSMA-)


title: DSP-1001250001619-A06 (D20_HeartLV_ROI4_alphaSMA-)


title: DSP-1001250001619-A08 (D20_HeartLV_ROI5_alphaSMA-)


title: DSP-1001250001619-A10 (D20_HeartLV_ROI7_alphaSMA+)


title: DSP-1001250001619-A05 (D20_HeartLV_ROI4_alphaSMA+)


title: DSP-1001660004763-F06 (D19_LLL_ROI11_PanCK-)

source_name: LLL

value: PanCK-

value: Alveolar

value: Other

value: Hispanic/Latino


title: DSP-1001250001619-A07 (D20_HeartLV_ROI5_alphaSMA+)

value: unannotated

value: not provided


title: DSP-1001250001619-A04 (D20_HeartLV_ROI3_alphaSMA-)

value: alphaSMA-

value: WTA

value: White


title: DSP-1001660004763-F08 (D19_LLL_ROI13_PanCK-)


title: DSP-1001660004763-F09 (D19_LLL_ROI15_PanCK+)

value: PanCK+


title: DSP-1001660004763-F07 (D19_LLL_ROI12_PanCK-)


title: DSP-1001660004763-F11 (D19_LLL_ROI16_PanCK+)


title: DSP-1001660004763-F12 (D19_LLL_ROI16_PanCK-)


title: DSP-1001660004763-F10 (D19_LLL_ROI15_PanCK-)


title: DSP-1001660004763-F04 (D19_LLL_ROI10_PanCK-)


title: DSP-1001250001620-H12 (D20_HeartLV_ROI1_alphaSMA+)

value: alphaSMA+

value: F

value: Lung, heart


title: DSP-1001250001619-B05 (D20_HeartLV_ROI10_alphaSMA-)


title: DSP-1001660004763-F01 (D19_LLL_ROI8_PanCK-)


title: DSP-1001660004763-E12 (D19_LLL_ROI7_PanCK-)


title: DSP-1001660004763-F02 (D19_LLL_ROI9_PanCK-)


title: DSP-1001660004763-F05 (D19_LLL_ROI11_PanCK+)


title: DSP-1001660004763-E11 (D19_LLL_ROI6_PanCK-)


title: DSP-1001250001619-B01 (D20_HeartLV_ROI8_alphaSMA-)


title: DSP-1001250001619-A02 (D20_HeartLV_ROI1_alphaSMA-)


title: DSP-1001660004763-E10 (D19_LLL_ROI6_PanCK+)


title: DSP-1001660004763-E06 (D19_LLL_ROI3_PanCK-)


title: DSP-1001660004763-F03 (D19_LLL_ROI10_PanCK+)


title: DSP-1001660004763-D10 (D18_RUL_ROI14_PanCK+)

source_name: RUL

value: Black/AA


title: DSP-1001660004763-E01 (D18_RUL_ROI15_PanCK-)

value: Bronchi


title: DSP-1001660004763-E05 (D19_LLL_ROI3_PanCK+)

value: M

value: Lung


title: DSP-1001660004763-D12 (D18_RUL_ROI15_PanCK+)


title: DSP-1001660004763-E08 (D19_LLL_ROI5_PanCK+)

value: Basal pore


title: DSP-1001660004763-E04 (D19_LLL_ROI2_PanCK-)

value: PanCK-

value: Artery


title: DSP-1001660004763-E09 (D19_LLL_ROI5_PanCK-)

value: Other

value: Hispanic/Latino


title: DSP-1001660004763-E07 (D19_LLL_ROI4_PanCK-)

value: Alveolar


title: DSP-1001660004763-E03 (D19_LLL_ROI1_PanCK-)


title: DSP-1001660004763-D08 (D18_RUL_ROI13_PanCK+)

value: not provided


title: DSP-1001660004763-D11 (D18_RUL_ROI14_PanCK-)

value: WTA


title: DSP-1001660004763-D06 (D18_RUL_ROI11_PanCK-)


title: DSP-1001660004763-D05 (D18_RUL_ROI11_PanCK+)


title: DSP-1001660004763-E02 (D19_LLL_ROI1_PanCK+)


title: DSP-1001660004763-D09 (D18_RUL_ROI13_PanCK-)


title: DSP-1001660004763-D07 (D18_RUL_ROI12_PanCK-)


title: DSP-1001660004763-D03 (D18_RUL_ROI10_PanCK+)


title: DSP-1001660004763-D04 (D18_RUL_ROI10_PanCK-)


title: DSP-1001660004763-D01 (D18_RUL_ROI9_PanCK+)


title: DSP-1001660004763-C11 (D18_RUL_ROI7_PanCK-)

value: Lymphoid


title: DSP-1001660004763-C10 (D18_RUL_ROI6_PanCK-)


title: DSP-1001660004763-C09 (D18_RUL_ROI5_PanCK-)


title: DSP-1001660004763-C08 (D18_RUL_ROI4_PanCK-)


title: DSP-1001660004763-C07 (D18_RUL_ROI4_PanCK+)

value: PanCK+


title: DSP-1001660004763-C12 (D18_RUL_ROI8_PanCK-)


title: DSP-1001660004763-C06 (D18_RUL_ROI3_PanCK-)


title: DSP-1001660004763-C05 (D18_RUL_ROI3_PanCK+)


title: DSP-1001660004763-C04 (D18_RUL_ROI2_PanCK-)


title: DSP-1001660004763-C03 (D18_RUL_ROI2_PanCK+)


title: DSP-1001660004763-C02 (D18_RUL_ROI1_PanCK-)


title: DSP-1001250001621-H06 (D12_LUL_ROI17_PanCK-)

source_name: LUL

value: White

value: Not Hispanic/Latino

value: Multi-organ


title: DSP-1001250001621-H05 (D12_LUL_ROI17_PanCK+)


title: DSP-1001250001621-H04 (D12_LUL_ROI16_PanCK-)

value: Large airway


title: DSP-1001660004763-D02 (D18_RUL_ROI9_PanCK-)

value: Bronchi

value: Black/AA

value: F


title: DSP-1001250001621-H01 (D12_LUL_ROI15_PanCK+)

value: Seromucinous glands

value: M


title: DSP-1001250001621-G11 (D12_LUL_ROI14_PanCK+)


title: DSP-1001250001621-H09 (D12_LUL_ROI19_PanCK+)


title: DSP-1001250001621-H10 (D12_LUL_ROI19_PanCK-)

value: PanCK-


title: DSP-1001250001621-H08 (D12_LUL_ROI18_PanCK-)


title: DSP-1001250001621-H03 (D12_LUL_ROI16_PanCK+)


title: DSP-1001250001621-G09 (D12_LUL_ROI13_PanCK+)


title: DSP-1001250001621-G07 (D12_LUL_ROI11_PanCK-)


title: DSP-1001250001621-H07 (D12_LUL_ROI18_PanCK+)


title: DSP-1001250001621-G12 (D12_LUL_ROI14_PanCK-)


title: DSP-1001250001621-G04 (D12_LUL_ROI10_PanCK+)


title: DSP-1001250001621-G03 (D12_LUL_ROI9_PanCK-)


title: DSP-1001250001621-H02 (D12_LUL_ROI15_PanCK-)


title: DSP-1001250001621-G05 (D12_LUL_ROI10_PanCK-)


title: DSP-1001250001621-G08 (D12_LUL_ROI12_PanCK-)

value: Artery


title: DSP-1001250001621-G06 (D12_LUL_ROI11_PanCK+)


title: DSP-1001250001621-G10 (D12_LUL_ROI13_PanCK-)


title: DSP-1001250001621-F12 (D12_LUL_ROI8_PanCK+)


title: DSP-1001250001621-G02 (D12_LUL_ROI9_PanCK+)


title: DSP-1001250001621-F11 (D12_LUL_ROI7_PanCK-)


title: DSP-1001250001621-F10 (D12_LUL_ROI7_PanCK+)


title: DSP-1001250001621-F09 (D12_LUL_ROI6_PanCK-)


title: DSP-1001250001621-F08 (D12_LUL_ROI6_PanCK+)


title: DSP-1001250001621-F07 (D12_LUL_ROI5_PanCK-)


title: DSP-1001250001621-F06 (D12_LUL_ROI5_PanCK+)


title: DSP-1001250001621-F05 (D12_LUL_ROI4_PanCK-)


title: DSP-1001250001621-G01 (D12_LUL_ROI8_PanCK-)


title: DSP-1001250001621-F02 (D12_LUL_ROI2_PanCK-)

value: Basal pore


title: DSP-1001250001621-F03 (D12_LUL_ROI3_PanCK+)

value: Alveolar


title: DSP-1001250001621-F04 (D12_LUL_ROI3_PanCK-)


title: DSP-1001250001621-E12 (D12_LUL_ROI1_PanCK-)


title: DSP-1001250001621-F01 (D12_LUL_ROI2_PanCK+)


title: DSP-1001250001621-E09 (D11_LUL_ROI22_PanCK+)

value: not provided

value: Lung, kidney


title: DSP-1001250001621-E11 (D12_LUL_ROI1_PanCK+)

value: WTA


title: DSP-1001250001621-E06 (D11_LUL_ROI20_PanCK-)


title: DSP-1001250001621-E03 (D11_LUL_ROI19_PanCK+)

value: PanCK+

value: Terminal bronchiole


title: DSP-1001250001621-E08 (D11_LUL_ROI21_PanCK-)

value: White


title: DSP-1001250001621-E05 (D11_LUL_ROI20_PanCK+)


title: DSP-1001250001621-E07 (D11_LUL_ROI21_PanCK+)


title: DSP-1001250001621-D12 (D11_LUL_ROI16_PanCK-)

value: Vein


title: DSP-1001250001621-E10 (D11_LUL_ROI22_PanCK-)


title: DSP-1001250001621-E04 (D11_LUL_ROI19_PanCK-)


title: DSP-1001250001621-D08 (D11_LUL_ROI13_PanCK-)


title: DSP-1001250001621-D11 (D11_LUL_ROI15_PanCK-)


title: DSP-1001250001621-E02 (D11_LUL_ROI18_PanCK-)


title: DSP-1001250001621-D10 (D11_LUL_ROI15_PanCK+)


title: DSP-1001250001621-D07 (D11_LUL_ROI12_PanCK-)


title: DSP-1001250001621-D09 (D11_LUL_ROI14_PanCK-)


title: DSP-1001250001621-D06 (D11_LUL_ROI12_PanCK+)


title: DSP-1001250001621-D05 (D11_LUL_ROI11_PanCK-)


title: DSP-1001250001621-D04 (D11_LUL_ROI10_PanCK-)


title: DSP-1001250001621-E01 (D11_LUL_ROI17_PanCK-)


title: DSP-1001250001621-D01 (D11_LUL_ROI8_PanCK-)


title: DSP-1001250001621-C11 (D11_LUL_ROI7_PanCK-)


title: DSP-1001250001621-D02 (D11_LUL_ROI9_PanCK-)


title: DSP-1001250001621-C12 (D11_LUL_ROI8_PanCK+)


title: DSP-1001250001621-C05 (D11_LUL_ROI3_PanCK-)


title: DSP-1001250001621-C09 (D11_LUL_ROI6_PanCK-)


title: DSP-1001250001621-C10 (D11_LUL_ROI7_PanCK+)


title: DSP-1001250001621-C03 (D11_LUL_ROI2_PanCK-)


title: DSP-1001250001621-C01 (D11_LUL_ROI1_PanCK+)


title: DSP-1001660004761-H11 (D10_LUL_ROI16_PanCK+)

value: Not Hispanic/Latino

value: Multi-organ


title: DSP-1001660004761-H12 (D10_LUL_ROI16_PanCK-)


title: DSP-1001250001621-C02 (D11_LUL_ROI1_PanCK-)


title: DSP-1001660004761-H10 (D10_LUL_ROI15_PanCK-)


title: DSP-1001660004761-H08 (D10_LUL_ROI13_PanCK-)


title: DSP-1001250001621-C07 (D11_LUL_ROI4_PanCK-)


title: DSP-1001660004761-H06 (D10_LUL_ROI12_PanCK-)


title: DSP-1001250001621-C04 (D11_LUL_ROI3_PanCK+)


title: DSP-1001660004761-H05 (D10_LUL_ROI12_PanCK+)


title: DSP-1001660004761-H07 (D10_LUL_ROI13_PanCK+)


title: DSP-1001660004761-H09 (D10_LUL_ROI14_PanCK-)


title: DSP-1001660004761-H04 (D10_LUL_ROI11_PanCK-)


title: DSP-1001250001621-C08 (D11_LUL_ROI5_PanCK-)


title: DSP-1001250001621-D03 (D11_LUL_ROI10_PanCK+)


title: DSP-1001660004761-H03 (D10_LUL_ROI11_PanCK+)


title: DSP-1001660004761-G11 (D10_LUL_ROI8_PanCK-)


title: DSP-1001660004761-H01 (D10_LUL_ROI10_PanCK+)


title: DSP-1001660004761-H02 (D10_LUL_ROI10_PanCK-)


title: DSP-1001660004761-G12 (D10_LUL_ROI9_PanCK-)


title: DSP-1001660004761-G10 (D10_LUL_ROI7_PanCK-)


title: DSP-1001660004761-G09 (D10_LUL_ROI7_PanCK+)


title: DSP-1001250001621-C06 (D11_LUL_ROI4_PanCK+)


title: DSP-1001660004761-G08 (D10_LUL_ROI6_PanCK-)


title: DSP-1001660004761-G07 (D10_LUL_ROI6_PanCK+)


title: DSP-1001660004761-G05 (D10_LUL_ROI5_PanCK+)


title: DSP-1001660004761-G04 (D10_LUL_ROI4_PanCK-)


title: DSP-1001660004761-F11 (D9_LUL_ROI14_PanCK-)

value: Black/AA

value: Lung


title: DSP-1001660004761-F10 (D9_LUL_ROI13_PanCK-)

value: F


title: DSP-1001660004761-F09 (D9_LUL_ROI12_PanCK-)


title: DSP-1001660004761-F08 (D9_LUL_ROI12_PanCK+)


title: DSP-1001660004761-F07 (D9_LUL_ROI11_PanCK-)


title: DSP-1001660004761-G03 (D10_LUL_ROI4_PanCK+)

value: M


title: DSP-1001660004761-G01 (D10_LUL_ROI2_PanCK-)

value: PanCK-


title: DSP-1001660004761-F04 (D9_LUL_ROI9_PanCK-)


title: DSP-1001660004761-F06 (D9_LUL_ROI11_PanCK+)


title: DSP-1001660004761-F03 (D9_LUL_ROI9_PanCK+)


title: DSP-1001660004761-E11 (D9_LUL_ROI7_PanCK+)


title: DSP-1001660004761-F02 (D9_LUL_ROI8_PanCK-)


title: DSP-1001660004761-F01 (D9_LUL_ROI8_PanCK+)


title: DSP-1001660004761-E08 (D9_LUL_ROI5_PanCK-)

value: Artery


title: DSP-1001660004761-E12 (D9_LUL_ROI7_PanCK-)


title: DSP-1001660004761-E02 (D9_LUL_ROI2_PanCK+)


title: DSP-1001660004761-E10 (D9_LUL_ROI6_PanCK-)


title: DSP-1001660004761-E09 (D9_LUL_ROI6_PanCK+)


title: DSP-1001660004761-E07 (D9_LUL_ROI4_PanCK-)


title: DSP-1001660004761-E06 (D9_LUL_ROI4_PanCK+)


title: DSP-1001660004761-F05 (D9_LUL_ROI10_PanCK-)


title: DSP-1001660004761-E05 (D9_LUL_ROI3_PanCK-)


title: DSP-1001660004761-E04 (D9_LUL_ROI3_PanCK+)


title: DSP-1001660004761-G06 (D10_LUL_ROI5_PanCK-)


title: DSP-1001660004761-E03 (D9_LUL_ROI2_PanCK-)


title: DSP-1001660004761-D06 (D8_LUL_ROI12_PanCK-)

value: Hispanic/Latino


title: DSP-1001660004761-G02 (D10_LUL_ROI3_PanCK-)

value: Alveolar


title: DSP-1001660004761-D02 (D8_LUL_ROI9_PanCK-)


title: DSP-1001660004761-D01 (D8_LUL_ROI8_PanCK-)

value: Large airway


title: DSP-1001660004761-F12 (D10_LUL_ROI1_PanCK-)


title: DSP-1001660004761-C12 (D8_LUL_ROI8_PanCK+)

value: Lung, kidney


title: DSP-1001660004761-E01 (D9_LUL_ROI1_PanCK-)

value: WTA


title: DSP-1001660004761-D12 (D9_LUL_ROI1_PanCK+)

value: PanCK+


title: DSP-1001660004761-D11 (D8_LUL_ROI15_PanCK-)


title: DSP-1001660004761-D10 (D8_LUL_ROI14_PanCK-)


title: DSP-1001660004761-C09 (D8_LUL_ROI6_PanCK+)


title: DSP-1001660004761-D08 (D8_LUL_ROI13_PanCK-)


title: DSP-1001660004761-D09 (D8_LUL_ROI14_PanCK+)


title: DSP-1001660004761-D05 (D8_LUL_ROI11_PanCK-)


title: DSP-1001660004761-D07 (D8_LUL_ROI13_PanCK+)


title: DSP-1001660004761-C04 (D8_LUL_ROI3_PanCK+)


title: DSP-1001660004761-C02 (D8_LUL_ROI2_PanCK+)

value: Basal pore


title: DSP-1001660004761-C03 (D8_LUL_ROI2_PanCK-)


title: DSP-1001660004761-D03 (D8_LUL_ROI10_PanCK-)


title: DSP-1001660004761-C05 (D8_LUL_ROI3_PanCK-)


title: DSP-1001660004761-C07 (D8_LUL_ROI5_PanCK+)


title: DSP-1001660004761-C06 (D8_LUL_ROI4_PanCK-)


title: DSP-1001660004763-H10 (D21_LUL_ROI13_PanCK+)

value: not provided


title: DSP-1001660004761-C01 (D8_LUL_ROI1_PanCK-)


title: DSP-1001660004761-D04 (D8_LUL_ROI11_PanCK+)


title: DSP-1001660004761-C08 (D8_LUL_ROI5_PanCK-)


title: DSP-1001660004762-A02 (D21_LUL_ROI14_PanCK-)


title: DSP-1001660004763-H09 (D21_LUL_ROI12_PanCK-)

value: Vein


title: DSP-1001660004763-H02 (D21_LUL_ROI8_PanCK+)

value: Terminal bronchiole


title: DSP-1001660004763-H03 (D21_LUL_ROI8_PanCK-)


title: DSP-1001660004763-H06 (D21_LUL_ROI10_PanCK+)


title: DSP-1001660004763-H04 (D21_LUL_ROI9_PanCK+)


title: DSP-1001660004763-H01 (D21_LUL_ROI7_PanCK-)


title: DSP-1001660004763-G11 (D21_LUL_ROI6_PanCK-)


title: DSP-1001660004763-H12 (D21_LUL_ROI14_PanCK+)


title: Zsphere-scRNA

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

description: single cell RNA

data_processing:
We used cell-ranger version 2.1.1 to deconvolve, align and quantify the per-cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release-89 from Ensembl (software available from 10x genomics).
From these alignments we were able to identify 2,644 high quality cells with a mean reads per cell value of 59,754 and a median genes per cell count of 3,807.  All other QC metrics were within thresholds set by 10x Genomics
Genome_build: GRCz10 release-89 from Ensembl
Supplementary_files_format_and_content: tar file containing 10x counts matrix, features and barcode data

molecule: polyA RNA

organism: Danio rerio

source_name: Zebrafish embryos

growth_protocol: Zebrafish embryos were grown in embryo media, for dissection of the blastula cup, embryos were transferred in DMEM-F12 media

extract_protocol:
At high stage, embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage, the embryo media was sequentially replaced with Dulbecco Modified Eagle’s Medium (DMEM F-12) with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100µl of DMEM-F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200µl of ice-cold PBS+0.04% BSA to which 800µl of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to -20°C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4°C. Cells were resuspended in 100µl ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3′ Chip
The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing, the ample was diluted to a concentration of ~1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000.
10x Chromium Single Cell 3'

tag: Stage

value: sphere


title: DSP-1001660004763-H07 (D21_LUL_ROI10_PanCK-)


title: DSP-1001660004763-G10 (D21_LUL_ROI6_PanCK+)


title: DSP-1001660004763-G09 (D21_LUL_ROI5_PanCK-)

value: Connective


title: DSP-1001660004761-C10 (D8_LUL_ROI6_PanCK-)

value: Black/AA


title: DSP-1001660004763-H08 (D21_LUL_ROI11_PanCK-)

value: Lung


title: DSP-1001660004761-C11 (D8_LUL_ROI7_PanCK-)

value: M


title: DSP-1001660004763-H05 (D21_LUL_ROI9_PanCK-)

value: PanCK-


title: DSP-1001660004761-B12 (D8_LUL_ROI1_PanCK+)


title: DSP-1001660004763-G08 (D21_LUL_ROI4_PanCK-)


title: DSP-1001660004763-G12 (D21_LUL_ROI7_PanCK+)


title: DSP-1001660004763-G05 (D21_LUL_ROI3_PanCK+)


title: DSP-1001660004763-G07 (D21_LUL_ROI4_PanCK+)


title: DSP-1001660004763-H11 (D21_LUL_ROI13_PanCK-)


title: DSP-1001660004763-G06 (D21_LUL_ROI3_PanCK-)


title: DSP-1001250001620-H10 (D20_LUL_ROI25_PanCK+)

value: White

value: F

value: Lung, heart


title: DSP-1001250001620-H11 (D20_LUL_ROI25_PanCK-)

value: Large airway


title: DSP-1001660004763-G02 (D21_LUL_ROI1_PanCK-)

value: Alveolar

value: Hispanic/Latino


title: DSP-1001250001620-H09 (D20_LUL_ROI24_PanCK-)

value: WTA


title: DSP-1001660004763-G01 (D21_LUL_ROI1_PanCK+)

value: PanCK+


title: DSP-1001250001620-H08 (D20_LUL_ROI24_PanCK+)

value: not provided


title: DSP-1001250001620-H06 (D20_LUL_ROI23_PanCK+)


title: Ovary rep2

city: Hangzhou

first: Jindong

last: Ren

address: No.198, Shiqiao Road

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
The libraries were sequenced on an Illumina Hiseq 4000 platform (Illumina, San Diego, CA, USA) and 150 bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1)  with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: No reference
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Macrobrachium rosenbergii

source_name: Ovary

extract_protocol:
Each shrimp was put on ice 1 min for anesthetizing, firstly. After anesthetizing, samples of ovaries (Ov), testicles (Tt) and androgenic gland (Ag) were collected separately and dissected. Each fresh sample was washed in phosphate-buffered saline (PBS; Gibco, Fisher Scientific, Waltham, MA, USA) and immediately frozen in liquid nitrogen. Total RNA was extracted from each sample using an RNeasy Plus Micro Kit (QIGEN Group, Germany)
Total RNA was used to generate sequencing libraries with varied index label using a NEBNextUltra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions

tag: strain

value: female

value: adult

tag: tissue

value: Ovary


title: Ovary rep3


title: Androgenic_gland rep3

source_name: Androgenic gland

value: male

value: Androgenic gland


title: DSP-1001250001620-H07 (D20_LUL_ROI23_PanCK-)


title: CHD who did not have PAH_control_Plasma_rep3

type: RNA

city: Nanning

first: Danyan

last: Su

address: 22, Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

description: circRNA expression profile

hyb_protocol: The labeled circRNAs were hybridized to the Arraystar Human circRNA Array (8× 15K) and incubated in an Agilent Hybridization Oven at 65°C for 17 h

scan_protocol: After washing the slides, the arrays were scanned with an Agilent G2505C scanner.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 5 out of 10 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.

source_name: CHD patients who did not have PAH_Plasma

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide

growth_protocol: Before the surgery, blood was taken from the femoral vein by cardiac catheterization. The blood samples were then centrifuged at 1000 × g for 15 min to completely remove the cellular components. The plasma samples were then stored at -80°C until total RNA were isolated.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000.The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

value: plasma

tag: gender


title: Ovary rep1


title: CHD who did not have PAH_control_Plasma_rep2

description: circRNA expression profile

treatment_protocol: The plasma samples were then stored at -80°C until total RNA were isolated.

value: M


title: CHD who did not have PAH_control_Plasma_rep5

description: circRNA expression profile


title: CHD who did not have PAH_control_Plasma_rep4

description: circRNA expression profile


title: CHD combined with PAH_Plasma_rep8

description: circRNA expression profile

source_name: CHD patients combined with PAH_Plasma


title: CHD combined with PAH_Plasma_rep2

description: circRNA expression profile


title: CHD combined with PAH_Plasma_rep4

description: circRNA expression profile


title: CHD combined with PAH_Plasma_rep3

description: circRNA expression profile


title: CHD who did not have PAH_control_Plasma_rep1

description: circRNA expression profile


title: DSP-1001660004763-G03 (D21_LUL_ROI2_PanCK+)

value: Lung


title: DSP-1001250001620-H05 (D20_LUL_ROI22_PanCK-)

value: PanCK-

value: Vein

value: White


title: CHD combined with PAH_Plasma_rep6

description: circRNA expression profile


title: CHD combined with PAH_Plasma_rep1

description: circRNA expression profile


title: CHD combined with PAH_Plasma_rep5

description: circRNA expression profile

value: F


title: Androgenic_gland rep2


title: CHD combined with PAH_Plasma_rep7

description: circRNA expression profile


title: DSP-1001660004763-G04 (D21_LUL_ROI2_PanCK-)

value: Alveolar


title: DSP-1001250001620-H04 (D20_LUL_ROI21_PanCK-)

value: Lung, heart


title: Androgenic_gland rep1


title: DSP-1001250001620-H02 (D20_LUL_ROI20_PanCK-)

value: WTA


title: Testis rep2

source_name: Testis

value: Testis


title: DSP-1001250001620-H01 (D20_LUL_ROI20_PanCK+)

value: PanCK+

value: not provided


title: Testis rep1

value: adult


title: DSP-1001250001620-G11 (D20_LUL_ROI19_PanCK+)


title: DSP-1001250001620-G10 (D20_LUL_ROI18_PanCK-)

value: Basal pore


title: DSP-1001250001620-G12 (D20_LUL_ROI19_PanCK-)


title: DSP-1001250001620-G09 (D20_LUL_ROI18_PanCK+)


title: D12 | 019 | PanCK-

type: other

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_11.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

hyb_protocol: Oligonucleotides were then hybridized to fluorescent barcodes and run through the nCounter MAX analysis system to generate raw digital counts. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)

data_processing: The raw counts were inputted into the DSP for calibration (adjusting for oligo-barcode binding efficiency) and for generation of a protein expression matrix; this matrix was subsequently normalized to internal spike-in positive controls (ERCC) to account for system variation. The calibrated and ERRC-normalized expression matrix was then normalized to the geometric mean of housekeeping genes99 as follows: first, the geometric mean of three housekeeping genes, histone H6, GAPDH, and S6, was calculated for each AOI; next, normalization factors were calculated as the geometric mean in each AOI dividing by the geometric mean of geometric means across all AOIs; finally, raw expression values were divided by the calculated normalization factors to give normalized protein expression levels.

molecule: other

extract_protocol:
[sample isolation protocol]  Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.
Sample extraction was performed according to NanoString GeoMx manufacturer instructions. Slides were stained with antibody panels and a SARS-CoV-2 panel spike-ins, all consisting of RNA-ISH probes conjugated with a UV-photocleavable barcodes; along with Syto13, Anti-PanCK, and Anti-CD45 morphological markers. ROIs were selected based on pathologist annotation of morphology, PanCK signal, and S-gene RNAScope from sequential slides. ROIs were segmented into PanCK+ and PanCK- for LUL samples. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform.

tag: infection

value: SARS-CoV-2 infected

tag: x coordinate

tag: y coordinate

tag: aoi surface area

tag: binding density

value: Large airway

value: Not Hispanic/Latino

value: Multi-organ


title: D12 | 019 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_10.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

scan_protocol: Oligonucleotides were then hybridized to fluorescent barcodes and run through the nCounter MAX analysis system to generate raw digital counts. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)

tag: segment

value: M


title: Testis rep3

value: male


title: D12 | 016 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: race


title: D12 | 017 | PanCK-

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: PanCK-

tag: ethnicity


title: D12 | 018 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_08.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: White

tag: Sex


title: D12 | 018 | PanCK-

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: age


title: DSP-1001250001620-H03 (D20_LUL_ROI21_PanCK+)

tag: morphology

tag: assay

value: F

tag: organ failure


title: DSP-1001250001620-G07 (D20_LUL_ROI17_PanCK+)

tag: s/s to death (days)

tag: donor


title: DSP-1001250001620-G06 (D20_LUL_ROI16_PanCK-)

value: Alveolar


title: DSP-1001250001620-G02 (D20_LUL_ROI14_PanCK-)

value: Lung, heart


title: DSP-1001250001620-G04 (D20_LUL_ROI15_PanCK-)

value: Airway

value: WTA


title: DSP-1001250001620-G05 (D20_LUL_ROI16_PanCK+)

value: PanCK+


title: DSP-1001250001620-G08 (D20_LUL_ROI17_PanCK-)

value: not provided


title: DSP-1001250001620-G03 (D20_LUL_ROI15_PanCK+)


title: DSP-1001250001620-G01 (D20_LUL_ROI14_PanCK+)


title: D12 | 015 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Seromucinous glands


title: D12 | 017 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Basal pore


title: D12 | 015 | PanCK-

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected


title: DSP-1001250001620-F12 (D20_LUL_ROI13_PanCK-)


title: D12 | 014 | PanCK+

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_12.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-F11 (D20_LUL_ROI13_PanCK+)


title: D12 | 013 | PanCK+


title: DSP-1001250001620-F10 (D20_LUL_ROI12_PanCK-)

value: Connective


title: D12 | 013 | PanCK-

value: Not Hispanic/Latino


title: DSP-1001250001620-F09 (D20_LUL_ROI12_PanCK+)


title: D12 | 016 | PanCK-

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Large airway

value: Multi-organ


title: DSP-1001250001620-F08 (D20_LUL_ROI11_PanCK-)


title: D12 | 012 | PanCK-

value: Artery

value: M


title: DSP-1001250001620-F07 (D20_LUL_ROI11_PanCK+)

value: White


title: D12 | 011 | PanCK+


title: D12 | 011 | PanCK-

value: PanCK-


title: DSP-1001250001620-F05 (D20_LUL_ROI9_PanCK-)

value: Alveolar

value: F


title: DSP-1001250001620-F04 (D20_LUL_ROI8_PanCK-)

value: Lung, heart


title: D12 | 010 | PanCK+


title: D12 | 014 | PanCK-

description:
raw data file: 20200924_P1001250001716A_P1001250001716A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-F01 (D20_LUL_ROI7_PanCK+)

value: WTA


title: DSP-1001250001620-E12 (D20_LUL_ROI6_PanCK-)


title: DSP-1001250001620-F03 (D20_LUL_ROI8_PanCK+)

value: PanCK+


title: DSP-1001250001620-F02 (D20_LUL_ROI7_PanCK-)

value: not provided


title: D12 | 009 | PanCK+


title: D12 | 009 | PanCK-


title: D12 | 008 | PanCK-


title: D12 | 008 | PanCK+


title: DSP-1001250001620-E11 (D20_LUL_ROI5_PanCK-)


title: D12 | 007 | PanCK+

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_11.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-E10 (D20_LUL_ROI5_PanCK+)


title: D12 | 007 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_12.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D12 | 006 | PanCK+

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-E09 (D20_LUL_ROI4_PanCK-)

description: sample isolation protocol: Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.


title: DSP-1001250001620-F06 (D20_LUL_ROI10_PanCK-)

value: Vein


title: D12 | 006 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_10.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D12 | 005 | PanCK+

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-E07 (D20_LUL_ROI3_PanCK-)


title: DSP-1001250001620-E06 (D20_LUL_ROI3_PanCK+)


title: D12 | 005 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_08.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-E05 (D20_LUL_ROI2_PanCK-)


title: D12 | 010 | PanCK-


title: D12 | 004 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D12 | 003 | PanCK+

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001620-E03 (D20_LUL_ROI1_PanCK-)


title: DSP-1001250001620-E04 (D20_LUL_ROI2_PanCK+)


title: D12 | 002 | PanCK+

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Basal pore


title: DSP-1001250001620-E01 (D19_LUL_ROI15_PanCK-)

value: Other

value: Hispanic/Latino

value: Lung


title: D12 | 001 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected

value: Not Hispanic/Latino


title: DSP-1001250001620-E02 (D20_LUL_ROI1_PanCK+)

value: Large airway


title: DSP-1001250001620-D12 (D19_LUL_ROI15_PanCK+)

value: M


title: DSP-1001250001620-E08 (D20_LUL_ROI4_PanCK+)

value: White


title: DSP-1001250001620-D10 (D19_LUL_ROI14_PanCK+)

value: Terminal bronchiole


title: D12 | 002 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: PanCK-

value: Multi-organ


title: DSP-1001250001620-D09 (D19_LUL_ROI13_PanCK-)


title: D11 | 022 | PanCK+

value: Lung, kidney


title: DSP-1001250001620-D11 (D19_LUL_ROI14_PanCK-)

value: WTA


title: DSP-1001250001620-D08 (D19_LUL_ROI13_PanCK+)

value: PanCK+


title: D11 | 021 | PanCK+

value: not provided


title: D11 | 021 | PanCK-


title: D11 | 020 | PanCK+


title: DSP-1001250001620-D07 (D19_LUL_ROI12_PanCK-)

value: Artery


title: DSP-1001250001620-D06 (D19_LUL_ROI11_PanCK-)

value: Alveolar


title: DSP-1001250001620-D05 (D19_LUL_ROI11_PanCK+)

value: Other


title: DSP-1001250001620-D04 (D19_LUL_ROI10_PanCK-)

value: Vein

value: Hispanic/Latino


title: D12 | 003 | PanCK-

description:
raw data file: 20200929_P1001250001717A_P1001250001717A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected


title: DSP-1001250001620-D03 (D19_LUL_ROI10_PanCK+)

value: Lung


title: D11 | 019 | PanCK+


title: D11 | 018 | PanCK-


title: D11 | 020 | PanCK-

value: Basal pore


title: D12 | 001 | PanCK+

value: Not Hispanic/Latino

value: M


title: DSP-1001250001620-D02 (D19_LUL_ROI9_PanCK-)


title: DSP-1001250001620-D01 (D19_LUL_ROI8_PanCK-)


title: D11 | 017 | PanCK-

value: White


title: D11 | 022 | PanCK-

value: PanCK-


title: D11 | 016 | PanCK-


title: DSP-1001250001620-C09 (D19_LUL_ROI5_PanCK+)


title: DSP-1001250001620-C10 (D19_LUL_ROI5_PanCK-)


title: D11 | 015 | PanCK+


title: DSP-1001250001620-C08 (D19_LUL_ROI4_PanCK-)


title: DSP-1001250001620-C12 (D19_LUL_ROI7_PanCK-)


title: DSP-1001250001620-C11 (D19_LUL_ROI6_PanCK-)


title: D11 | 015 | PanCK-


title: D11 | 013 | PanCK-


title: D11 | 012 | PanCK+


title: D11 | 012 | PanCK-


title: D11 | 011 | PanCK-


title: DSP-1001250001620-C07 (D19_LUL_ROI4_PanCK+)


title: D11 | 014 | PanCK-


title: DSP-1001250001620-C05 (D19_LUL_ROI3_PanCK+)


title: D11 | 019 | PanCK-

value: Terminal bronchiole


title: D11 | 010 | PanCK+

value: Lung, kidney


title: D11 | 010 | PanCK-


title: DSP-1001250001620-C04 (D19_LUL_ROI2_PanCK-)

value: WTA


title: DSP-1001250001620-C03 (D19_LUL_ROI1_PanCK-)


title: DSP-1001250001620-C02 (D19_LUL_ROI1_PanCK+)

value: PanCK+


title: D11 | 009 | PanCK-

value: not provided


title: DSP-1001250001620-C01 (D18_LUL_ROI19_PanCK-)

value: Black/AA

value: F


title: DSP-1001250001620-B12 (D18_LUL_ROI19_PanCK+)


title: DSP-1001250001620-B11 (D18_LUL_ROI18_PanCK-)


title: D11 | 008 | PanCK-

value: Alveolar


title: D11 | 008 | PanCK+


title: D11 | 007 | PanCK-


title: D11 | 007 | PanCK+


title: DSP-1001250001620-B10 (D18_LUL_ROI17_PanCK-)


title: DSP-1001250001620-B08 (D18_LUL_ROI15_PanCK-)

value: Artery


title: DSP-1001250001620-C06 (D19_LUL_ROI3_PanCK-)

value: Other

value: Hispanic/Latino


title: DSP-1001250001620-B09 (D18_LUL_ROI16_PanCK-)

value: Lung


title: D11 | 004 | PanCK+

value: SARS-CoV-2 infected


title: D11 | 005 | PanCK-


title: D11 | 006 | PanCK-

value: Vein


title: DSP-1001250001620-B05 (D18_LUL_ROI13_PanCK-)


title: DSP-1001250001620-B07 (D18_LUL_ROI14_PanCK-)


title: D11 | 003 | PanCK+

value: M


title: DSP-1001250001620-B04 (D18_LUL_ROI13_PanCK+)


title: D11 | 003 | PanCK-

value: White


title: DSP-1001250001620-B06 (D18_LUL_ROI14_PanCK+)


title: D11 | 004 | PanCK-

value: PanCK-


title: D11 | 002 | PanCK-


title: DSP-1001250001620-B02 (D18_LUL_ROI11_PanCK-)


title: D11 | 001 | PanCK+


title: D11 | 001 | PanCK-


title: DSP-1001250001620-B03 (D18_LUL_ROI12_PanCK-)


title: DSP-1001250001620-B01 (D18_LUL_ROI10_PanCK-)


title: DSP-1001250001620-A12 (D18_LUL_ROI10_PanCK+)


title: D10 | 015 | PanCK-

value: Not Hispanic/Latino

value: Multi-organ


title: D10 | 016 | PanCK-

value: Terminal bronchiole


title: DSP-1001250001620-A11 (D18_LUL_ROI9_PanCK-)

value: WTA


title: DSP-1001250001620-A10 (D18_LUL_ROI8_PanCK-)

value: not provided


title: DSP-1001250001620-A09 (D18_LUL_ROI7_PanCK-)

value: Black/AA


title: D10 | 014 | PanCK-


title: DSP-1001250001620-A07 (D18_LUL_ROI5_PanCK-)

value: F


title: DSP-1001250001620-A08 (D18_LUL_ROI6_PanCK-)

value: Alveolar


title: DSP-1001250001620-A06 (D18_LUL_ROI4_PanCK-)


title: D10 | 013 | PanCK+

value: PanCK+


title: D10 | 013 | PanCK-


title: DSP-1001250001620-A04 (D18_LUL_ROI3_PanCK-)


title: DSP-1001250001620-A05 (D18_LUL_ROI4_PanCK+)


title: DSP-1001250001620-A03 (D18_LUL_ROI2_PanCK-)


title: D10 | 011 | PanCK+


title: D10 | 012 | PanCK+


title: D10 | 011 | PanCK-


title: DSP-1001250001620-A02 (D18_LUL_ROI1_PanCK-)


title: D10 | 012 | PanCK-


title: D10 | 010 | PanCK+


title: D10 | 010 | PanCK-


title: DSP-1001660004763-B11 (D24_Parenchyma_ROI14_PanCK-)

value: Multi organ


title: DSP-1001660004763-B12 (D24_Parenchyma_ROI15_PanCK+)


title: D10 | 009 | PanCK-

value: Artery


title: D10 | 016 | PanCK+


title: D10 | 008 | PanCK-


title: D10 | 007 | PanCK+


title: DSP-1001660004763-B10 (D24_Parenchyma_ROI14_PanCK+)


title: DSP-1001660004763-B09 (D24_Parenchyma_ROI13_PanCK-)


title: D10 | 007 | PanCK-


title: DSP-1001660004763-B08 (D24_Parenchyma_ROI13_PanCK+)


title: DSP-1001660004763-B07 (D24_Parenchyma_ROI12_PanCK-)


title: DSP-1001660004763-B06 (D24_Parenchyma_ROI12_PanCK+)


title: D10 | 006 | PanCK+


title: D10 | 006 | PanCK-


title: D10 | 005 | PanCK+


title: D10 | 005 | PanCK-


title: D10 | 004 | PanCK+


title: DSP-1001660004763-B05 (D24_Parenchyma_ROI11_PanCK-)


title: DSP-1001660004763-C01 (D24_Parenchyma_ROI15_PanCK-)


title: DSP-1001660004763-B03 (D24_Parenchyma_ROI10_PanCK-)


title: DSP-1001660004763-B02 (D24_Parenchyma_ROI10_PanCK+)


title: D10 | 004 | PanCK-


title: D10 | 003 | PanCK-


title: DSP-1001660004763-B01 (D24_Parenchyma_ROI9_PanCK-)


title: D10 | 001 | PanCK-


title: DSP-1001660004763-A11 (D24_Parenchyma_ROI7_PanCK-)


title: D9 | 014 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_11.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Lung


title: DSP-1001660004763-A12 (D24_Parenchyma_ROI8_PanCK-)


title: D10 | 002 | PanCK-

value: SARS-CoV-2 infected


title: DSP-1001660004763-A10 (D24_Parenchyma_ROI7_PanCK+)


title: D9 | 013 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_10.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Vein


title: D9 | 011 | PanCK+

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004763-A09 (D24_Parenchyma_ROI6_PanCK-)

value: M


title: DSP-1001660004763-A07 (D24_Parenchyma_ROI4_PanCK-)

value: White


title: D9 | 012 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: PanCK-


title: DSP-1001660004763-A08 (D24_Parenchyma_ROI5_PanCK-)

value: Not Hispanic/Latino


title: D9 | 012 | PanCK+

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_08.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004763-A06 (D24_Parenchyma_ROI4_PanCK+)


title: D9 | 010 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D9 | 011 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004763-A04 (D24_Parenchyma_ROI3_PanCK+)

description: sample isolation protocol: Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.


title: DSP-1001660004763-A05 (D24_Parenchyma_ROI3_PanCK-)


title: DSP-1001660004763-B04 (D24_Parenchyma_ROI11_PanCK+)


title: DSP-1001660004763-A03 (D24_Parenchyma_ROI2_PanCK-)


title: D9 | 009 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D9 | 009 | PanCK+

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004763-A02 (D24_Parenchyma_ROI1_PanCK-)


title: DSP-1001250001621-B10 (D23_Parenchyma_ROI12_PanCK+)

value: Heart


title: DSP-1001250001621-B11 (D23_Parenchyma_ROI12_PanCK-)

value: Terminal bronchiole


title: D9 | 007 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_12.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D9 | 008 | PanCK+

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001621-B09 (D23_Parenchyma_ROI11_PanCK-)

value: WTA


title: D9 | 008 | PanCK-

description:
raw data file: 20201006_P1001250001718A_P1001250001718A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001621-B07 (D23_Parenchyma_ROI10_PanCK-)


title: DSP-1001250001621-B08 (D23_Parenchyma_ROI11_PanCK+)


title: D9 | 007 | PanCK+


title: DSP-1001250001621-B06 (D23_Parenchyma_ROI10_PanCK+)


title: D9 | 004 | PanCK+


title: D9 | 006 | PanCK-


title: D9 | 005 | PanCK-


title: DSP-1001250001621-B05 (D23_Parenchyma_ROI8_PanCK-)


title: DSP-1001250001621-B12 (D23_Parenchyma_ROI13_PanCK-)


title: D9 | 003 | PanCK+


title: D9 | 004 | PanCK-


title: D9 | 003 | PanCK-


title: DSP-1001250001621-B03 (D23_Parenchyma_ROI7_PanCK-)


title: D9 | 002 | PanCK+


title: DSP-1001250001621-B02 (D23_Parenchyma_ROI7_PanCK+)


title: DSP-1001250001621-B01 (D23_Parenchyma_ROI6_PanCK-)


title: D9 | 002 | PanCK-


title: D9 | 001 | PanCK+


title: D8 | 015 | PanCK-

value: Hispanic/Latino

value: Lung, kidney


title: D9 | 006 | PanCK+

value: Black/AA

value: F


title: DSP-1001250001621-A11 (D23_Parenchyma_ROI5_PanCK-)

value: Alveolar


title: DSP-1001250001621-A10 (D23_Parenchyma_ROI5_PanCK+)

value: PanCK+


title: DSP-1001250001621-A08 (D23_Parenchyma_ROI4_PanCK+)


title: DSP-1001250001621-A09 (D23_Parenchyma_ROI4_PanCK-)


title: D8 | 014 | PanCK+


title: D8 | 013 | PanCK-


title: D8 | 013 | PanCK+


title: DSP-1001250001621-B04 (D23_Parenchyma_ROI8_PanCK+)


title: D8 | 012 | PanCK-


title: D8 | 011 | PanCK+


title: DSP-1001250001621-A04 (D23_Parenchyma_ROI2_PanCK+)


title: DSP-1001250001621-A05 (D23_Parenchyma_ROI2_PanCK-)


title: D8 | 011 | PanCK-


title: DSP-1001250001621-A12 (D23_Parenchyma_ROI6_PanCK+)


title: DSP-1001250001621-A02 (D23_Parenchyma_ROI1_PanCK+)


title: D9 | 001 | PanCK-


title: D8 | 009 | PanCK-


title: DSP-1001660004761-B11 (D22_Parenchyma_ROI12_PanCK-)

value: Multi organ


title: DSP-1001660004761-B10 (D22_Parenchyma_ROI12_PanCK+)


title: D8 | 008 | PanCK-

value: Large airway


title: DSP-1001660004761-B09 (D22_Parenchyma_ROI11_PanCK-)

value: Artery


title: DSP-1001660004761-B08 (D22_Parenchyma_ROI10_PanCK-)


title: DSP-1001250001621-A07 (D23_Parenchyma_ROI3_PanCK-)


title: D8 | 007 | PanCK-

value: SARS-CoV-2 infected


title: DSP-1001250001621-A06 (D23_Parenchyma_ROI3_PanCK+)


title: D8 | 006 | PanCK+

value: M


title: DSP-1001660004761-B06 (D22_Parenchyma_ROI9_PanCK-)

value: White


title: D8 | 006 | PanCK-

value: PanCK-


title: D8 | 014 | PanCK-


title: DSP-1001660004761-B07 (D22_Parenchyma_ROI10_PanCK+)

value: Not Hispanic/Latino


title: D8 | 005 | PanCK+


title: DSP-1001250001621-A03 (D23_Parenchyma_ROI1_PanCK-)

value: Heart


title: DSP-1001660004761-B04 (D22_Parenchyma_ROI8_PanCK-)


title: D8 | 010 | PanCK-


title: D8 | 008 | PanCK+


title: D8 | 003 | PanCK+


title: DSP-1001660004761-B03 (D22_Parenchyma_ROI7_PanCK-)


title: DSP-1001660004761-B02 (D22_Parenchyma_ROI7_PanCK+)


title: DSP-1001660004761-B01 (D22_Parenchyma_ROI6_PanCK-)

value: Basal pore


title: D8 | 003 | PanCK-


title: D8 | 002 | PanCK-


title: DSP-1001660004761-A11 (D22_Parenchyma_ROI5_PanCK-)

value: WTA


title: D8 | 002 | PanCK+

value: Hispanic/Latino


title: D8 | 001 | PanCK-

value: Lung, kidney


title: D8 | 001 | PanCK+

value: Black/AA


title: DSP-1001660004761-A12 (D22_Parenchyma_ROI6_PanCK+)


title: DSP-1001660004761-A10 (D22_Parenchyma_ROI5_PanCK+)


title: D21 | 014 | PanCK+

value: not provided

value: Lung


title: DSP-1001660004761-A09 (D22_Parenchyma_ROI4_PanCK-)

value: Alveolar


title: DSP-1001660004761-B05 (D22_Parenchyma_ROI9_PanCK+)

value: PanCK+

value: Multi organ


title: DSP-1001660004761-A08 (D22_Parenchyma_ROI4_PanCK+)


title: DSP-1001660004761-A06 (D22_Parenchyma_ROI3_PanCK+)


title: D21 | 014 | PanCK-


title: D8 | 005 | PanCK-


title: DSP-1001660004761-A04 (D22_Parenchyma_ROI2_PanCK+)


title: D21 | 013 | PanCK-


title: D8 | 004 | PanCK-

value: Vein


title: D21 | 013 | PanCK+

value: SARS-CoV-2 infected


title: DSP-1001660004761-A03 (D22_Parenchyma_ROI1_PanCK-)

value: M


title: D21 | 012 | PanCK-


title: D21 | 011 | PanCK-


title: DSP-1001660004761-A02 (D22_Parenchyma_ROI1_PanCK+)

value: White


title: D21 | 010 | PanCK-

value: PanCK-


title: D21 | 009 | PanCK+


title: DSP-1001250001622-H03 (D12_LUL_ROI19_PanCK-)

value: Large airway

value: CTA

value: Not Hispanic/Latino

value: Multi-organ


title: DSP-1001250001622-H02 (D12_LUL_ROI19_PanCK+)


title: DSP-1001250001622-H01 (D12_LUL_ROI18_PanCK-)


title: D21 | 009 | PanCK-

value: Hispanic/Latino


title: D21 | 008 | PanCK+

value: Terminal bronchiole


title: DSP-1001250001622-G12 (D12_LUL_ROI18_PanCK+)


title: D21 | 007 | PanCK+


title: DSP-1001660004761-A07 (D22_Parenchyma_ROI3_PanCK-)

value: WTA


title: D21 | 008 | PanCK-

value: not provided


title: DSP-1001250001622-G11 (D12_LUL_ROI17_PanCK-)

value: Basal pore


title: DSP-1001660004761-A05 (D22_Parenchyma_ROI2_PanCK-)

value: Alveolar


title: DSP-1001250001622-G10 (D12_LUL_ROI17_PanCK+)

value: PanCK+


title: DSP-1001250001622-G09 (D12_LUL_ROI16_PanCK-)


title: D21 | 007 | PanCK-

value: Lung


title: D21 | 006 | PanCK-


title: DSP-1001250001622-G08 (D12_LUL_ROI16_PanCK+)


title: DSP-1001250001622-G07 (D12_LUL_ROI15_PanCK-)

value: Seromucinous glands


title: DSP-1001250001622-G06 (D12_LUL_ROI15_PanCK+)


title: DSP-1001250001622-G05 (D12_LUL_ROI14_PanCK-)


title: D21 | 005 | PanCK-

value: SARS-CoV-2 infected

value: Connective


title: D21 | 004 | PanCK+

value: M


title: D21 | 004 | PanCK-

value: PanCK-


title: D21 | 003 | PanCK+


title: DSP-1001250001622-G04 (D12_LUL_ROI14_PanCK+)

value: White


title: DSP-1001250001622-G03 (D12_LUL_ROI13_PanCK-)

value: CTA


title: D21 | 002 | PanCK+


title: D21 | 003 | PanCK-


title: D21 | 002 | PanCK-


title: DSP-1001250001622-G02 (D12_LUL_ROI13_PanCK+)

value: Not Hispanic/Latino


title: DSP-1001250001622-G01 (D12_LUL_ROI12_PanCK-)

value: Artery

value: Multi-organ


title: D21 | 001 | PanCK+

value: Hispanic/Latino


title: DSP-1001250001622-F11 (D12_LUL_ROI11_PanCK+)


title: DSP-1001250001622-F10 (D12_LUL_ROI10_PanCK-)


title: DSP-1001250001622-F09 (D12_LUL_ROI10_PanCK+)


title: D21 | 006 | PanCK+

value: Terminal bronchiole


title: D21 | 001 | PanCK-

value: not provided


title: D20 | 025 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_10.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Large airway

value: F

value: Lung, heart


title: D20 | 025 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: PanCK+


title: D20 | 024 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001622-F06 (D12_LUL_ROI8_PanCK-)

value: Alveolar


title: DSP-1001250001622-F08 (D12_LUL_ROI9_PanCK-)


title: DSP-1001250001622-F07 (D12_LUL_ROI9_PanCK+)


title: D20 | 024 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_08.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected


title: D20 | 023 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: D20 | 022 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Vein


title: DSP-1001250001622-F05 (D12_LUL_ROI8_PanCK+)

value: M


title: DSP-1001250001622-F03 (D12_LUL_ROI7_PanCK+)


title: D20 | 023 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: PanCK-


title: D20 | 021 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: White


title: DSP-1001250001622-F04 (D12_LUL_ROI7_PanCK-)

value: CTA


title: D20 | 021 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001622-F02 (D12_LUL_ROI6_PanCK-)

value: Not Hispanic/Latino


title: D20 | 020 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_12.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001250001622-E12 (D12_LUL_ROI5_PanCK-)


title: Healthy control [Ctrl-2]

city: Daejeon

first: Kijong

last: Yi

state: Daejeon

address: 291 Daehak-ro, #N26

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
10x Chromium V3 3' single cell RNA sequencing library
Ctrl-2

data_processing:
Fastq generated using Cellranger bcl2fastq
Alignment and quantification using Cellranger 3.0.2
Post processing is done with R package "Seurat"
Processed files were stored with "readr" package using "write_rds" function
Genome_build: NC_045512.2 and MusPutFur1.0
Supplementary_files_format_and_content: "*.Rds" files contain Seurat objects and can be read with "readRds" function in R
Supplementary_files_format_and_content: ".tsv" files contain metadata and cell annotation information

organism: Mustela putorius furo

source_name: Ferret's bronchoalveolar lavage

extract_protocol:
After 2 days and 5 days injection, lungs were extracted from euthanized ferrets. Brochoalveolar lavage was performed to enrich immune cells in the lung. Cells were treated with RBC lysis buffer and washed twice.
Single cell RNA-sequencing libraries were constructed using Chromium 3' scRNA seq kit as manufacturer's instruction

treatment_protocol: Ferrets were nasal injected with SARS-CoV-2 virus.

tag: cell type

value: bronchoalveolar lavage

tag: disease state

value: healthy


title: Healthy control [Ctrl-3]

description:
10x Chromium V3 3' single cell RNA sequencing library
Ctrl-3


title: DSP-1001250001622-F12 (D12_LUL_ROI11_PanCK-)

description: sample isolation protocol: Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.

value: Seromucinous glands

value: Multi-organ


title: D20 | 019 | PanCK+

tag: infection

value: not provided


title: D20 | 020 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: x coordinate


title: 5 dpi of SARS-CoV-2 [C5-3]

description:
10x Chromium V3 3' single cell RNA sequencing library
C5-3

value: infected with SARS-CoV-2 5 dpi


title: 5 dpi of SARS-CoV-2 [C5-2]

description:
10x Chromium V3 3' single cell RNA sequencing library
C5-2


title: Healthy control [Ctrl-1]

description:
10x Chromium V3 3' single cell RNA sequencing library
Ctrl-1


title: DSP-1001250001622-E11 (D12_LUL_ROI5_PanCK+)


title: 5 dpi of SARS-CoV-2 [C5-4]

description:
10x Chromium V3 3' single cell RNA sequencing library
C5-4


title: D20 | 019 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_11.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: y coordinate

value: F


title: D20 | 018 | PanCK+

tag: aoi surface area

value: Basal pore

value: Lung, heart


title: D20 | 018 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: binding density


title: 2 dpi of SARS-CoV-2 [C2-2]

description:
10x Chromium V3 3' single cell RNA sequencing library
C2-2

value: infected with SARS-CoV-2 2 dpi


title: DSP-1001250001622-E09 (D12_LUL_ROI3_PanCK-)

tag: segment

value: Alveolar


title: DSP-1001250001622-E08 (D12_LUL_ROI3_PanCK+)

value: PanCK+

tag: race


title: 5 dpi of SARS-CoV-2 [C5-1]

description:
10x Chromium V3 3' single cell RNA sequencing library
C5-1


title: 2 dpi of SARS-CoV-2 [C2-1]

description:
10x Chromium V3 3' single cell RNA sequencing library
C2-1


title: DSP-1001250001622-F01 (D12_LUL_ROI6_PanCK+)

tag: ethnicity

value: M


title: DSP-1001250001622-E07 (D12_LUL_ROI2_PanCK-)

value: PanCK-

tag: Sex


title: DSP-1001660004762-A01 (Blank control)

organism: blank sample

source_name: blank sample

value: blank sample

value: WTA

tag: Sex:

tag: age


title: D20 | 017 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected

value: White


title: DSP-1001250001620-A01 (Blank control)

tag: morphology

tag: assay


title: D20 | 017 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: organ failure

tag: s/s to death (days)


title: DSP-1001250001622-E06 (D12_LUL_ROI2_PanCK+)

value: CTA

value: Not Hispanic/Latino

tag: donor


title: DSP-1001660004763-A01 (Blank control)


title: DSP-1001250001622-E05 (D12_LUL_ROI1_PanCK-)

value: Multi-organ


title: DSP-1001250001621-A01 (Blank control)


title: D20 | 016 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: not provided


title: DSP-1001250001622-E10 (D12_LUL_ROI4_PanCK-)

value: Artery


title: D20 | 016 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: F


title: 2 dpi of SARS-CoV-2 [C2-3]

description:
10x Chromium V3 3' single cell RNA sequencing library
C2-3

tag: cell type

value: bronchoalveolar lavage

tag: disease state


title: DSP-1001250001622-E04 (D12_LUL_ROI1_PanCK+)

value: Basal pore


title: DSP-1001250001622-E03 (D11_LUL_ROI18_PanCK-)

value: Vein

value: Lung, kidney


title: DSP-1001660004759-A01 (Blank control)


title: D20 | 015 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: infection

tag: x coordinate

value: Airway

value: Lung, heart


title: mouse lung conditioned medium

city: Matsumoto

first: Sachie

last: Hiratsuka

address: 3-1-1 Asahi

department: Medicine

country: Japan

institute: Shinshu University

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with Clariom S Assay, Mouse (Thermo) in a GeneChip Hybridization Oven 645 (Thermo) at 45C, 16 hrs, 60 rpm. In this procedure, Hybridization, Wash, and Stain Kit (Thermo) was used. The microarray was washed by a GeneChip Fluidics Station 450.

scan_protocol: Array scanning was performed by using a GeneChip Scanner 3000 7G (Thermo).

data_processing: Raw data was obtained with GeneChip Command Console (AGCC) 4.0 (Thermo) and Expression Cosole Software (Thermo). Labeling, Hybridization, Scanning, and Data Procceing procedures were done at Filgen Inc. (Nagoya, Japan)

label: biotin

organism: Mus musculus

source_name: lung

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the GeneChip 3' IVT Pico Kit (Thermo).

growth_protocol: Mouse lungs were diced and placed in a tissue culture insert. The culture insert was placed into a 24-well plate to culture 24 hrs. RNAs were isolated from the culture medium.

extract_protocol: After DNase treatment, RNA in the medium outside the culture insert was isolated by using TRIZOL (Thermo). Sample was treated with GeneChip 3'IVT Pico Kit to generate amplified cRNA

tag: strain

tag: tissue

value: lung

value: female


title: primary root -N_plus_TIS108_Rep3

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

data_processing:
base-calling and demultiplexing with Illumina CASAVA 1.8
adapter clipping and quality filtering with Trimmomatic 0.39
mapping with tophat-2.0.13; parameters: ' -N 3 --read-gap-length 3 --read-edit-dist 3 -p 8 --b2-very-sensitive -i 10 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis usignDESeq2 (v1.30)
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: tab-delimited matrix with normalized FPKM values for all the samples

organism: Zea mays

source_name: primary root

growth_protocol: Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, each seedling was moved to a controlled environmental chamber in 30 ml glass tube containing a nutrient medium (Manoli et al. 2014).

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma, St Louis, MO, USA)
TruSeq RNA Library Prep Kit - paired end

treatment_protocol: 24h of growth in nutrient solution supplemented with 1 mM NO3-, 2 µM TIS108 and 1 mM NO3- plus 10 µM PCIB

tag: inbred

tag: treatment


title: primary root +NO3_plus_PCIB_Rep1


title: primary root +NO3_plus_PCIB_Rep3


title: primary root +NO3_plus_PCIB_Rep2


title: DSP-1001250001622-E01 (D11_LUL_ROI16_PanCK-)

description: sample isolation protocol: Autopsies were performed at Brigham and Women's Hospital in a negative pressure isolation room by personnel equipped with powered air-purifying or N95 respirators. Organs were removed from the body en bloc, and subsequently dissected for individual organ examination, including weighing and photographing. Representative samples of lung, trachea, and heart were fixed in 10% formalin, processed and paraffin embedded using standard protocols. 5 µm-thick slides were prepared from the FFPE tissue blocks and transferred to the Broad Institute.

tag: segment

value: PanCK-

tag: race

tag: ethnicity

value: M


title: DSP-1001250001622-A01 (Blank control)

value: blank sample

tag: Sex:

tag: age


title: DSP-1001250001619-A01 (Blank control)

tag: morphology

tag: assay

value: WTA


title: primary root -N_plus_TIS108_Rep2


title: DSP-1001250001622-D12 (D11_LUL_ROI15_PanCK-)

value: Alveolar

value: CTA

value: White

tag: Sex

tag: organ failure

tag: s/s to death (days)


title: primary root +NO3_Rep3


title: D20 | 015 | PanCK+

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected

tag: y coordinate

tag: aoi surface area

tag: binding density

value: PanCK+

value: not provided


title: primary root +NO3_Rep2


title: D20 | 014 | PanCK+

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_12.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: infection

tag: x coordinate

value: F


title: primary root +NO3_Rep1

tag: inbred


title: D20 | 013 | PanCK+

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_10.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004761-A01 (Blank control)

tag: donor


title: primary root -N_plus_TIS108_Rep1

tag: treatment


title: D20 | 013 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_11.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: segment

tag: race


title: DSP-1001250001622-D11 (D11_LUL_ROI15_PanCK+)

tag: ethnicity


title: primary root -N_control_Rep3

value: control


title: DSP-1001250001622-D10 (D11_LUL_ROI14_PanCK-)

tag: age

value: Lung, kidney


title: primary root -N_control_Rep2


title: D20 | 012 | PanCK+

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_08.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Connective


title: DSP-1001250001622-E02 (D11_LUL_ROI17_PanCK-)

tag: morphology

value: Artery


title: DSP-1001250001622-D09 (D11_LUL_ROI13_PanCK-)

tag: assay


title: D20 | 014 | PanCK-

description:
raw data file: 20201006_P1001250001722A_P1001250001722A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: Sex

value: Lung, heart


title: D20 | 012 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_09.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: organ failure


title: DSP-1001660004765-E03 (D20_LUL_ROI23_COVID-)

value: COVID-

tag: s/s to death (days)


title: DSP-1001660004765-E01 (D20_LUL_ROI21_COVID-)


title: DSP-1001250001622-D08 (D11_LUL_ROI12_PanCK-)

value: PanCK-


title: DSP-1001660004765-D12 (D20_LUL_ROI21_COVID+)

value: COVID+


title: DSP-1001250001622-D07 (D11_LUL_ROI12_PanCK+)

value: M


title: D20 | 011 | PanCK+

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_06.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: y coordinate


title: D20 | 011 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_07.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: aoi surface area


title: DSP-1001660004765-D11 (D20_LUL_ROI20_COVID-)


title: DSP-1001660004765-D10 (D20_LUL_ROI20_COVID+)


title: DSP-1001660004765-D09 (D20_LUL_ROI19_COVID-)


title: DSP-1001250001622-D06 (D11_LUL_ROI11_PanCK-)


title: DSP-1001660004765-D08 (D20_LUL_ROI18_COVID-)

value: Basal pore


title: DSP-1001250001622-D04 (D11_LUL_ROI10_PanCK+)

value: Alveolar


title: D20 | 009 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_04.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: binding density


title: D20 | 010 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_05.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

tag: infection

value: Vein


title: DSP-1001660004765-D07 (D20_LUL_ROI17_COVID-)

value: CTA

value: White


title: DSP-1001660004765-D05 (D20_LUL_ROI15_COVID-)

value: Airway


title: DSP-1001660004765-D04 (D20_LUL_ROI14_COVID-)

value: not provided


title: DSP-1001660004765-D03 (D20_LUL_ROI13_COVID-)

value: F


title: DSP-1001660004765-D06 (D20_LUL_ROI16_COVID-)


title: primary root -N_control_Rep1

value: control


title: D20 | 008 | PanCK+

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_02.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: SARS-CoV-2 infected

tag: x coordinate

value: PanCK+


title: DSP-1001660004765-D02 (D20_LUL_ROI12_COVID-)

value: Connective


title: D20 | 008 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_03.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc

value: Lung, heart


title: DSP-1001250001622-D03 (D11_LUL_ROI9_PanCK-)

value: Lung, kidney


title: DSP-1001250001622-D05 (D11_LUL_ROI10_PanCK-)

value: PanCK-


title: DSP-1001660004765-D01 (D20_LUL_ROI11_COVID-)

value: COVID-


title: DSP-1001660004765-C12 (D20_LUL_ROI10_COVID-)


title: D20 | 007 | PanCK+


title: DSP-1001660004765-C11 (D20_LUL_ROI9_COVID-)


title: DSP-1001660004765-C10 (D20_LUL_ROI8_COVID-)


title: D20 | 007 | PanCK-

description:
raw data file: 20201004_P1001250001721A_P1001250001721A_01.RCC
processed data files:
Hs P CellDeath v1.0.pkc
Hs P COVID19 v1.0.pkc
Hs P ImmuneActivation v1.0.pkc
Hs P ImmuneCellProfile v1.1.pkc
Hs P ImmuneCellTyping v1.0.pkc
Hs P IODrugTarget v1.1.pkc
Hs P PI3K AKT v1.0.pkc
SubR5 Hs P MAPK v1.0.pkc


title: DSP-1001660004765-C09 (D20_LUL_ROI7_COVID-)


title: DSP-1001250001622-C12 (D11_LUL_ROI7_PanCK-)

value: M


title: DSP-1001250001622-D02 (D11_LUL_ROI8_PanCK-)


title: DSP-1001250001622-D01 (D11_LUL_ROI8_PanCK+)


title: D20 | 005 | PanCK+


title: DSP-1001250001622-C11 (D11_LUL_ROI7_PanCK+)


title: DSP-1001660004765-C07 (D20_LUL_ROI5_COVID-)


title: D20 | 006 | PanCK-


title: DSP-1001660004765-C08 (D20_LUL_ROI6_COVID-)


title: DSP-1001250001622-C10 (D11_LUL_ROI6_PanCK-)


title: DSP-1001660004765-C06 (D20_LUL_ROI4_COVID-)


title: DSP-1001660004765-C05 (D20_LUL_ROI3_COVID-)

value: Large airway


title: DSP-1001660004765-C03 (D20_LUL_ROI1_COVID-)


title: D20 | 005 | PanCK-

value: Alveolar


title: DSP-1001250001622-C09 (D11_LUL_ROI5_PanCK-)


title: DSP-1001660004765-C02 (D20_Trachea_ROI32_COVID-)

source_name: Trachea

value: Submucosa


title: D20 | 004 | PanCK+


title: D20 | 004 | PanCK-


title: DSP-1001660004765-C01 (D20_Trachea_ROI31_COVID-)

value: CTA


title: DSP-1001250001622-C07 (D11_LUL_ROI4_PanCK+)

value: White


title: DSP-1001660004765-B12 (D20_Trachea_ROI30_COVID-)


title: DSP-1001250001622-C08 (D11_LUL_ROI4_PanCK-)


title: DSP-1001660004765-B10 (D20_Trachea_ROI28_COVID-)


title: DSP-1001660004765-B11 (D20_Trachea_ROI29_COVID-)


title: D20 | 003 | PanCK+


title: DSP-1001250001622-C06 (D11_LUL_ROI3_PanCK-)


title: DSP-1001660004765-B09 (D20_Trachea_ROI27_COVID-)


title: DSP-1001660004765-C04 (D20_LUL_ROI2_COVID-)


title: DSP-1001660004765-B07 (D20_Trachea_ROI26_COVID+)

value: COVID+

value: Mucosa


title: DSP-1001660004765-B06 (D20_Trachea_ROI25_COVID-)

value: not provided

value: F


title: D20 | 002 | PanCK-

value: SARS-CoV-2 infected


title: DSP-1001250001622-C05 (D11_LUL_ROI3_PanCK+)

value: PanCK+


title: D20 | 002 | PanCK+


title: D20 | 001 | PanCK+


title: DSP-1001660004765-B02 (D20_Trachea_ROI13_COVID-)


title: D20 | 003 | PanCK-


title: DSP-1001660004765-B04 (D20_Trachea_ROI17_COVID-)


title: DSP-1001250001622-C03 (D11_LUL_ROI2_PanCK+)


title: DSP-1001660004765-B01 (D20_Trachea_ROI8_COVID-)


title: DSP-1001250001622-C02 (D11_LUL_ROI1_PanCK-)


title: DSP-1001660004765-B03 (D20_Trachea_ROI17_COVID+)


title: DSP-1001660004765-A12 (D20_Trachea_ROI7_COVID-)


title: DSP-1001660004765-A11 (D20_Trachea_ROI7_COVID+)


title: D20 | 001 | PanCK-


title: D19 | 015 | PanCK+

value: Basal pore

value: Other

value: Hispanic/Latino

value: Lung


title: DSP-1001660004765-B08 (D20_Trachea_ROI26_COVID-)

value: COVID-

value: Lung, heart


title: DSP-1001660004765-A10 (D20_Trachea_ROI6_COVID-)


title: DSP-1001660004759-D12 (D10_LUL_ROI16_PanCK-)

value: PanCK-

value: Terminal bronchiole

value: Not Hispanic/Latino

value: M

value: Multi-organ


title: DSP-1001250001622-C01 (D11_LUL_ROI1_PanCK+)

value: Alveolar

value: CTA

value: White

value: Lung, kidney


title: DSP-1001660004765-A09 (D20_Trachea_ROI5_COVID-)

value: Submucosa

value: not provided

value: F


title: D19 | 015 | PanCK-

value: SARS-CoV-2 infected

value: Basal pore

value: Other


title: DSP-1001660004765-E02 (D20_LUL_ROI22_COVID-)

value: COVID-

value: Vein


title: DSP-1001660004765-A08 (D20_Trachea_ROI5_COVID+)

value: COVID+

value: Mucosa

value: Lung, heart


title: DSP-1001250001622-C04 (D11_LUL_ROI2_PanCK-)

value: PanCK-

value: M


title: DSP-1001660004765-A07 (D20_Trachea_ROI4_COVID-)


title: DSP-1001660004759-D11 (D10_LUL_ROI16_PanCK+)

value: PanCK+

value: Terminal bronchiole

value: Not Hispanic/Latino

value: Multi-organ


title: DSP-1001660004765-A06 (D20_Trachea_ROI3_COVID-)

value: Submucosa

value: CTA

value: White


title: DSP-1001660004759-D10 (D10_LUL_ROI15_PanCK-)

value: Artery


title: DSP-1001660004765-A05 (D20_Trachea_ROI3_COVID+)

value: not provided

value: F


title: D19 | 014 | PanCK+

value: SARS-CoV-2 infected

value: Other

value: Hispanic/Latino

value: Lung


title: D19 | 014 | PanCK-


title: DSP-1001660004765-A03 (D20_Trachea_ROI2_COVID+)

value: COVID+

value: Mucosa

value: Lung, heart


title: DSP-1001660004765-A04 (D20_Trachea_ROI2_COVID-)

value: COVID-


title: DSP-1001660004759-D09 (D10_LUL_ROI14_PanCK-)

value: PanCK-

value: Alveolar

value: M


title: DSP-1001660004764-H12 (D21_LUL_ROI14_PanCK-)


title: DSP-1001660004764-H09 (D21_LUL_ROI13_PanCK+)

value: PanCK+


title: DSP-1001660004765-A02 (D20_Trachea_ROI1_COVID-)

value: Submucosa

value: CTA


title: DSP-1001660004764-H10 (D21_LUL_ROI13_PanCK-)


title: DSP-1001660004759-D07 (D10_LUL_ROI13_PanCK+)

value: White

value: Not Hispanic/Latino

value: Multi-organ


title: D19 | 013 | PanCK-

value: SARS-CoV-2 infected

value: Basal pore


title: DSP-1001660004764-H11 (D21_LUL_ROI14_PanCK+)

value: not provided

value: Hispanic/Latino


title: DSP-1001660004759-D06 (D10_LUL_ROI12_PanCK-)


title: DSP-1001660004759-D08 (D10_LUL_ROI13_PanCK-)


title: DSP-1001660004764-H07 (D21_LUL_ROI11_PanCK-)

value: Vein

value: Lung


title: DSP-1001660004764-H08 (D21_LUL_ROI12_PanCK-)


title: D19 | 011 | PanCK+

value: Other


title: D19 | 011 | PanCK-


title: DSP-1001660004764-H06 (D21_LUL_ROI10_PanCK-)


title: D19 | 013 | PanCK+


title: DSP-1001660004759-D05 (D10_LUL_ROI12_PanCK+)


title: DSP-1001660004765-B05 (D20_Trachea_ROI24_COVID-)

value: COVID-

value: F

value: Lung, heart


title: DSP-1001660004764-H05 (D21_LUL_ROI9_PanCK-)

value: PanCK-

value: Alveolar

value: M


title: DSP-1001660004759-D04 (D10_LUL_ROI11_PanCK-)

value: CTA


title: D19 | 012 | PanCK-

value: Artery


title: DSP-1001660004764-H04 (D21_LUL_ROI9_PanCK+)

value: PanCK+


title: DSP-1001660004764-H02 (D21_LUL_ROI8_PanCK+)

value: Terminal bronchiole


title: DSP-1001660004764-H03 (D21_LUL_ROI8_PanCK-)


title: DSP-1001660004759-D03 (D10_LUL_ROI11_PanCK+)

value: White

value: Not Hispanic/Latino

value: Multi-organ


title: D19 | 010 | PanCK-

value: SARS-CoV-2 infected

value: Hispanic/Latino


title: D19 | 010 | PanCK+

value: Lung


title: DSP-1001660004764-H01 (D21_LUL_ROI7_PanCK-)

value: not provided


title: DSP-1001660004759-D02 (D10_LUL_ROI10_PanCK-)


title: DSP-1001660004764-G12 (D21_LUL_ROI7_PanCK+)


title: D19 | 009 | PanCK-

value: Other


title: D19 | 008 | PanCK-


title: DSP-1001660004764-G11 (D21_LUL_ROI6_PanCK-)


title: DSP-1001660004759-C12 (D10_LUL_ROI9_PanCK-)


title: DSP-1001660004764-G09 (D21_LUL_ROI5_PanCK-)

value: Connective


title: DSP-1001660004759-C11 (D10_LUL_ROI8_PanCK-)

value: Vein


title: DSP-1001660004764-G10 (D21_LUL_ROI6_PanCK+)


title: DSP-1001660004764-G05 (D21_LUL_ROI3_PanCK+)


title: DSP-1001660004764-G07 (D21_LUL_ROI4_PanCK+)


title: D19 | 006 | PanCK-

value: PanCK-


title: DSP-1001660004764-G06 (D21_LUL_ROI3_PanCK-)

value: Alveolar


title: DSP-1001660004764-G04 (D21_LUL_ROI2_PanCK-)

value: M


title: DSP-1001660004759-C10 (D10_LUL_ROI7_PanCK-)

value: CTA


title: D19 | 005 | PanCK+


title: DSP-1001660004764-G03 (D21_LUL_ROI2_PanCK+)


title: DSP-1001660004759-C09 (D10_LUL_ROI7_PanCK+)


title: DSP-1001660004764-G02 (D21_LUL_ROI1_PanCK-)


title: DSP-1001660004764-G01 (D21_LUL_ROI1_PanCK+)


title: DSP-1001660004765-H12 (D20_LUL_ROI23_PanCK-)

value: F

value: Lung, heart


title: D19 | 004 | PanCK+

value: PanCK+


title: DSP-1001660004759-C07 (D10_LUL_ROI6_PanCK+)

value: White


title: DSP-1001660004759-D01 (D10_LUL_ROI10_PanCK+)

value: Not Hispanic/Latino


title: DSP-1001660004765-H10 (D20_LUL_ROI22_PanCK-)


title: DSP-1001660004765-H09 (D20_LUL_ROI21_PanCK-)


title: D19 | 004 | PanCK-


title: DSP-1001660004764-G08 (D21_LUL_ROI4_PanCK-)

value: Terminal bronchiole


title: D19 | 007 | PanCK-

value: SARS-CoV-2 infected


title: DSP-1001660004759-C05 (D10_LUL_ROI5_PanCK+)

value: Multi-organ


title: DSP-1001660004765-H08 (D20_LUL_ROI21_PanCK+)


title: DSP-1001660004765-H05 (D20_LUL_ROI19_PanCK-)


title: DSP-1001660004759-C04 (D10_LUL_ROI4_PanCK-)


title: D19 | 005 | PanCK-

value: Hispanic/Latino

value: Lung


title: D19 | 003 | PanCK-

value: Other


title: D19 | 003 | PanCK+


title: D19 | 002 | PanCK-


title: DSP-1001660004765-H03 (D20_LUL_ROI18_PanCK-)

value: Basal pore

value: not provided


title: DSP-1001660004765-H04 (D20_LUL_ROI19_PanCK+)


title: DSP-1001660004759-C08 (D10_LUL_ROI6_PanCK-)

value: PanCK-


title: DSP-1001660004759-C03 (D10_LUL_ROI4_PanCK+)


title: DSP-1001660004765-H02 (D20_LUL_ROI18_PanCK+)


title: DSP-1001660004765-H11 (D20_LUL_ROI23_PanCK+)

value: Alveolar


title: DSP-1001660004765-G12 (D20_LUL_ROI17_PanCK+)


title: DSP-1001660004759-C02 (D10_LUL_ROI3_PanCK-)

value: M


title: D19 | 001 | PanCK-


title: DSP-1001660004765-G11 (D20_LUL_ROI16_PanCK-)

value: CTA


title: DSP-1001660004765-G10 (D20_LUL_ROI16_PanCK+)

value: F


title: DSP-1001660004759-C06 (D10_LUL_ROI5_PanCK-)


title: DSP-1001660004765-H07 (D20_LUL_ROI20_PanCK-)

value: Lung, heart


title: DSP-1001660004759-C01 (D10_LUL_ROI3_PanCK+)

value: PanCK+


title: DSP-1001660004765-G09 (D20_LUL_ROI15_PanCK-)

value: Airway

value: White


title: DSP-1001660004765-G08 (D20_LUL_ROI15_PanCK+)


title: DSP-1001660004765-H06 (D20_LUL_ROI20_PanCK+)


title: DSP-1001660004759-B12 (D10_LUL_ROI2_PanCK-)

value: Not Hispanic/Latino


title: D18 | 019 | PanCK+

value: SARS-CoV-2 infected

value: Terminal bronchiole

value: Black/AA


title: DSP-1001660004759-B11 (D10_LUL_ROI1_PanCK-)

value: Multi-organ


title: D19 | 001 | PanCK+

value: Other

value: Hispanic/Latino

value: Lung


title: DSP-1001660004765-G06 (D20_LUL_ROI14_PanCK+)

value: not provided


title: D18 | 018 | PanCK-

value: PanCK-

value: Vein


title: DSP-1001660004765-G04 (D20_LUL_ROI13_PanCK+)

value: Alveolar

value: CTA