title: DSP-1001660004765-G05 (D20_LUL_ROI13_PanCK-)

value: F

value: Lung, heart


title: DSP-1001660004765-H01 (D20_LUL_ROI17_PanCK-)

status: Public on Apr 11 2021

type: SRA

city: Cambridge

first: Samouil

last: Farhi

state: Massachusetts

address: 415 Main St.

country: USA

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.

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: LUL

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.

tag: segment

value: PanCK-

tag: morphology

value: Basal pore

tag: assay

value: CTA

tag: race

value: White

tag: ethnicity

value: not provided

tag: Sex

tag: age

tag: organ failure

tag: s/s to death (days)

tag: donor


title: DSP-1001660004765-G03 (D20_LUL_ROI12_PanCK-)

value: Connective


title: DSP-1001660004765-G02 (D20_LUL_ROI12_PanCK+)

value: PanCK+


title: DSP-1001660004759-F11 (D9_LUL_ROI13_PanCK-)

value: Vein

value: Black/AA

value: Not Hispanic/Latino

value: Lung


title: DSP-1001660004765-F12 (D20_LUL_ROI11_PanCK+)

value: Alveolar


title: DSP-1001660004765-G01 (D20_LUL_ROI11_PanCK-)


title: D18 | 017 | PanCK-

type: other

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

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


title: D18 | 016 | 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

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)


title: DSP-1001660004759-F10 (D9_LUL_ROI12_PanCK-)


title: DSP-1001660004765-F11 (D20_LUL_ROI10_PanCK-)


title: D18 | 019 | 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

value: Terminal bronchiole


title: DSP-1001660004759-F09 (D9_LUL_ROI12_PanCK+)


title: D18 | 015 | 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

value: Artery


title: D18 | 014 | 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

value: F


title: DSP-1001660004765-F10 (D20_LUL_ROI10_PanCK+)

value: Lung, heart


title: DSP-1001660004765-F09 (D20_LUL_ROI9_PanCK-)

value: PanCK-


title: DSP-1001660004765-G07 (D20_LUL_ROI14_PanCK-)


title: DSP-1001660004765-F07 (D20_LUL_ROI8_PanCK-)


title: D18 | 014 | 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


title: DSP-1001660004759-F12 (D9_LUL_ROI14_PanCK-)


title: DSP-1001660004765-F08 (D20_LUL_ROI9_PanCK+)


title: D18 | 013 | 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


title: DSP-1001660004765-F05 (D20_LUL_ROI7_PanCK-)


title: DSP-1001660004759-F06 (D9_LUL_ROI10_PanCK-)


title: DSP-1001660004765-F04 (D20_LUL_ROI7_PanCK+)


title: DSP-1001660004759-F05 (D9_LUL_ROI9_PanCK-)


title: DSP-1001660004765-F03 (D20_LUL_ROI6_PanCK-)


title: D18 | 012 | 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


title: BFAR-KO2

city: Shanghai

first: Siyu

last: Pei

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: Th9 differentiation condition for 3 days

data_processing:
Transcriptomic reads from the RNA-Seq experiments were mapped to a reference genome (GRCm38/mm10) using Bowtie.
Gene expression levels were quantified using the RSEM software package.
Differentially expressed genes were subsequently analyzed using the DAVID bioinformatics platformand IPA and GraphPad.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Processed data were txt format and all gene FPKM of each sample were contained in each txt file.

organism: Mus musculus

source_name: CD4+ T cells

growth_protocol: The 6-8-week-old wild-type and T cells-conditional deficient mice were sacrificed, and primary T cells were isolated from the spleen and lymph nodes. Naive CD4+CD44loCD62Lhi T cells were purified by flow cytometry and clutured for 3 days in RPMI medium supplemented with anti-CD3 and anti-CD28.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen) cleanup. Total RNA was subjected to Hiseq RNA-Seq, performed by BGI Tech Solutions Co., Ltd.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Stimulated for 3 days in Th9 differentiation condition

tag: strain

tag: genotype

value: BFAR-/-

tag: tissue

value: spleen and lymph nodes


title: DSP-1001660004759-F04 (D9_LUL_ROI9_PanCK+)

tag: segment

tag: morphology

value: CTA


title: DSP-1001660004765-F02 (D20_LUL_ROI6_PanCK+)

tag: assay

tag: race

value: White

value: not provided


title: BFAR-KO1


title: DSP-1001660004759-F08 (D9_LUL_ROI11_PanCK-)

tag: ethnicity

tag: Sex


title: DSP-1001660004765-F01 (D20_LUL_ROI5_PanCK-)

tag: age

tag: organ failure


title: D18 | 013 | 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: s/s to death (days)


title: DSP-1001660004759-F02 (D9_LUL_ROI8_PanCK+)

value: PanCK+

tag: donor


title: DSP-1001660004759-F07 (D9_LUL_ROI11_PanCK+)


title: WT1

value: wild type


title: WT2


title: DSP-1001660004765-E11 (D20_LUL_ROI4_PanCK-)


title: D18 | 010 | 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: infection

tag: x coordinate

value: Black/AA


title: D18 | 009 | 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

tag: y coordinate

tag: aoi surface area

value: Vein


title: DSP-1001660004759-F03 (D9_LUL_ROI8_PanCK-)

value: Not Hispanic/Latino

value: Lung


title: DSP-1001660004759-F01 (D9_LUL_ROI7_PanCK-)

value: Alveolar


title: DSP-1001660004765-E12 (D20_LUL_ROI5_PanCK+)


title: DSP-1001660004765-E10 (D20_LUL_ROI4_PanCK+)


title: input_Col-0_rep1

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq version 2.16.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
The SICER was used to identify ChIP-enriched peaks between wild type and mutant.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated using bamCoverage.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with H3K9Ac antibody.
Libraries were built for ChIP-seq (Illumina HiSeq X 10; 150-bp pair-end sequencing)

value: seedlings

tag: chip antibody

value: none (input)


title: input_Col-0_rep2

tag: genotype


title: DSP-1001660004759-E12 (D9_LUL_ROI7_PanCK+)

value: F


title: D18 | 010 | PanCK-

value: SARS-CoV-2 infected

tag: binding density


title: D18 | 007 | PanCK-

tag: segment

value: PanCK-


title: D18 | 008 | PanCK-


title: DSP-1001660004765-F06 (D20_LUL_ROI8_PanCK+)

tag: morphology

value: Lung, heart


title: scs1-scs2a_rep2

tag: tissue

value: anti-H3K9Ac (Millipore, 07-352)


title: DSP-1001660004765-E09 (D20_LUL_ROI3_PanCK-)

value: Large airway

tag: assay

value: CTA

tag: race


title: DSP-1001660004765-E08 (D20_LUL_ROI3_PanCK+)

value: White

tag: ethnicity

value: not provided

tag: Sex


title: D18 | 005 | PanCK-

tag: age

tag: organ failure


title: scs1-scs2a_rep1


title: DSP-1001660004759-E10 (D9_LUL_ROI6_PanCK+)

value: PanCK+

tag: s/s to death (days)

tag: donor


title: DSP-1001660004765-E07 (D20_LUL_ROI2_PanCK-)


title: DSP-1001660004759-E09 (D9_LUL_ROI5_PanCK-)

value: Artery

value: Black/AA


title: ada2b_rep2


title: D18 | 004 | PanCK+

tag: infection

tag: x coordinate


title: DSP-1001660004759-E08 (D9_LUL_ROI4_PanCK-)

value: Not Hispanic/Latino


title: DSP-1001660004759-E07 (D9_LUL_ROI4_PanCK+)

value: Lung


title: ada2b_rep1


title: DSP-1001660004765-E06 (D20_LUL_ROI2_PanCK+)

value: Alveolar


title: DSP-1001660004765-E04 (D20_LUL_ROI1_PanCK+)


title: DSP-1001660004759-E06 (D9_LUL_ROI3_PanCK-)

value: Terminal bronchiole


title: D18 | 003 | PanCK-

tag: y coordinate

tag: aoi surface area


title: D18 | 004 | PanCK-


title: DSP-1001660004764-F12 (D19_LUL_ROI15_PanCK-)

value: Basal pore

value: Other

value: Hispanic/Latino

value: M


title: DSP-1001660004759-E11 (D9_LUL_ROI6_PanCK-)

value: PanCK-

value: F


title: DSP-1001660004765-E05 (D20_LUL_ROI1_PanCK-)

value: Large airway

value: Lung, heart


title: hag1_rep1

value: seedlings

tag: genotype

tag: chip antibody

value: anti-H3K9Ac (Millipore, 07-352)


title: D18 | 006 | PanCK-

value: SARS-CoV-2 infected

tag: binding density

tag: segment

value: not provided


title: DSP-1001660004759-E05 (D9_LUL_ROI3_PanCK+)

value: PanCK+

tag: morphology

value: CTA

value: Black/AA


title: Col-0_rep1

tag: tissue

value: wild type


title: D18 | 002 | PanCK-

value: Alveolar

tag: race

value: Lung


title: D18 | 001 | 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

tag: ethnicity


title: D24 | 015 | 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

source_name: Parenchyma

value: control

value: Terminal bronchiole

value: White

value: Not Hispanic/Latino

tag: Sex

value: Multi organ


title: Col-0_rep2


title: DSP-1001660004764-F11 (D19_LUL_ROI15_PanCK+)

value: Basal pore

tag: assay

value: Other

value: Hispanic/Latino

value: M

tag: age


title: DSP-1001660004764-F10 (D19_LUL_ROI14_PanCK-)

value: PanCK-

tag: organ failure

tag: s/s to death (days)


title: hag1_rep2

value: seedlings

value: anti-H3K9Ac (Millipore, 07-352)


title: DSP-1001660004759-E04 (D9_LUL_ROI2_PanCK-)

value: CTA

value: F

tag: donor


title: DSP-1001660004759-E02 (D9_LUL_ROI1_PanCK-)

value: Black/AA


title: DSP-1001660004764-F09 (D19_LUL_ROI14_PanCK+)

value: PanCK+


title: D24 | 014 | 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

tag: infection

tag: x coordinate


title: scs1-scs2a_rep1

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The DEGs (log2 (fold-change) > 1 or < -1, FDR < 0.05) were obtained with the R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy on the BGISEQ500 platform).


title: ada2b_rep2


title: scs1-scs2a_rep2


title: DSP-1001660004759-E01 (D9_LUL_ROI1_PanCK+)

value: Alveolar

value: Lung


title: DSP-1001660004759-H12 (D8_LUL_ROI15_PanCK-)

value: Vein

value: Lung, kidney


title: DSP-1001660004764-F06 (D19_LUL_ROI12_PanCK-)

value: Artery


title: DSP-1001660004764-F07 (D19_LUL_ROI13_PanCK+)


title: D24 | 013 | 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

value: control

tag: y coordinate

tag: aoi surface area

value: Terminal bronchiole

value: White

value: Not Hispanic/Latino

value: Multi organ


title: ada2b_rep1

tag: genotype


title: D24 | 014 | 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

tag: binding density

value: PanCK-

value: M


title: DSP-1001660004759-H09 (D8_LUL_ROI13_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: Hispanic/Latino


title: DSP-1001660004759-H11 (D8_LUL_ROI14_PanCK-)

tag: morphology

value: CTA


title: DSP-1001660004759-H10 (D8_LUL_ROI14_PanCK+)


title: DSP-1001660004764-F05 (D19_LUL_ROI11_PanCK-)

value: Other


title: D24 | 013 | 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: D24 | 012 | 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


title: hag1_rep1

tag: tissue

value: seedlings


title: D24 | 015 | 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

tag: race


title: DSP-1001660004764-F04 (D19_LUL_ROI11_PanCK+)

value: PanCK+

tag: ethnicity


title: DSP-1001660004759-E03 (D9_LUL_ROI2_PanCK+)

value: Alveolar

value: Black/AA

tag: Sex

value: F


title: Col-0_rep2

value: wild type


title: DSP-1001660004764-F03 (D19_LUL_ROI10_PanCK-)

value: Vein

tag: assay

value: Lung


title: Col-0_rep1


title: D24 | 011 | 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: control

tag: age


title: DSP-1001660004764-F08 (D19_LUL_ROI13_PanCK-)

value: Basal pore

tag: organ failure


title: D24 | 012 | 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

value: Terminal bronchiole

value: White

value: Not Hispanic/Latino

tag: s/s to death (days)


title: DSP-1001660004764-F02 (D19_LUL_ROI10_PanCK+)

value: M

tag: donor


title: DSP-1001660004759-H08 (D8_LUL_ROI13_PanCK+)

value: Hispanic/Latino

value: Lung, kidney


title: DSP-1001660004764-F01 (D19_LUL_ROI9_PanCK-)

value: PanCK-

value: CTA

value: Other


title: DSP-1001660004759-H07 (D8_LUL_ROI12_PanCK-)

value: Alveolar


title: hag1_rep2

value: seedlings


title: DSP-1001660004759-H06 (D8_LUL_ROI11_PanCK-)

value: Black/AA


title: D24 | 010 | 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

tag: infection

value: PanCK+

value: Multi organ


title: DSP-1001660004764-E12 (D19_LUL_ROI8_PanCK-)

value: Lung


title: D24 | 010 | 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: control

tag: x coordinate


title: D24 | 009 | PanCK-

tag: y coordinate

value: Artery


title: DSP-1001660004759-H05 (D8_LUL_ROI11_PanCK+)


title: DSP-1001660004764-E11 (D19_LUL_ROI7_PanCK-)


title: DSP-1001660004759-H04 (D8_LUL_ROI10_PanCK-)


title: DSP-1001660004759-H03 (D8_LUL_ROI9_PanCK-)


title: DSP-1001660004764-E10 (D19_LUL_ROI6_PanCK-)


title: DSP-1001660004764-E09 (D19_LUL_ROI5_PanCK-)


title: DSP-1001660004759-H02 (D8_LUL_ROI8_PanCK-)

value: Large airway


title: D24 | 007 | PanCK+

tag: aoi surface area

value: White


title: D24 | 011 | 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

value: Not Hispanic/Latino


title: D24 | 008 | PanCK-

value: M


title: OsbR overexpression regulon replicate 3

type: RNA

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

country: Brazil

institute: Universidade de Sao Paulo

description: Biological replicate 3 of 3

hyb_protocol: Pooled labeled cRNA samples were fragmented and hybridized to the C. violaceum microarray slides. After hybridization, slides were washed sequential according to the Agilent Two-Color Microarray-Based Exon Analysis Protocol, version 1.0 (Agilent Technologies)

scan_protocol: The slides were scanned with the G2505C Agilent DNA Microarray Scanner

data_processing: Data were extracted and normalized (LOWESS normalization) using the Agilent Feature Extraction software, version 10.7.3

organism: Chromobacterium violaceum

source_name: C. violaceum WT(osbR)

label_protocol: The fluorescence-labeled cRNA (complementary RNA) was generated of total RNA derived from each experimental condition using the Low Input Quick Amp WT Two-Color kit (Agilent Technologies)

growth_protocol: Bacteria were grown at 37 °C in LB medium until mid-log phase (OD600 of 0.8 to 1.2)

extract_protocol: Total RNA was extracted using Trizol reagent (Ambion) and purified with the illustra RNAspin Mini RNA Isolation Kit (GE Healthcare)

tag: strain

tag: growth

value: midlog phase LB

source_name: C. violaceum ∆osbR(pJN105)

value: [delta]osbR mutant (JF3905 with empty vector)


title: D24 | 007 | PanCK-

tag: binding density

tag: segment

value: PanCK-


title: DSP-1001660004759-H01 (D8_LUL_ROI8_PanCK+)

tag: morphology

value: CTA

value: Hispanic/Latino

value: Lung, kidney


title: DSP-1001660004764-E07 (D19_LUL_ROI4_PanCK-)

value: Alveolar

tag: race

value: Other


title: DSP-1001660004759-G12 (D8_LUL_ROI7_PanCK-)

value: Black/AA

tag: ethnicity


title: OsbR overexpression regulon replicate 2

description: Biological replicate 2 of 3


title: OsbR overexpression regulon replicate 1

description: Biological replicate 1 of 3


title: OsbR deletion regulon replicate 2

description: Biological replicate 2 of 3

source_name: C. violaceum WT control

source_name: C. violaceum ∆osbR

value: [delta]osbR mutant (JF3905)


title: WT-PH-C-rep_1

city: Jeddah

first: Haroon

last: Butt

state: Makkah

address: King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900

department: BESE

country: Saudi Arabia

institute: KAUST

description: High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol

data_processing:
Basecalls performed using CASAVA version 1.4
Trimming library adapters and quality controls with Trimmomatic using the following arguments; TrimmomaticPE - LEADING:25 TRAILING:25 CROP:120 MINLEN:120. Illumina adapters were removed and read pairs were trimmed to the same length
Alignement with STAR with the following arguments: --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --readFilesCommand zcat, --quantMode GeneCounts, --outFilterMultimapNmax 1.
bigwig files generated with deeptools BamCoverage

molecule: polyA RNA

organism: Oryza sativa Japonica Group

source_name: Seedlings

growth_protocol: 7-day-old seedlings

extract_protocol:
Direct-zol RNA MiniPrep Plus (Zymo Research) according to the manufacturer’s instructions
The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol and sequenced on the HiSeq-4000 platform to generate high-quality paired-end reads.

treatment_protocol: six hours treatment with 0.3 uM GEX1A

tag: tissue

value: Seedlings

tag: cultivar

value: Nipponbare

tag: genotype

value: Wild type

tag: treatment

value: Mock, 6hours


title: D24 | 006 | PanCK-

value: control

value: White

tag: Sex

tag: age

tag: organ failure

value: Multi organ

tag: s/s to death (days)


title: DSP-1001660004764-E06 (D19_LUL_ROI4_PanCK+)

value: PanCK+

tag: assay

value: M

value: Lung

tag: donor


title: WT-PH-C-rep_2


title: DSP-1001660004759-G11 (D8_LUL_ROI6_PanCK-)

value: PanCK-

value: CTA


title: D24 | 005 | PanCK-

tag: infection

tag: x coordinate

tag: y coordinate

tag: aoi surface area

value: Not Hispanic/Latino


title: OGR-1-C-rep_2


title: OGR-1-C-rep_1


title: DSP-1001660004764-E04 (D19_LUL_ROI3_PanCK+)

tag: segment

tag: morphology

value: Alveolar

value: Hispanic/Latino


title: DSP-1001660004764-E05 (D19_LUL_ROI3_PanCK-)

tag: race

value: Other

tag: ethnicity


title: DSP-1001660004759-G09 (D8_LUL_ROI5_PanCK-)

value: Black/AA

value: Lung, kidney


title: DSP-1001660004759-G10 (D8_LUL_ROI6_PanCK+)


title: PGR-4-C-rep_2

tag: tissue

value: Seedlings

tag: cultivar

value: Nipponbare


title: D24 | 004 | PanCK+

tag: binding density


title: DSP-1001660004764-E03 (D19_LUL_ROI2_PanCK-)

tag: Sex


title: D24 | 004 | PanCK-

tag: age


title: DSP-1001660004759-G08 (D8_LUL_ROI5_PanCK+)

tag: organ failure


title: OsbR deletion regulon replicate 3

description: Biological replicate 3 of 3

tag: strain

tag: growth

value: midlog phase LB

value: [delta]osbR mutant (JF3905)


title: DSP-1001660004764-E08 (D19_LUL_ROI5_PanCK+)

tag: assay

tag: s/s to death (days)

tag: donor


title: D24 | 003 | PanCK+

tag: infection

value: control

tag: x coordinate

tag: y coordinate

value: White


title: PGR-4-C-rep_1

tag: genotype

tag: treatment

value: Mock, 6hours


title: DSP-1001660004764-E02 (D19_LUL_ROI1_PanCK-)

tag: segment

tag: morphology

tag: race

tag: ethnicity

value: M


title: PGR-3-C-rep_2

tag: tissue

tag: cultivar


title: OsbR deletion regulon replicate 1

description: Biological replicate 1 of 3


title: D24 | 003 | PanCK-

tag: aoi surface area

tag: binding density

tag: Sex

tag: age

tag: organ failure

value: Multi organ


title: DSP-1001660004764-E01 (D19_LUL_ROI1_PanCK+)

value: PanCK+

tag: assay

value: Lung

tag: s/s to death (days)

tag: donor


title: DSP-1001660004759-G07 (D8_LUL_ROI4_PanCK-)

value: PanCK-

value: Vein

value: CTA


title: D24 | 002 | PanCK-

tag: infection

tag: x coordinate

tag: y coordinate

value: Alveolar

value: Not Hispanic/Latino


title: DSP-1001660004759-G06 (D8_LUL_ROI3_PanCK-)

tag: segment

value: Black/AA

value: Hispanic/Latino

value: Lung, kidney


title: PGR-3-C-rep_1

value: Seedlings

value: Nipponbare

tag: genotype

tag: treatment


title: DSP-1001660004759-G05 (D8_LUL_ROI3_PanCK+)

tag: morphology

tag: race

tag: ethnicity


title: DSP-1001660004764-D12 (D18_LUL_ROI19_PanCK-)

value: Terminal bronchiole

value: not provided

value: F


title: PGR-2-C-rep_2

tag: tissue

tag: cultivar

value: Mock, 6hours


title: DSP-1001660004764-D11 (D18_LUL_ROI19_PanCK+)

tag: Sex


title: DSP-1001660004759-G04 (D8_LUL_ROI2_PanCK-)

value: Basal pore

value: M

tag: age


title: D23 | 012 | 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: control

tag: aoi surface area

tag: binding density

value: Artery

tag: organ failure

value: Heart


title: D24 | 001 | PanCK-

value: PanCK-

value: White

value: Multi organ

tag: s/s to death (days)


title: DSP-1001660004764-D10 (D18_LUL_ROI18_PanCK-)

value: Vein

tag: assay

value: CTA

value: Black/AA

value: Lung

tag: donor


title: PGR-2-C-rep_1

value: Seedlings

value: Nipponbare


title: DSP-1001660004759-G03 (D8_LUL_ROI2_PanCK+)

value: PanCK+

value: Hispanic/Latino

value: Lung, kidney


title: DSP-1001660004764-D09 (D18_LUL_ROI17_PanCK-)

value: Alveolar

value: not provided

value: F


title: DSP-1001660004759-G02 (D8_LUL_ROI1_PanCK-)

value: Basal pore

value: M


title: D23 | 011 | 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

tag: infection

value: control

tag: x coordinate

tag: y coordinate

value: Terminal bronchiole

value: Not Hispanic/Latino

value: Heart


title: DSP-1001660004759-G01 (D8_LUL_ROI1_PanCK+)

tag: segment

value: CTA


title: D23 | 011 | 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: PanCK-

value: Black/AA


title: DSP-1001660004764-D07 (D18_LUL_ROI15_PanCK-)

tag: morphology

value: Artery

value: Lung


title: D23 | 010 | 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

value: PanCK+

tag: race


title: DSP-1001250001622-B12 (D23_Parenchyma_ROI12_PanCK-)

tag: ethnicity


title: WT-PH-X-rep_1

tag: tissue

value: Seedlings

value: Nipponbare

tag: genotype

value: Wild type

tag: treatment

value: 0.3 µM GEX1A, 6hours


title: DSP-1001660004764-D06 (D18_LUL_ROI14_PanCK-)

value: Alveolar

value: not provided

tag: Sex

value: F

tag: age


title: DSP-1001660004764-D08 (D18_LUL_ROI16_PanCK-)


title: WT-PH-X-rep_2

tag: cultivar


title: DSP-1001250001622-B11 (D23_Parenchyma_ROI12_PanCK+)

tag: organ failure


title: D23 | 010 | 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

value: control

tag: aoi surface area

tag: binding density

tag: s/s to death (days)


title: DSP-1001660004764-D05 (D18_LUL_ROI14_PanCK+)

tag: assay

tag: donor


title: OGR-1-X-rep_2


title: DSP-1001250001622-B10 (D23_Parenchyma_ROI11_PanCK-)


title: D23 | 009 | 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

tag: infection

tag: x coordinate

tag: y coordinate


title: DSP-1001660004764-D04 (D18_LUL_ROI13_PanCK-)

tag: segment

tag: morphology

tag: race


title: D23 | 008 | 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

value: Terminal bronchiole

tag: ethnicity


title: D23 | 009 | 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

value: Not Hispanic/Latino


title: PGR-1-C-rep_2

tag: tissue

tag: genotype

tag: treatment

value: Mock, 6hours


title: PGR-4-X-rep_2

tag: cultivar

tag: age


title: DSP-1001250001622-B08 (D23_Parenchyma_ROI10_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: CTA

tag: Sex

tag: organ failure

value: Heart


title: OGR-1-X-rep_1


title: PGR-1-C-rep_1


title: DSP-1001660004764-D03 (D18_LUL_ROI13_PanCK+)

value: Black/AA

tag: s/s to death (days)


title: DSP-1001250001622-B07 (D23_Parenchyma_ROI10_PanCK+)

value: Artery

tag: assay


title: D23 | 008 | 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

tag: aoi surface area

tag: binding density

value: PanCK-


title: PGR-4-X-rep_1


title: DSP-1001660004764-D02 (D18_LUL_ROI12_PanCK-)

value: Lung

tag: donor


title: PGR-3-X-rep_2

value: Seedlings


title: DSP-1001250001622-B06 (D23_Parenchyma_ROI9_PanCK-)


title: D23 | 007 | 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

tag: infection

tag: x coordinate

tag: y coordinate

value: PanCK+


title: PGR-3-X-rep_1

value: Nipponbare


title: D23 | 007 | 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

tag: segment

tag: race


title: DSP-1001660004764-D01 (D18_LUL_ROI11_PanCK-)

tag: morphology

tag: ethnicity


title: DSP-1001250001622-B05 (D23_Parenchyma_ROI8_PanCK-)


title: DSP-1001660004764-C12 (D18_LUL_ROI10_PanCK-)


title: PGR-2-X-rep_2

tag: tissue

tag: genotype

tag: treatment

value: 0.3 µM GEX1A, 6hours


title: D23 | 006 | PanCK+

tag: Sex

tag: age


title: DSP-1001250001622-B04 (D23_Parenchyma_ROI8_PanCK+)

tag: organ failure

tag: s/s to death (days)


title: PGR-2-X-rep_1

tag: cultivar


title: DSP-1001250001622-B09 (D23_Parenchyma_ROI11_PanCK+)

value: Alveolar

tag: assay


title: D23 | 006 | 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

tag: aoi surface area

tag: binding density


title: D23 | 005 | PanCK+

tag: infection

tag: x coordinate


title: DSP-1001660004764-C10 (D18_LUL_ROI9_PanCK-)

tag: segment

value: Vein

value: not provided

tag: donor


title: DSP-1001660004764-C11 (D18_LUL_ROI10_PanCK+)

tag: morphology

tag: race

value: F


title: DSP-1001250001622-B03 (D23_Parenchyma_ROI7_PanCK-)

tag: ethnicity


title: DSP-1001250001622-B02 (D23_Parenchyma_ROI7_PanCK+)


title: PGR-1-X-rep_2

tag: tissue

tag: genotype


title: PGR-1-X-rep_1

tag: treatment


title: D23 | 005 | PanCK-

value: control

tag: y coordinate

tag: Sex

tag: age


title: DSP-1001660004764-C09 (D18_LUL_ROI8_PanCK-)

tag: organ failure

tag: s/s to death (days)


title: D23 | 004 | PanCK+

tag: aoi surface area

value: Not Hispanic/Latino


title: DSP-1001660004764-C08 (D18_LUL_ROI7_PanCK-)

tag: assay


title: DSP-1001250001622-B01 (D23_Parenchyma_ROI6_PanCK-)

value: Terminal bronchiole


title: DSP-1001250001622-A12 (D23_Parenchyma_ROI6_PanCK+)

value: CTA


title: DSP-1001660004764-C07 (D18_LUL_ROI6_PanCK-)


title: WT-SF-X-rep_2

tag: cultivar

value: Wild type


title: D23 | 004 | PanCK-

tag: infection

tag: x coordinate

tag: binding density

value: Black/AA

value: Heart


title: DSP-1001660004764-C06 (D18_LUL_ROI5_PanCK-)

tag: segment

value: PanCK-

tag: morphology

tag: donor


title: DSP-1001250001622-A11 (D23_Parenchyma_ROI5_PanCK-)

tag: race

tag: ethnicity


title: DSP-1001250001622-A10 (D23_Parenchyma_ROI5_PanCK+)


title: SGS-1-X-rep_2

tag: tissue

tag: genotype

tag: treatment


title: WT-SF-X-rep_1

tag: age


title: SGS-1-X-rep_1


title: DSP-1001660004764-C05 (D18_LUL_ROI4_PanCK-)

tag: Sex

tag: organ failure

value: Lung


title: SGR-6-X-rep_2

value: Seedlings


title: D23 | 003 | PanCK+

tag: y coordinate

tag: aoi surface area

value: PanCK+

tag: s/s to death (days)


title: DSP-1001660004764-C04 (D18_LUL_ROI4_PanCK+)

tag: assay


title: DSP-1001250001622-A09 (D23_Parenchyma_ROI4_PanCK-)


title: D23 | 003 | PanCK-

tag: infection

tag: x coordinate


title: DSP-1001660004764-C03 (D18_LUL_ROI3_PanCK-)

tag: segment


title: D23 | 002 | PanCK+

tag: binding density


title: D23 | 001 | PanCK+


title: D23 | 002 | PanCK-


title: SGR-5-X-rep_2

tag: cultivar

value: Nipponbare


title: DSP-1001660004764-C02 (D18_LUL_ROI2_PanCK-)

tag: morphology

tag: race

tag: donor


title: SGR-6-X-rep_1

tag: tissue

tag: genotype

value: 0.3 µM GEX1A, 6hours


title: DSP-1001250001622-A06 (D23_Parenchyma_ROI3_PanCK+)

tag: ethnicity

tag: age


title: DSP-1001250001622-A05 (D23_Parenchyma_ROI2_PanCK-)

tag: Sex

tag: organ failure


title: DSP-1001250001622-A08 (D23_Parenchyma_ROI4_PanCK+)

value: Alveolar


title: SGR-5-X-rep_1

tag: treatment


title: DSP-1001250001622-A07 (D23_Parenchyma_ROI3_PanCK-)

tag: s/s to death (days)


title: D23 | 001 | PanCK-

tag: y coordinate

tag: aoi surface area


title: D22 | 014 | 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: infection

tag: x coordinate

value: White

value: M

value: Multi organ


title: DSP-1001660004764-C01 (D18_LUL_ROI1_PanCK-)

tag: segment

tag: assay

value: not provided

value: F


title: DSP-1001250001622-A04 (D23_Parenchyma_ROI2_PanCK+)

tag: morphology

value: Terminal bronchiole

value: Not Hispanic/Latino


title: SGR-4-X-rep_1

tag: cultivar


title: D22 | 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

value: control

tag: binding density

value: Vein

tag: race


title: DSP-1001660004764-B10 (D24_Parenchyma_ROI13_PanCK-)

value: CTA

tag: donor


title: DSP-1001250001622-A03 (D23_Parenchyma_ROI1_PanCK-)

value: PanCK-

value: Black/AA

tag: ethnicity

value: Heart


title: SGR-3-X-rep_2

tag: tissue

value: Seedlings

tag: genotype

tag: age


title: D22 | 011 | 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

value: PanCK+

value: Artery

tag: Sex

tag: organ failure


title: DSP-1001660004764-B08 (D24_Parenchyma_ROI12_PanCK-)

tag: s/s to death (days)


title: DSP-1001250001622-A02 (D23_Parenchyma_ROI1_PanCK+)

value: Alveolar


title: DSP-1001660004764-B09 (D24_Parenchyma_ROI13_PanCK+)

value: White


title: DSP-1001660004759-B10 (D22_Parenchyma_ROI12_PanCK-)

value: M


title: SGR-3-X-rep_1

description: High-quality RNA samples with RNA integrity number (RIN) 7.0 were selected for library construction. The RNA-seq libraries were constructed using TruSeq mRNA stranded kit following the standard protocol

value: Nipponbare

tag: treatment

value: 0.3 µM GEX1A, 6hours


title: SGR-2-X-rep_2


title: SGR-4-X-rep_2


title: DSP-1001660004764-B12 (D24_Parenchyma_ROI14_PanCK-)

value: Multi organ


title: D22 | 010 | 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: infection

tag: y coordinate

tag: aoi surface area


title: D22 | 011 | 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

tag: x coordinate

tag: segment


title: SGR-2-X-rep_1

tag: cultivar


title: DSP-1001660004764-B06 (D24_Parenchyma_ROI11_PanCK-)

tag: morphology

tag: assay


title: D22 | 010 | 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

tag: binding density

tag: race


title: DSP-1001660004759-B08 (D22_Parenchyma_ROI11_PanCK-)

tag: ethnicity

tag: donor


title: DSP-1001660004764-B11 (D24_Parenchyma_ROI14_PanCK+)

value: Terminal bronchiole

tag: age


title: DSP-1001660004759-B07 (D22_Parenchyma_ROI10_PanCK-)

value: Not Hispanic/Latino

tag: Sex


title: DSP-1001660004764-B05 (D24_Parenchyma_ROI11_PanCK+)

tag: organ failure


title: SGR-1-X-rep_2

tag: tissue

tag: genotype


title: D22 | 009 | 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: control

tag: s/s to death (days)


title: SGR-1-X-rep_1

tag: treatment


title: D22 | 009 | 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: x coordinate

tag: y coordinate

tag: aoi surface area


title: DSP-1001660004764-B04 (D24_Parenchyma_ROI10_PanCK-)

tag: segment

tag: morphology


title: WT-SF-C-rep_2

tag: cultivar

value: Wild type

value: Mock, 6hours


title: DSP-1001660004759-B05 (D22_Parenchyma_ROI9_PanCK-)

value: PanCK-

tag: assay

value: CTA

tag: race


title: DSP-1001660004764-B03 (D24_Parenchyma_ROI10_PanCK+)

tag: ethnicity

tag: donor


title: D22 | 008 | 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

tag: Sex

tag: age


title: DSP-1001660004764-B02 (D24_Parenchyma_ROI9_PanCK-)

tag: organ failure


title: DSP-1001660004759-B09 (D22_Parenchyma_ROI12_PanCK+)


title: DSP-1001660004764-B07 (D24_Parenchyma_ROI12_PanCK+)


title: D22 | 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

tag: infection


title: DSP-1001660004759-B04 (D22_Parenchyma_ROI9_PanCK+)

tag: s/s to death (days)


title: DSP-1001660004759-B03 (D22_Parenchyma_ROI8_PanCK-)


title: DSP-1001660004764-B01 (D24_Parenchyma_ROI8_PanCK-)


title: DSP-1001660004759-B02 (D22_Parenchyma_ROI7_PanCK-)


title: SGR-6-C-rep_2

tag: tissue

tag: genotype

tag: treatment


title: DSP-1001660004764-A11 (D24_Parenchyma_ROI7_PanCK+)


title: D22 | 007 | 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

tag: x coordinate

tag: y coordinate

tag: aoi surface area


title: D22 | 006 | PanCK+

tag: segment

value: Basal pore


title: DSP-1001660004759-B06 (D22_Parenchyma_ROI10_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: morphology

tag: assay


title: DSP-1001660004764-A10 (D24_Parenchyma_ROI6_PanCK-)

tag: race

tag: ethnicity


title: D22 | 006 | PanCK-

tag: binding density


title: DSP-1001660004759-A12 (D22_Parenchyma_ROI6_PanCK-)

tag: Sex

tag: donor


title: D22 | 005 | PanCK-

tag: age

tag: organ failure


title: D22 | 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

tag: infection

tag: s/s to death (days)


title: D22 | 004 | PanCK+


title: WT-SF-C-rep_1

tag: tissue

value: Seedlings

tag: cultivar

tag: genotype


title: DSP-1001660004764-A09 (D24_Parenchyma_ROI6_PanCK+)

value: PanCK+


title: DSP-1001660004759-A11 (D22_Parenchyma_ROI6_PanCK+)


title: SGS-1-C-rep_2

tag: treatment


title: SGS-1-C-rep_1


title: DSP-1001660004764-A08 (D24_Parenchyma_ROI5_PanCK-)


title: SGR-5-C-rep_1


title: D22 | 004 | PanCK-

tag: x coordinate

tag: y coordinate

tag: aoi surface area


title: DSP-1001660004764-A12 (D24_Parenchyma_ROI7_PanCK-)

tag: segment

tag: morphology

tag: assay


title: DSP-1001660004759-A10 (D22_Parenchyma_ROI5_PanCK-)

tag: race

tag: ethnicity


title: SGR-4-C-rep_2


title: DSP-1001660004764-A07 (D24_Parenchyma_ROI4_PanCK-)

tag: Sex

tag: donor


title: DSP-1001660004759-A09 (D22_Parenchyma_ROI5_PanCK+)

tag: age

tag: organ failure


title: DSP-1001660004759-B01 (D22_Parenchyma_ROI7_PanCK+)

tag: s/s to death (days)


title: SGR-4-C-rep_1

tag: tissue


title: D22 | 003 | PanCK+

tag: infection

tag: binding density


title: DSP-1001660004764-A06 (D24_Parenchyma_ROI4_PanCK+)


title: SGR-5-C-rep_2

tag: cultivar

tag: genotype

tag: treatment


title: SGR-6-C-rep_1


title: SGR-3-C-rep_2


title: DSP-1001660004764-A05 (D24_Parenchyma_ROI3_PanCK-)


title: DSP-1001660004759-A08 (D22_Parenchyma_ROI4_PanCK-)


title: DSP-1001660004764-A04 (D24_Parenchyma_ROI3_PanCK+)


title: SGR-3-C-rep_1


title: SGR-2-C-rep_2


title: DSP-1001660004759-A06 (D22_Parenchyma_ROI3_PanCK-)


title: D22 | 003 | PanCK-

tag: x coordinate

tag: y coordinate

tag: aoi surface area


title: DSP-1001660004759-A05 (D22_Parenchyma_ROI3_PanCK+)

tag: segment

tag: morphology

tag: assay


title: SGR-2-C-rep_1


title: DSP-1001660004764-A03 (D24_Parenchyma_ROI2_PanCK-)

tag: race

tag: ethnicity

tag: Sex


title: D22 | 002 | PanCK+

tag: age

tag: organ failure


title: D22 | 001 | PanCK+

tag: s/s to death (days)


title: D22 | 002 | PanCK-

tag: infection


title: DSP-1001660004759-A04 (D22_Parenchyma_ROI2_PanCK-)

tag: donor


title: DSP-1001660004764-A02 (D24_Parenchyma_ROI1_PanCK-)


title: D22 | 001 | PanCK-

tag: binding density


title: DSP-1001660004765-A01 (Blank control)

organism: blank sample

source_name: blank sample

value: blank sample

tag: Sex:


title: Normoxia-treated BG01 hESC-CMs

city: Seoul

first: Seung-Cheol

last: Choi

address: Anamdong 5-Ga

department: Cardiology

country: South Korea

institute: College of Medicine, Korea University

data_processing:
Differentially expressed genes were analyzed using the ExDEGA software (EBIOGEN, Inc., Seoul, Korea).
Gene classification was based on searches performed using the DAVID (http://david.abcc.ncifcrf.gov/), Medline databases (http://www.ncbi.nlm.nih.gov/), KEGG pathway (http://www.genome.jp/kegg/tool/map_pathway2.html) and STRING (http://www.string-db.org/).
Heat maps of hypoxia-induced genes in hESC-CMs were performed using software MultiExperiment Viewer (Mev)
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: BG01 hESCs

growth_protocol: For cardiac differentiation, BG01 hESCs were dissociated into single cells with Accutase (Sigma-Aldrich, Saint Louis, MO, USA) and then seeded onto a Matrigel-coated at 32,000 cells/cm2 in E8 supplemented with 2 μM Thiazovivin (Sigma-Aldrich), a Rho kinase inhibitor from day -3 to day 0. At day 0, cells were treated with 6 µM CHIR99021 (Sigma-Aldrich) in the basal medium RPMI 1640 (Thermo Fisher Scientific), L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma-Aldrich), and bovine serum albumin (BSA, Sigma-Aldrich) medium for 1 days. At 2 day, cells were then treated with 2 µM IWP2 (Tocris Bioscience, Ellisville, MO, USA) in RPMI 1640 + B27 minus insulin (RPMI/B27-Insulin, Thermo Fisher Scientific) medium for 48 hr.

extract_protocol:
Total RNA was extracted from normoxia- and hypoxia-treated BG01 hESC-CMs for 24 hr after treatment with FGF4+AA between days 5 and 15 of differentiation with TRIzol reagent.
For each RNA sample, the library construction was performed using QuantSeq Library Prep kit (Lexogen, Inc., Vienna, Austria) according to the manufacturer's instructions.

treatment_protocol: Normoxia- and hypoxia-treated BG01 hESC-CMs for 24 hr after treatment with FGF4+AA between days 5 and 15 of differentiation

tag: cell type

value: Cardiomyocytes derived from BG01 hESCs

tag: treatment

value: Normoxia for 24 hr

tag: disease state

value: Normal


title: DSP-1001660004764-A01 (Blank control)


title: Hypoxia-treated BG01 hESC-CMs

value: hypoxia (2% O2) for 24 hr

value: Ischemia


title: DSP-1001660004759-A02 (D22_Parenchyma_ROI1_PanCK+)

value: Alveolar

value: White

value: M

value: Multi organ


title: DSP-1001660004759-A03 (D22_Parenchyma_ROI1_PanCK-)

value: Not Hispanic/Latino


title: SGR-1-C-rep_1

tag: tissue

tag: cultivar

value: Nipponbare

tag: genotype

value: Mock, 6hours


title: DSP-1001660004759-A07 (D22_Parenchyma_ROI4_PanCK+)

tag: segment

tag: morphology

tag: assay

value: CTA


title: IMR90_HMGB1_pro_ChIP_rep2

status: Public on Apr 10 2021

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

country: Germany

institute: University Medical Center Goettingen

description:
ChIP
IMR90_pro_HMGB1_pooled_replicates_fc.bigwig

data_processing:
Encode ChIP-seq pipeline for single-end sequencing.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files of ChIP over Input fold change.

source_name: Normal lung fibroblast IMR90

growth_protocol: Single IMR90 isolates (I90-10 and/or -79, passage 5; Coriell Biorepository) were continuously passaged until replicative exhaustion in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
~25 million cells per sample were double crosslinked in EGS/PFA and processed with ChIP-IT high sensitivity kit (Active motif) as per manufacturer instructions. Immunoprecipitation was carried out with 4 ug of HMGB1 antibody (Hybridoma, PCRP-HMGB1-4F10) in 30 ug of chromatin. DNA was purified with ChIP DNA Clean & Concentrator kit (Zymo).
TruSeq Library Preparation Kit (Illumina).

treatment_protocol: Normal growth conditions for proliferating samples and until replicative exhaustion for senescent samples.

tag: cell line

tag: condition

value: Proliferating

tag: chip antibody

value: HMGB1 Hybridoma Ab (PCRP-HMGB1-4F10)


title: HUVEC_HMGB1_pro_Input_rep1

description:
Input
HUVEC_pro_HMGB1_pooled_replicates_fc.bigwig

source_name: Umbilical vein endothelial cells HUVEC

value: HUVEC

value: No antibody


title: IMR90_HMGB1_sen_ChIP_rep2

description:
ChIP
IMR90_sen_HMGB1_pooled_replicates_fc.bigwig

value: Senescent


title: Pro_rep1_rna

data_processing:
For both the Ribo-seq and the RNA-seq the linker adapters have been removed from the demultiplexed FASTQ files.
For Ribo-seq, the reads were collapsed and the UMIs were removed using cutadapt (version 1.18) -u 2 -u -5 to
After filtering of reads that map to rRNA, both the Ribo-seq and RNA-seq reads were aligned to RefSeq version 91 using bowtie version 1.0.1 with the following parameters: bowtie -a -m 100 -l 25 -n 2 -S --norc
The bowtie output .sam files were converted to bam files using samtools (Version: 1.8).
Differential gene expression with DESeq2 (version 1.22.2) VST normalization and Anota2seq (version 1.7.0).
Genome_build: Transcriptome RefSeq version 91
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include raw read quantifications.
Supplementary_files_format_and_content: DatasetEV5_RiboSeq.xlsx: Excel datasheet containing results of differential expression for Ribo-seq and RNA-seq in proliferative and senescent conditions.

source_name: Normal lung fibroblasts IMR90

growth_protocol: Single IMR90 isolates (I90-10 and -79, passage 5; Coriell Biorepository) were continuously passaged to replicative exhaustion in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
Three independent replicas of proliferating or senescent IMR90 were grown, harvested in ice-cold polysome isolation buffer supplemented with cyclohexamide. Approx. 15% of each lysate was kept for isolation of RNA and used for RNA-seq.
Cell lysates digested with RNase1, ribosomes purified, RNA extracted, ribosome protected fragments (28-32nt) isolated by urea-PAGE then NGS libraries prepared by 3' linker ligation followed by reverse transcriptase with a circularisation primer (same as doi.org/10.1016/j.ymeth.2017.05.028).

treatment_protocol: Replicative exhaustion.


title: IMR90_HMGB1_sen_Input_rep2

description:
Input
IMR90_sen_HMGB1_pooled_replicates_fc.bigwig


title: SGR-1-C-rep_2

value: Seedlings

tag: age


title: Sen_rep3_rna


title: Pro_rep3_rna


title: IMR90_HMGB1_sen_ChIP_rep1


title: Sen_rep1_rna


title: IMR90_HMGB1_pro_Input_rep2

description:
Input
IMR90_pro_HMGB1_pooled_replicates_fc.bigwig


title: Pro_rep3_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx

data_processing:
Library strategy: Ribo-seq
For both the Ribo-seq and the RNA-seq the linker adapters have been removed from the demultiplexed FASTQ files.
For Ribo-seq, the reads were collapsed and the UMIs were removed using cutadapt (version 1.18) -u 2 -u -5 to
After filtering of reads that map to rRNA, both the Ribo-seq and RNA-seq reads were aligned to RefSeq version 91 using bowtie version 1.0.1 with the following parameters: bowtie -a -m 100 -l 25 -n 2 -S --norc
The bowtie output .sam files were converted to bam files using samtools (Version: 1.8).
Differential gene expression with DESeq2 (version 1.22.2) VST normalization and Anota2seq (version 1.7.0).
Genome_build: Transcriptome RefSeq version 91
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include raw read quantifications.
Supplementary_files_format_and_content: DatasetEV5_RiboSeq.xlsx: Excel datasheet containing results of differential expression for Ribo-seq and RNA-seq in proliferative and senescent conditions.


title: Pro_rep2_rna


title: Sen_rep2_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx


title: Sen_rep1_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx


title: Pro_rep2_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx


title: HUVEC_HMGB1_pro_ChIP_rep1

description:
ChIP
HUVEC_pro_HMGB1_pooled_replicates_fc.bigwig


title: IMR90_HMGB1_sen_Input_rep1


title: Sen_rep3_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx


title: Control_rep2

description:
mRNA-Seq
IMR90_HMGB1_KD_RNAseq_DESeq2_results.xlsx

data_processing:
Alignment with STAR aligner.
Count quantification with featureCounts.
Normalization with RUV-seq.
Differential gene expression analysis with DESeq2.
Genome_build: hg19 GRCh37)
Supplementary_files_format_and_content: *_sorted_featurecounts.txt: Tab-delimited text files include raw read counts for all the samples.
Supplementary_files_format_and_content: IMR90_HMGB1_KD_RNAseq_DESeq2_results.xlsx: Excel table of differentially expressed genes.

growth_protocol: Single IMR90 isolates (I90-10 and -79, passage 5; Coriell Biorepository) were continuously passaged in MEM (M4655, Sigma-Aldrich) supplemented with non-essential amino acids and 10% FBS under 5% CO2.

extract_protocol:
After knock-down cells were collected in TRIzol (Life Technologies), RNA purified and DNaseI treated with Direct-zol RNA Purification Kit (Zymo) and sent to sequencing facility for library construction and sequencing.
TruSeq RNA library kit (Illumina).

treatment_protocol: Knock-down experiment performed with NTC (non-targeting control) or siRNA targeting HMGB1 mRNA with RNAiMAX (Invitrogen) for 72h.

tag: isolate

tag: sirna

value: Non-targeting control (NTC)


title: HMGB1_KD_rep2

value: siHMGB1 knock-down


title: IMR90_HMGB1_pro_Input_rep1


title: Sen_rep2_rna


title: Pro_rep1_rpf

description:
rRNA
DatasetEV5_RiboSeq.xlsx


title: HMGB1_KD_rep1


title: Control_rep1


title: IMR90_HMGB1_pro_ChIP_rep1


title: H18673-L1_S30_L003

city: Kiel

first: Joana

middle: Pimenta

last: Bernardes

address: Am Botanischen Garten 11

department: Systems Immunology

institute: Institute of Clinical Molecular Biology

data_processing:
Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter and quality trimming (Trim Galore!)
Removal of ribosomal RNA (SortMeRNA)
Alignment using  STAR
Sort and index alignments (SAMtools)
Duplicate read marking (picard MarkDuplicates)
Transcript assembly and quantification (StringTie)
Create bigWig coverage files (BEDTools, bedGraphToBigWig)
Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts for individual samples
Supplementary_files_format_and_content: Metadata including Sample ID, demographics, histology and clinical information

source_name: biopsy

extract_protocol:
Whole blood and sigmoid mucosal biopsy samples (collected from the most inflamed region within 30 cm of colon sigmoideum) were collected as a longitudinal dataset from which the RNA for transcriptome analyses was isolated.
Whole RNA libraries were prepared using TruSeq RNA Library Prep technology and samples were sequenced using HiSeq 4000 (2x75bp).

treatment_protocol: 600 mg of olamkicept were administered by intravenous infusion every 2 weeks for 12 weeks (i.e. 7 infusions).

value: biopsy

tag: diagnosis

value: CD

tag: response

value: NoResp

tag: remission

value: NR

tag: patient

tag: timepoint

tag: location


title: H18671-L1_S28_L003

tag: tissue

value: UC


title: H18672-L1_S29_L003


title: H18668-L1_S19_L002


title: H18667-L1_S18_L002

value: Resp


title: H18662-L1_S13_L002


title: H18664-L1_S15_L002


title: H18661-L1_S12_L002


title: H18666-L1_S17_L002

value: R


title: H18659-L1_S10_L001


title: H18665-L1_S16_L002


title: H18663-L1_S14_L002


title: H18657-L1_S8_L001


title: H18669-L1_S20_L002


title: SF-35_ICM_GSCN176

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

country: France

institute: INRAE

data_processing:
The cDNA sequence database for Bos taurus was obtained from Ensembl genome browser (release-98101; Bos_taurus.ARS-UCD1.2.cdna.all.fa) and used to build a reference index for the bovine transcriptome.
RNA-Seq reads were pseudo-aligned to the reference index with Salmon (Release 1.1.0).
Gene-level counts were prepared for differential expression analysis with tximport (release 1.14.2) as part of the Bioconductor package.
Differential expression was measured using DESeq2 (release 1.26.0) with default parameters as part of the Bioconductor package.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content:
GSCN*.quant.sf is the quantification file output of Salmon (quasi-mapping and transcript quantification tool for RNA-seq data). This is a plain text, tab-separated file. The columns have the following interpretation:
Name: the name of the target transcript.
Length: the length of the target transcript in nucleotides.
EffectiveLength: the computed effective length of the target transcript.
TPM: salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). TPM is the recommended relative abundance measure to use for downstream analysis.
NumReads: Salmon's estimate of the number of reads mapping to each transcript that was quantified. It is an estimate insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely mapping and multi-mapping reads and the relative abundance estimates for each transcript.

organism: Bos taurus

source_name: embryo

extract_protocol:
Total RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems, Life Technologies), according to the manufacturer’s instructions
Full length cDNA were generated from 300 pg of total RNA  using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.

treatment_protocol: The inner cell mass are dissected from the blastocyst by a mixed procedure including both immunosurgery and manual cutting to remove trophoblastic cells

tag: developmental satge

value: day-7 blastocyst

tag: sample type

value: inner cell mass

tag: treatment

value: serum-free conditions of IVM, IVF and IVD


title: H18656-L1_S7_L001


title: H18655-L1_S6_L001


title: H18658-L1_S9_L001


title: H18654-L1_S5_L001


title: SC-33_ICM_GSCN174

value: serum-supplementation of IVM, IVF and IVP


title: H18653-L1_S4_L001


title: SF-PGE2-15_ICM_GSCN156

value: serum-free conditions + PGE2 supplementation of IVM, IVF and IVD


title: SF-13_ICM_GSCN154


title: H18650-L1_S1_L001


title: H18651-L1_S2_L001


title: H18652-L1_S3_L001


title: SF-PGE2-37_ICM_GSCN178


title: SF-PGE2-27_ICM_GSCN168


title: H18649-L1_S80_L008


title: SC-25_ICM_GSCN166


title: H18648-L1_S79_L008


title: SC-23_ICM_GSCN164


title: H18660-L1_S11_L002


title: H18647-L1_S78_L008


title: H18643-L1_S74_L008


title: H18646-L1_S77_L008


title: SF-1_ICM_GSCN142


title: SF-3_ICM_GSCN144


title: H18642-L1_S73_L008


title: H18641-L1_S72_L008


title: H18640-L1_S71_L008


title: Weri-RB1/CRP-shSNHG1#2-3

city: harbin

first: shoubin

last: sun

address: baojian road 157

institute: harbin medical university

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads   containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) [2]. Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12) [4] . The heatmap was drawn by pheatmap (v1.0.8) [5] according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)[6] with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni [7] .
Genome_build: GCF_000001405.39
Supplementary_files_format_and_content: Excel files including FPKM of each sample

source_name: SNHG1-specific shSNHG1#2 were designed to knockdown SNHG1 in Weri-RB1/CRP

growth_protocol: The cells were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS) at 37 °C in the presence of 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: Weri-RB1/CRP-shSNHG1#1 and Weri-RB1/CRP-shSNHG1#2 were designed to knockdown SNHG1 in Weri-RB1/CRP.Weri-RB1/CRP-shNC was control.

value: carboplatin resistance retinoblastoma cell line


title: Weri-RB1/CRP-shSNHG1#2-2


title: Weri-RB1/CRP-shSNHG1#2-1


title: Weri-RB1/CRP-shSNHG1#1-3

source_name: SNHG1-specific shSNHG1#1 were designed to knockdown SNHG1 in Weri-RB1/CRP


title: H18639-L1_S70_L007


title: Weri-RB1/CRP-shNC-3

source_name: SNHG1-specific shNC were designed in Weri-RB1/CRP


title: H18637-L1_S68_L007


title: Weri-RB1/CRP-shNC-2


title: 154-rep2

first: James

last: Locke

address: Bateman street

country: United Kingdom

institute: SLCU

data_processing:
The raw reads were analysed using a combination of publicly available software and in-house scripts. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the Bacillus subtilis PY79 transcriptome using Salmon (Patro et al. 2017). Read counts for each gene were imported using the tximport R package (Soneson et al. 2015).
Genome_build: Bacillus subtilis PY79
Supplementary_files_format_and_content: counts

organism: Bacillus subtilis PY79

growth_protocol: Overnight cultures were prepared as for snap shot or movie experiments. Briefly, cultures were started from frozen stock in SMM and grown overnight at 30°C to an OD between 0.3 and 0.8. The overnight cultures were resuspended to an OD of 0.01 and regrown to an OD of 0.1 at 37°C.

extract_protocol:
10 ml of B. subtilis at OD 0.1-0.2 were centrifuged in 15 ml falcon tubes for 10 min at 4000 rpm. Cell pellets were resuspended in 1 ml of Qiagen RNAprotect Bacteria Reagent, and flash frozen in liquid nitrogen.     Defrosted cells were pelleted by a quick centrifugation. After removing the supernatant, cells were resuspended in 1 ml buffer RLT from Qiagen RNeasy kit. Resuspended cells were transferred in a Fastprep Lysing Matrix B tube (MP Bio) and processed in Fastprep apparatus 45 seconds at speed 6.5M/s. 700 µl of the supernatant, containing lysed cells, was transferred to a new microcentrifuge tube, to which 500 µl of absolute ethanol was added. After vortexing, the lysate was transferred to a RNeasy spin column and centrifuged 15 seconds at > 10000 rpm. RNA purification was then carried out following the instructions of the Quiagen RNeasy kit. RNA quality and integrity were assessed on the Agilent 2200 TapeStation, and RNA concentration was assessed using Qubit RNA HS assay kit.
Library preparation was performed using ScriptSeq™ Complete Kit (Illumina, BB1224), for 2 µg of high integrity total RNA (RIN>8). The libraries were sequenced on a NextSeq500 using paired-end sequencing of 75 bp in length.

treatment_protocol: Once the cultures had reached an OD of 0.1, they were split into aliquots of 10 ml to which either 0 µg/ml or 1 µg/ml lysozyme from hen eggs white (Sigma Aldrich, St. Louis, MO, USA) were added. The aliquots were then incubated at 37°C for 30 min before snap freezing them.

tag: genotype

value: No lysosyme treatment

tag: replicate


title: Weri-RB1/CRP-shNC-1

tag: cell line


title: 154-rep1


title: H18636-L1_S67_L007


title: SF-PGE2-5_ICM_GSCN146


title: 154-lysosyme-rep2

value: Lysosyme treatment (1 microg/ml lysozyme for 30min)


title: H18635-L1_S66_L007


title: 154-lysosyme-rep1


title: H18634-L1_S65_L007


title: 130-rep2


title: Weri-RB1/CRP-shSNHG1#1-2


title: H18632-L1_S63_L007


title: H18633-L1_S64_L007


title: H17537-L1_S44_L006

source_name: blood

value: blood


title: H17540-L1_S47_L006


title: H17539-L1_S46_L006


title: 130-lysosyme-rep2


title: H17541-L1_S48_L006


title: H17536-L1_S43_L006


title: H18638-L1_S69_L007


title: Weri-RB1/CRP-shSNHG1#1-1


title: H17535-L1_S42_L006


title: H18629-L1_S60_L006


title: H17534-L1_S41_L005


title: 130-lysosyme-rep1


title: H18628-L1_S59_L006


title: H17533-L1_S40_L005


title: H17532-L1_S39_L005


title: H18627-L1_S58_L006


title: H17531-L1_S38_L005


title: 130-rep1


title: H17538-L1_S45_L006


title: H17528-L1_S35_L005


title: H18626-L1_S57_L006


title: H17526-L1_S33_L005


title: H17524-L1_S31_L004


title: H18625-L1_S56_L006


title: LAIR-1- ILC2s 8-GH191105

city: Los Angeles

first: Georges Doumet

last: HELOU

state: California

address: 1450 Biggy St, NRT5505, Keck School of Medicine

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: WT LAIR-1- aILC2s

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M16 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M. Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10

source_name: Lungs

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted ILC2s after three intranasal administrations of rmIL-33 (0.5 μg per mouse), defined in this study as IL-33-activated ILC2s (aILC2s), were incubated with rmIL-2 (10 ng mL−1) and rmIL-7 (10 ng mL−1)  for 24 hours (5x104 mL−1).

tag: strain

value: 8 weeks

tag: genotype/variation

value: WT


title: LAIR-1- ILC2s 7-GH191105

description: WT LAIR-1- aILC2s

tag: age


title: H17525-L1_S32_L004

value: CD


title: H18624-L1_S55_L006

value: biopsy

value: NoResp


title: LAIR-1- ILC2s 10-GH191105

description: WT LAIR-1- aILC2s


title: H17520-L1_S27_L004

value: NR


title: LAIR-1+ ILC2s 3-GH191105

description: WT LAIR-1+ aILC2s


title: H17522-L1_S29_L004


title: H17527-L1_S34_L005


title: LAIR-1+ ILC2s 1-GH191105

description: WT LAIR-1+ aILC2s


title: H18623-L1_S54_L006

value: UC

value: Resp


title: LAIR-1+ ILC2s 2-GH191105

description: WT LAIR-1+ aILC2s


title: H17519-L1_S26_L004


title: H17521-L1_S28_L004


title: H18621-L1_S52_L006

value: R


title: H17529-L1_S36_L005


title: H17518-L1_S25_L004


title: H18622-L1_S53_L006


title: LAIR-1 KO -15

description: LAIR-1 KO aILC2s

value: LAIR-1 KO


title: LAIR-1 KO -14

description: LAIR-1 KO aILC2s


title: H17517-L1_S24_L003


title: H17514-L1_S21_L003


title: H17515-L1_S22_L003


title: H17513-L1_S20_L003


title: genomic DNA from DPSCs

type: genomic

city: Guangzhou

first: Tingting

last: Ai

address: 56# Lingyuan West Road

institute: Sun Yat-sen University School and Hospital of Stomatology

description:
SAMPLE 1
healthy young people

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio™ methylation module software (2010.3) according to manufacturer's user guide

label: Cy3, Cy5

source_name: stem cells from dental pulp

label_protocol: Standard Illumina Protocol

growth_protocol: After the isolation, suspension and seeding of human DFPCs, PDLSCs and DPSCs from corresponding tissues of each donor, all three primary culture cell types were subjected to morphological identification and characterization. Then PDLSCs, DFPCs and DPSCs were seeded separately in culture plates separately at a cell density of 5×10^4 cells/ml, and supplemented with a-MEM with 10% FBS.

extract_protocol: genomic DNA was extracted and purified from each stem cell type using QIAamp DNA mini kit according to standard instructions

tag: gender

value: 2 female and 2 male

value: dental pulp

tag: tooth site

value: premolar

tag: passage


title: H18617-L1_S49_L005

tag: diagnosis

tag: response

tag: remission


title: WT B6 -11

description: WT aILC2s


title: H17508-L1_S15_L002

tag: patient

tag: timepoint

tag: location


title: H18620-L1_S51_L006

tag: tissue


title: H18618-L1_S50_L005


title: WT B6 -9

description: WT aILC2s


title: WT B6 -10

description: WT aILC2s


title: H17510-L1_S17_L003


title: H17511-L1_S18_L003


title: H18615-L1_S47_L005


title: H17505-L1_S12_L002


title: H17506-L1_S13_L002


title: H17512-L1_S19_L003


title: H17504-L1_S11_L002


title: H17501-L1_S8_L001


title: H17500-L1_S7_L001


title: genomic DNA from DFPCs

description:
SAMPLE 2
healthy young people

source_name: stem cells from dental follicles

value: dental follicles

value: third molar


title: genomic DNA from PDLSCs

description:
SAMPLE 3
healthy young people

source_name: stem cells from periodontal ligament

value: periodontal ligament


title: H18614-L1_S46_L005


title: H18616-L1_S48_L005


title: LAIR-1 KO -13

description: LAIR-1 KO aILC2s


title: PMN from spleen of tumor burden mice, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
cellranger v3.1.0 was executed with refdata-cellranger-mm10-3.0.0 transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: standard cellranger output

source_name: polymorphonuclear neutrophils

extract_protocol:
FACS sorted PMNs were processed according to 10x genomics protocol
Single cell libraries were prepared with isolated PBMCs using Chromium Single Cell 3’ v2 Reagent Kits
10x genomics single cell RNA-seq

value: spleen

tag: mouse

value: tumor burden


title: PMN from tumor of tumor burden mice, replicate 3

value: tumor


title: H18613-L1_S45_L005


title: H17507-L1_S14_L002

value: blood

value: CD


title: H17503-L1_S10_L002

value: NoResp


title: PMN from spleen of naïve mice, replicate 3

value: naive


title: H18612-L1_S44_L005

value: biopsy

value: NR


title: H17498-L1_S5_L001


title: H17497-L1_S4_L001


title: H17495-L1_S2_L001

value: UC

value: Resp

value: R


title: H18608-L1_S40_L004


title: H18609-L1_S41_L005


title: H17493-L1_S60_L008


title: H17492-L1_S59_L008


title: H17494-L1_S1_L001


title: PMN from tumor of tumor burden mice


title: H18606-L1_S38_L004


title: PMN from tumor of tumor burden mice, replicate 2


title: PMN from spleen of tumor burden mice, replicate 2


title: H18605-L1_S37_L004


title: PMN from spleen of naïve mice, replicate 2


title: H17490-L1_S57_L008


title: H18604-L1_S36_L004


title: H17485-L1_S52_L007


title: H17484-L1_S51_L007


title: H17486-L1_S53_L008


title: H18603-L1_S35_L004


title: H17483-L1_S50_L007


title: PMN from spleen of naïve mice


title: PMN from spleen of tumor burden mice


title: H17491-L1_S58_L008


title: H17488-L1_S55_L008


title: H17499-L1_S6_L001


title: H17487-L1_S54_L008


title: H18602-L1_S34_L004


title: Nas2Del_WT_1026

city: Brisbane

first: David

last: Simmons

state: Queensland

address: The Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

description: Paired-end bulk RNA-seq of NasDel wild type

data_processing:
Illumina Casava1.7 software used for basecalling.
Quantifying the samples using salmon software v1.2.0
Obtaining a transcriptome and building an index using salmon software v1.2.0
Importing the quantification data to R using tximport (Soneson, Love, and Robinson 2015)
Standard differential expression analysis steps was done with the single function DESeq in R
Results tables are generated using log2 fold change and Wald test p value on normalized counts
Supplementary_files_format_and_content: quant.sf salmon file

source_name: Forebrain

extract_protocol:
The whole forebrain was removed and flash frozen on dry ice. RNA was extracted using Qiagen RNeasy miniprep kit. Sample quality was confirmed using a Nanodrop and QC analysis was performed using a bioanalyzer to obtain RIN values.  Samples with appropriate RIN values were then chosen such that we had three independent triplicate samples for Nas2Del+/- Het and wild type.
RNA-seq libraries were prepared for sequencing using TruSeq strandard total RNA kit from illumina. The library pool was diluted and denatured according to the standard NextSeq protocol (Document # 15048776 v02).
Sequencing was performed using the Illumina NextSeq500 (NextSeq control software v2.1.0 / Real Time Analysis v2.4.11) to generate paired-end 76 bp reads using a 150 cycle NextSeq500/550 High Output reagent Kit v2 (illumina, FC-404-2002). Sequencing was performed at the Institute for Molecular Bioscience Sequencing Facility (University of Queensland).

value: Whole forebrain

value: Postnatal Day 20

tag: genotype

value: wild type


title: H17480-L1_S47_L007


title: Nas2Del_WT_1018


title: H17479-L1_S46_L007


title: H17478-L1_S45_L007


title: Nas2Del_WT_1016


title: H17473-L1_S40_L006


title: H18597-L1_S29_L003


title: H18598-L1_S30_L003


title: H17477-L1_S44_L006


title: H17471-L1_S38_L006


title: Nas2Del_Het_1027

description: Paired-end bulk RNA-seq of NasDel+/- Het

value: Nas2Del +/- Het


title: H17474-L1_S41_L006


title: H17472-L1_S39_L006


title: H17476-L1_S43_L006


title: H17470-L1_S37_L006


title: H18601-L1_S33_L004


title: Nas2Del_Het_1024


title: H18595-L1_S27_L003


title: H17467-L1_S34_L005


title: H18596-L1_S28_L003


title: H17466-L1_S33_L005


title: P_S1: HaCaT

city: Birmingham

first: Kasturi

last: Mitra

state: Alabama

address: University of Alabama, Birmingham

department: Genetics

institute: University of Alabama, Birmingham

data_processing:
Count matrix files were generated using 10x genomics cellranger (v.4.0) using hg38 as reference.
The matrix files where analyzed using Seurat package (v3.9.9).
Filter the data using nFeature_RNA > 2000 and the data is integrated using IntegrateData function of Seurat.
The clustering of the data were performed using 20 dimensions with resolution varied from 0.1-0.8.
The final seurat objects are saved using saveRDS function in R.
Genome_build: hg38
Supplementary_files_format_and_content: Seurat objects save using saveRDS function in R.

source_name: Parental HaCaT

growth_protocol: Parental, knockdown and transformed cells were grown in standard growth conditions in DMEM with 10% FBS.

extract_protocol:
Trypsinized single cells were washed in PBS (without ca++ or Mg++) with 0.04% BSA and tested for >90% viability. Single cell analysis was performed on a 10xGenomics platform according to 3’ v3.1 NextGem Dual Index manual.
The 3’-biased cDNA libraries were constructed through the following steps: cDNA fragmentation, end repair & A-tailing, and size selection by SPRIselect beads, adaptor ligation, and sample index PCR amplification, and then SPRIselect beads size selection again. The final constructed 3’-biased single cell libraries were sequenced by Illumina Nextseq500 machine, targeting total reads per cell for 20,000 at minimum, and the sequencing cycles consisted of 28bp for read 1, 90 bp for read 2, and 10 bp for i7 index, and 10bp for i5 index.

treatment_protocol: Stable transformed lines were derived with TCDD treatment and stable knckdown lines were selected with puromycin treatment

tag: cell type

value: Keratinocyte

value: HaCaT

tag: transformation status

value: Not transformed

tag: shRNA expression


title: H18594-L1_S26_L003


title: H17465-L1_S32_L005


title: H17464-L1_S31_L005


title: NT_S5: NT HaCaT

source_name: Control-knockdownParental HaCaT

tag: cell line

value: Control-knockdown


title: H17462-L1_S29_L005

value: blood


title: H18593-L1_S25_L003


title: 99_S5: Drp1-kd(s) HaCaT

source_name: Strong Drp1-knockdownParental HaCaT

value: Strong Drp1-knockdown


title: H18591-L1_S23_L003


title: H17461-L1_S28_L004

value: NoResp


title: Nas2Del_Het_1025

tag: age

tag: strain


title: 97_S4: Drp1-kd(w) HaCaT

source_name: Weak Drp1-knockdownParental HaCaT

value: Weak Drp1-knockdown


title: H17460-L1_S27_L004


title: H17459-L1_S26_L004


title: H17456-L1_S23_L004


title: H18590-L1_S22_L003

value: biopsy

value: CD


title: H17458-L1_S25_L004

value: UC

value: NR


title: H18589-L1_S21_L003

value: Resp


title: H17454-L1_S21_L004


title: H17453-L1_S20_L003


title: 1_S2: TF-1 HaCaT

source_name: TCDD-1 nM Transformed HaCaT

value: TCDD Transfomed


title: H17455-L1_S22_L004


title: H17449-L1_S16_L003


title: fve-4_siRNA_seq

first: Pei

last: Huang

address: Fenglin Road 300

institute: Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai

data_processing:
For sequencing data of sRNAs, adapters were trimmed using cutadapt (v1.16), low-quality tags were trimmed by Trimmomatic(version 0.36) (Bolger et al., 2014), and reads longer than 15-nt were retained for further analyses.
The trimmed siRNA reads were mapped to the Arabidopsis genome (TAIR10) using ShortStack (v3.8.5)  with either the multi-mapping mode (--mmap f) or the no-multi-mapping, none mode (--mmap n). A custom script was then used to retain only perfectly matching reads and reads with a single mismatch at their 3′ terminus.
The siRNA reads passing this custom filter were then used to call siRNA clusters using ShortStack with the --mincov 20, pad 100, --dicermin 21, and --dicermax 24 options.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files that represent the normalized number of reads at each position in genome

source_name: Seedlings

growth_protocol: Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose.

extract_protocol: Genomic small RNA samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, CAS (Shanghai, China) for library construction and Illumina sequencing.

value: fve-4 mutant

value: Seedlings


title: H17450-L1_S17_L003


title: H18586-L1_S18_L002

source_name: biopsy


title: H17448-L1_S15_L003


title: Col-0_siRNA_seq

value: wild type


title: H18587-L1_S19_L002


title: H18585-L1_S17_L002


title: H17446-L1_S13_L003


title: H17447-L1_S14_L003


title: H18584-L1_S16_L002


title: H17443-L1_S10_L002


title: 10_S3: TF-10 HaCaT

source_name: TCDD-10 nM Transformed HaCaT

value: Keratinocyte


title: H18588-L1_S20_L002


title: H18581-L1_S13_L002

value: R


title: H17452-L1_S19_L003


title: Input

data_processing:
Adapter and 3’-end of reads with sufficiently low quality scores (q<20) were trimmed, and clean reads that were shorter than 45 nt were discarded.
Clean paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with Bowtie2 (version 2.3.4.1) with default parameters (Langmead and Salzberg, 2012)
Samtools (Li et al., 2009) was used to remove potential PCR duplicates; only uniquely aligned reads were retained for the downstream analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files that represent the number  of reads at each position in genome normalized to the average base-pair count number

extract_protocol: ChIP samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, CAS (Shanghai, China) for library construction and Illumina sequencing.

tag: antibody

value: FLAG

tag: background

value: Col-0 WT

value: seedlings


title: FVE_ChIPSeq_Rep2

value: fve-4 backgroud


title: H17441-L1_S8_L002

value: blood

tag: diagnosis

value: NoResp


title: H17439-L1_S6_L002

tag: response


title: H17440-L1_S7_L002

tag: remission


title: BMDMs polarized with IL4 (total mRNA) replicate 3

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA sequencing reads were aligned to mm10 using HISAT2 (D. Kim, B. Langmead, S. L. Salzberg, HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360 (2015)) and reads mapping to multiple locations in the genome were discarded.
Gene expression was quantified as described using default settings (D. Ramskold, E. T. Wang, C. B. Burge, R. Sandberg, An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5, e1000598 (2009).) and RefSeq gene definitions (N. R. Coordinators, Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46, D8-D13 (2018).).
Only genes with <6 missing data points were included.
Raw counts were TMM normalized (M. D. Robinson, A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 (2010)) and log2 transformed using Voom (M. E. Ritchie et al., limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).) in R 3.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RNA sequencing counts and TMM-log2 normalized data

source_name: BMDM

growth_protocol: Bone marrow was extracted from naïve female FVB mice, differentiated into bone marrow-derived macrophages (BMDMs) as previously described (M. Wallerius et al., Cancer Res 76, 3166-3178 (2016).)

extract_protocol:
Polysome-profiling was performed  using polarized BMDMs. A fraction (~10%) of the obtained cell population was lysed in TRIzol reagent (ThermoFisher Scientific) and used for RNA sequencing with total RNA as input. Remaining cells were lysed in a hypotonic lysis buffer, as described and and lysates were  applied onto a 5%-50% (w/v) sucrose gradient, fractionated, and fractions corresponding to mRNA associated more than 3 ribosomes were collected in TRIzol reagent for subsequent RNA extraction. Such pooled samples were used for RNA sequencing of efficiently translated polysome-associated mRNA.
SmartSeq2 sequencing libraries were prepared

treatment_protocol: BMDMs were polarized with  IFNG (200 units/mL, Peprotech) or IL4 (40 ng/mL, Peprotech) for 4h.

value: Polarized BMDMs

tag: rna source

value: total mRNA

tag: polarization

tag: replicate


title: H18579-L1_S11_L002

tag: tissue

value: biopsy

value: CD

tag: patient

tag: timepoint

tag: location


title: b16_mac_cKO_rep4

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
For single cell RNAseq, 10X Genomics single cell RNA-seq data were aligned and quantified using the Cell Ranger Single-Cell Software Suit (version 3.0.2) against the mm10 reference genome.
For bulk RNAseq, The adaptor sequences were first trimmed from sequencing reads by using Trim Galore! with parameters --clip_R1 3, the remaining parameters default. Trimmed reads mapped to ribosomal RNA were removed using Bowtie2 (version 2.3.5). All remaining reads were mapped to the mouse genome mm9 using STAR (version 2.7.0f). Uniquely mapped reads were selected using SAMtools (version 1.9) with mapping quality ≥ 20.
For m6Aseq, Raw sequencing reads were trimmed by TrimGalore! with adjusting the parameter --clip_R1 3. Remaining trimmed reads were aligned to the mouse genome mm9 by STAR (version 2.7.0f). Uniquely mapped reads were selected using SAMtools (version 1.9) with mapping quality ≥ 20. The m6A-enriched regions (peaks) in each sample were detected by exomePeak R package (version2.16.0) with default paramters.
Genome_build: mm9

source_name: tumor infiltrating macrophage

extract_protocol:
For RNA seq, total RNA was extracted using Trizol. For m6A seq, total RNA in macrophage was extracted using Trizol and polyadenylated RNA was purified using the Dynabeads mRNA Purification Kit (Invitrogen). Fragment the RNAs into ~100-nucleotide-long fragments by 10X Fragmentation Reagent(Invitrogen) at 94℃ for 45s and stop it using the 10X Stop Solution(Invitrogen). EpiMark N6-methyladenosine enrichment kit (NEB E1610S) was used for m6A immunoprecipitation (m6A-IP) to enrich the m6A marked RNAs followed by RNA extraction by Trizol.
For RNA seq and m6A seq, the library construction was performed with SMARTer Stranded Total RNA-Seq Kit (Takara). For single cell RNA seq, the library was performed using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1(1000128) purchased from 10X Genomics according to the protocols provided by manufactures.

tag: technology

value: bulk RNA sequencing

tag: tumor type

tag: day

tag: genotype

value: Mettl14 cKO


title: BMDMs polarized with INFG (Polysome-associated mRNA) replicate 3

tag: cell type

value: Polysome-associated mRNA

value: INFG


title: b16_mac_cKO_rep3


title: BMDMs polarized with INFG (total mRNA) replicate 3


title: H18578-L1_S10_L001

value: Resp

value: NR


title: b16_mac_cKO_rep2


title: H17445-L1_S12_L002

source_name: blood

value: UC


title: H18576-L1_S8_L001


title: b16_mac_cKO_rep1


title: BMDMs polarized with IL4 (Polysome-associated mRNA) replicate 2


title: b16_mac_WT_rep2

value: wild-type


title: H18575-L1_S7_L001

value: R


title: FVE_ChIPSeq_Rep1

tag: antibody

value: FLAG

value: seedlings


title: H17442-L1_S9_L002

value: blood


title: b16_mac_WT_rep1