title: S-M001

status: Public on Feb 04 2021

first: Zemin

last: Zhang

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center

data_processing:
The libraries were sequenced using either DIPSEQ, BGISEQ or Illumina platforms.
Single-cell sequencing data were aligned and quantified using kallisto/bustools (KB, v0.24.4) . Unique molecular identifier (UMI) count matrices were imported into python (version 3.7.6) and were processed with python package Scanpy  (version 1.4.6).
Quality control was applied to cells based on three metrics step by step, including the total UMI counts, number of detected genes and proportion of mitochondrial gene counts per cell. Specifically, cells with less than 1000 UMI counts and 500 detected genes were filtered, as well as cells with more than 10% mitochondrial gene counts. To remove potential doublets, for PBMC samples, cells with UMI counts above 25,000 and detected genes above 5,000 are filtered out. For other tissues, cells with UMI counts above 70,000 and detected genes above 7,500 are filtered out. Additionally, we removed the potential doublets predicted by Scrublet (version 0.2.1), filtering cells with doubletScore > 0.25 as potential doublet.
We normalized the UMI counts with the deconvolution strategy implemented in the R package scran. Specifically, cell-specific size factors were computed by computeSumFactors function, and  were further used to scale the counts in each cell. Then the normalized data were logarithmized.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI count for each cell in mtx format and cell barcodes/genes in txt format

source_name: PBMC

extract_protocol: Cell suspensions were barcoded through the 10x Chromium Single Cell platform using Chromium Single Cell 5′ Library, Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10x Genomics). The loaded cell numbers range from 300-500,000 aiming for 300-14,000 single cells per reaction. Single-cell RNA libraries were prepared according to the manufacturer’s instructions using the Chromium Single Cell 3′ v2 Reagent (10x Genomics; PN-120237, PN-120236 and PN-120262), Chromium Single Cell 3′ v3 Reagent (10x Genomics; PN-1000075, PN-1000073 and PN-120262) and the Chromium Single Cell 5′ v2 Reagent (10x Genomics, 120237). Each sequencing library was generated with a unique sample index. The libraries were sequenced using either DIPSEQ, BGISEQ or Illumina platforms.

tag: patient

tag: datasets

tag: city

value: Zhuhai

value: M

tag: sample type

value: frozen PBMC

tag: covid-19 severity

value: mild/moderate

tag: sample time

value: convalescence

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

tag: outcome

value: discharged

tag: comorbidities

tag: covid-19-related medication and anti-microbials

value: Moxifloxacin, Ambroxol Hydrochloride

tag: leukocytes [g/l]

tag: neutrophils [g/l]

tag: lymphocytes [g/l]

tag: unpublished


title: S-HC020-1

type: SRA

city: Beijing

country: China

institute: Peking University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: PBMC-B

tag: patient

value: Wuhan

tag: age

tag: Sex

value: CD19+ B cell sorted from fresh PBMC (FACS)

value: control

value: negative

value: No


title: S-HC020-2

source_name: PBMC-T

tag: datasets

tag: city

tag: sample type

value: CD3+ T cell sorted from fresh PBMC (FACS)


title: S-HC024

value: Huanggang

value: fresh PBMC

tag: covid-19 severity

tag: sample time

tag: sampling day (days after symptom onset)


title: S-HC022

tag: single cell sequencing platform_id

tag: bcr single cell sequencing

tag: tcr single cell sequencing


title: S-HC025

tag: outcome

tag: comorbidities

tag: covid-19-related medication and anti-microbials


title: WT rep 2

status: Public on Feb 09 2021

city: Marseille

first: Antoine

last: de Chevigny

address: Campus de Luminy

country: France

institute: INMED INSERM U1249

description: 1 female mouse

data_processing:
Base-calling: Base calling was performed on the Illumina analysis platform Basespace Onsite using the Generate FASTQ application with default parameters
Trimming: Raw fastq reads were trimmed using sickle v1.33 (Joshin et al., 2011) with parameters –l 25 –q 20
Alignment: Trimmed fastq reads were aligned to mm10 using STAR v2.5.3a (Dobin et al., 2013) to produce BAM alignment files. Multi-mapped reads and reads with more than 0.08 mismatches per pair relative to read length were discarded
Transcriptome assembly: For each samples transcriptome assembly were performed with Cufflinks v2.2.1 (Trapnell C. et al 2010)  using the relative UCSC mm10 GTF file. The output GTF files from each of the Cufflinks analysis and the GTF annotation file were sent to Cuffmerge v2.2.1 (Trapnell C. et al 2010) to amalgamate them into a single unified transcript catalog
Gene counts: Gene counts were calculated with featureCounts v1.4.6-p4 (Liao Y et al., 2014) from a GTF containing known UCSC mm10 genes as well as the novel genes detected by Cufflinks (Cufflinks class code “u”) and alignment files.
Differential gene expression analysis: The R package DESeq2 v1.14.1 (Love MI et al., 2014) was then used to normalize counts and detect the differentially expressed genes (FDR < 0.05). Batch effect between replicates (1,2 and4) was added in the design formula of DESeqDataSetFromMatrix function to model it in the regression step and subtract it in the differential expression test.
Isoform expression analysis: Transcripts expression in fragments per kilobase of exon per million reads mapped (FPKM) were estimated and normalized with Cuffdiff v2.2.1 (Trapnell C. et al 2010) with default parameters from Cuffmerge GTF file result and alignment files
Genome_build: mm10
Supplementary_files_format_and_content: DEseq2 results table for the comparisons WT vs KO in txt format with gene names as rownames and the following columns: DESeq2_log2FoldChange, DESeq2_pvalue, DESeq2_padj (p value adjusted for multiple testing with Benjamini-Hochberg method) , WT_1 WT_3 WT_4 KO_1 KO_3 KO_4 the log2(normalised counts) for each sample; feaureCounts results table with raw counts on known and novel genes per samples

molecule: polyA RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Total RNA was purified using spin columns of the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
Library preparation was made with the TruSeq mRNA-seq Stranded v2 Kit sample preparation (Illumina) according to manufacturer’s instructions. One µg total RNA was used for poly(A)-selection and Elution-Fragmentation incubation time  was 8 min to obtain 120-210 bp fragments. Each library was barcoded using TruSeq Single Index (Illumina). After library preparation, Agencourt AMPure XP (Beckman Coulter, Inc.) was performed for 200 to 400 bp libraries size-selection (282 nt average final library size). Each library was examined on the Bioanalyzer with High Sensitivity DNA chip (Agilent), quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies), diluted to 4 nM and then pulled together at equimolar ratio.

tag: background strain

value: mixed C57BL/6 and Sv129/Sv

tag: tissue

value: motor plus somatosensory cortex

value: Post natal day 28

tag: genotype

value: wild type

value: female


title: WT rep 3

description: 1 male mouse

tag: age

value: male


title: KO rep 2

description: 1 female mouse

value: Neurod2 -/-

tag: Sex


title: KO rep 1

description: 1 male mouse


title: S-HC023

tag: patient

tag: datasets

value: M

value: Yes

tag: leukocytes [g/l]

tag: neutrophils [g/l]

tag: lymphocytes [g/l]

tag: unpublished


title: S-HC019-1

tag: city

value: Wuhan

tag: sample type

tag: covid-19 severity

tag: sample time

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id


title: WT rep 1

description: 4 mice (3males and 1 female)

tag: background strain

value: mixed


title: S-HC018-1

value: CD19+ B cell sorted from fresh PBMC (FACS)

value: control

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

tag: comorbidities

tag: covid-19-related medication and anti-microbials


title: S-HC019-2

tag: patient

tag: datasets

tag: age

tag: Sex

value: negative

value: No


title: S-HC017

value: F

value: frozen PBMC

tag: leukocytes [g/l]

tag: neutrophils [g/l]

tag: lymphocytes [g/l]

tag: unpublished


title: S-HC021

tag: city

value: Huanggang

tag: sample type

value: fresh PBMC

tag: covid-19 severity

tag: sample time


title: S-HC016

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: bcr single cell sequencing


title: S-HC013

tag: tcr single cell sequencing

tag: outcome

tag: comorbidities


title: S-HC014

tag: patient

tag: datasets

tag: covid-19-related medication and anti-microbials


title: S-HC015

tag: age

tag: Sex

tag: leukocytes [g/l]


title: S-HC009

value: Beijing

tag: neutrophils [g/l]

tag: lymphocytes [g/l]

tag: unpublished


title: WAT, 010_V2

status: Public on Feb 24 2021

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality bases removed, with resulting reads that were less than 25bp removed. Reads were then mapped to hg38.0 whole genome using TopHat, utilising bowtie2, with parameter --library-type fr-firststrand.
Number of reads aligned to each gene in the hg38.0 genome were quantified using HTSeq, using the following paratmers: --stranded=reverse -a 3, and the hg38.0 GTF file from ENSEMBL.
Genome_build: hg38.0
Supplementary_files_format_and_content: tab-delimited text files include the normalized counts per million normalized for library size, grouped by samples of the same BMI subgroup and treatment in a single file.

source_name: White adipose tissue

extract_protocol:
White adipose tissue was exctracted via scalpular incision, snap frozen in liquid nitrogen, and RNA was harvested using the Qiagen RNeasy lipid tissue mini RNA Isolation Kit.
RNA libraries were prepared for sequencing following standard Illumina protocols

treatment_protocol: Indviduals were supplemented with 3g Fish oil (1.1g EPA and 0.8g DHA) or 3g Corn oil/day for 12 weeks.

tag: bmi group

value: Normal weight

tag: tissue

value: White adipose tissue

tag: time point

tag: treatment group

value: Corn oil (3g/day)


title: KO rep 3

description: 1 male mouse

tag: background strain

value: mixed C57BL/6 and Sv129/Sv

value: motor plus somatosensory cortex

value: Post natal day 28

tag: genotype

value: Neurod2 -/-

value: male


title: S-HC008

tag: city

value: M

tag: sample type

tag: covid-19 severity

tag: sample time

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

tag: outcome


title: S-HC007

tag: patient

tag: datasets

value: Shanghai

tag: age

tag: Sex

value: control

value: negative

tag: comorbidities

tag: covid-19-related medication and anti-microbials

tag: leukocytes [g/l]

tag: neutrophils [g/l]

tag: lymphocytes [g/l]


title: S-HC006

tag: city

tag: sample type

tag: unpublished


title: S-HC018-2

value: Wuhan

value: CD3+ T cell sorted from fresh PBMC (FACS)

tag: covid-19 severity

tag: sample time

tag: sampling day (days after symptom onset)

value: No


title: S-HC002

source_name: PBMC-BT

value: Harbin

value: CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS)

tag: single cell sequencing platform_id

tag: bcr single cell sequencing

tag: tcr single cell sequencing


title: S-HC003

tag: patient

tag: datasets

value: Chongqing

value: fresh PBMC

tag: outcome


title: S-HC001

value: Suihua

tag: age

tag: Sex

value: F

tag: comorbidities


title: S-S090-2

value: Shenzhen

value: severe/critical

value: progression

value: positive

value: discharged

tag: covid-19-related medication and anti-microbials

value: Interferon atomization, Ribavirin

tag: leukocytes [g/l]

value: unknown

tag: neutrophils [g/l]


title: S-S090-1

source_name: BALF

tag: city

value: M

tag: sample type

value: fresh BALF

value: Yes

tag: lymphocytes [g/l]


title: S-HC004

tag: covid-19 severity

value: control

tag: sample time

value: negative

tag: unpublished


title: S-HC005

value: Shanghai

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: bcr single cell sequencing


title: S-S088-1

tag: patient

tag: datasets

value: No

tag: tcr single cell sequencing

value: Diabetes

value: Interferon atomization, Ribavirin, Methyl-prednisolone


title: S-S086-2

tag: age

tag: Sex

value: fresh PBMC

tag: outcome

value: deceased

value: Hyperpression


title: S-S087-2

value: Shenzhen

value: severe/critical

value: progression

tag: comorbidities

value: COPD

tag: covid-19-related medication and anti-microbials

tag: leukocytes [g/l]


title: S-S086-1

tag: city

tag: sample type

value: positive

value: Hypertension

value: unknown

tag: neutrophils [g/l]


title: S-S085-2

value: M

tag: covid-19 severity

tag: sample time

value: Yes

value: discharged

value: Interferon atomization, Ribavirin

tag: lymphocytes [g/l]


title: S-S089-2

value: F

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: unpublished


title: S-S089-1

tag: patient

tag: datasets

value: fresh BALF

tag: bcr single cell sequencing


title: S-HC012

value: Beijing

tag: age

tag: Sex

value: fresh PBMC

value: control

value: negative

tag: tcr single cell sequencing


title: S-S088-2

value: Shenzhen

value: severe/critical

tag: outcome

tag: comorbidities

value: Diabetes

tag: covid-19-related medication and anti-microbials

value: Interferon atomization, Ribavirin, Methyl-prednisolone


title: S-HC011

tag: city

tag: sample type

tag: leukocytes [g/l]


title: S-HC010

tag: covid-19 severity

tag: sample time

tag: neutrophils [g/l]


title: S-S082

value: Huanggang

value: convalescence

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

value: bronchial asthma

value: Steroids, antibiotics

tag: lymphocytes [g/l]


title: S-S083

tag: patient

tag: datasets

value: Yes

value: discharged

value: unknown

tag: unpublished


title: S-S080

tag: age

tag: Sex

value: M

tag: bcr single cell sequencing


title: S-S085-1

value: fresh BALF

value: progression

value: No

tag: tcr single cell sequencing

tag: outcome

tag: comorbidities

value: Interferon atomization, Ribavirin


title: S-S084

tag: city

value: F

tag: sample type

value: fresh PBMC

tag: covid-19-related medication and anti-microbials


title: S-S078

tag: covid-19 severity

value: severe/critical

tag: sample time

tag: leukocytes [g/l]


title: S-S087-1

value: Shenzhen

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: deceased

value: Sleep apnea

value: Interferon atomization, Ribavirin, Methyl-prednisolone

tag: neutrophils [g/l]


title: S-S075-1

tag: patient

tag: datasets

value: Wuhan

value: CD19+ B cell sorted from fresh PBMC (FACS)

value: positive

tag: lymphocytes [g/l]


title: S-S075-2

tag: age

tag: Sex

value: CD3+ T cell sorted from fresh PBMC (FACS)

value: discharged

tag: unpublished

value: Yes


title: S-S076-2

value: M

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

value: unknown


title: S-S073-2

tag: city

tag: sample type

value: progression

value: No

tag: comorbidities


title: S-S073-1

tag: covid-19 severity

tag: sample time

tag: covid-19-related medication and anti-microbials


title: S-S072-2

value: Zhuhai

value: frozen PBMC

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Controlled gout

value: Arbidol hydrochloride, Moxifloxacin, Lopinavir/ ritonavir tablet, Chloroquine

tag: leukocytes [g/l]


title: S-S079

tag: patient

tag: datasets

value: Huanggang

value: fresh PBMC

value: severe/critical

value: convalescence

value: Steroids, antibiotics

tag: neutrophils [g/l]


title: S-S071-1

tag: age

tag: Sex

value: positive

value: Controlled hypertension, hyperglycemia, diabetic retinopathy, gout, and renal disfunction

value: Arbidol hydrochloride, Moxifloxacin

tag: lymphocytes [g/l]


title: S-S070-3

value: F

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

value: Moxifloxacin, Lopinavir/ ritonavir tablet, Chloroquine

tag: unpublished


title: S-S077

tag: city

value: M

tag: sample type

value: Yes

tag: outcome

value: Antibiotics

value: unknown


title: S-S069-2

value: Zhuhai

value: frozen PBMC

tag: covid-19 severity

tag: sample time

value: progression

value: No

tag: comorbidities

value: Arbidol hydrochloride, Moxifloxacin, Lopinavir/ ritonavir tablet


title: S-S076-1

value: Wuhan

value: CD19+ B cell sorted from fresh PBMC (FACS)

value: severe/critical

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: covid-19-related medication and anti-microbials


title: S-S068

tag: patient

tag: datasets

value: convalescence

value: positive

value: Oseltamivir

tag: leukocytes [g/l]


title: S-S074-2

tag: age

tag: Sex

value: CD3+ T cell sorted from fresh PBMC (FACS)

value: deceased

tag: neutrophils [g/l]


title: S-S072-3

value: M

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

value: Controlled gout

value: Arbidol hydrochloride, Moxifloxacin, Lopinavir/ ritonavir tablet, Chloroquine

tag: lymphocytes [g/l]


title: S-S074-1

tag: city

tag: sample type

value: unknown

tag: unpublished

value: Yes


title: S-S072-1

value: Zhuhai

value: frozen PBMC

tag: covid-19 severity

tag: sample time

value: progression

tag: outcome


title: S-S070-2

value: F

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: comorbidities

value: Moxifloxacin, Lopinavir/ ritonavir tablet, Chloroquine


title: S-S070-1

tag: patient

tag: datasets

value: severe/critical

tag: covid-19-related medication and anti-microbials


title: S-S071-2

tag: age

tag: Sex

value: positive

value: Controlled hypertension, hyperglycemia, diabetic retinopathy, gout, and renal disfunction

value: Arbidol hydrochloride, Moxifloxacin

tag: leukocytes [g/l]


title: S-S058

value: Wuhan

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: deceased

value: tumor,cerebrovascular disease

value: Arbidol, Lopinavir and Ritonavir Tablets

tag: neutrophils [g/l]


title: S-S063

tag: city

tag: sample type

value: convalescence

value: hypertension,diabetes,coronary heart disease,cerebrovascular disease

tag: lymphocytes [g/l]


title: S-S092

value: Shenzhen

value: M

value: fresh PBMC

tag: covid-19 severity

tag: sample time

value: Yes

value: discharged

value: Bronchitis

value: unknown

tag: unpublished


title: S-S081

value: Huanggang

value: severe/critical

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: outcome

value: hyperthyreosis

value: Steroids, antibiotics


title: S-S056

tag: patient

tag: datasets

value: Beijing

value: F

value: progression

value: positive

tag: comorbidities

value: hypertension

value: Convalescent plasma, Interferon alpha 2 b,  Lopinavir/ ritonavir, steroids, Human immunoglobulin, antibiotics, antifungal


title: S-S091

value: Shenzhen

tag: age

tag: Sex

value: convalescence

value: No

tag: covid-19-related medication and anti-microbials

value: Interferon atomization, Ribavirin


title: S-S055

value: fresh PBMC

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

value: discharged

value: cervical spondylosis

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, steroids, Human immunoglobulin, antibiotics

tag: leukocytes [g/l]


title: S-S069-3

tag: city

value: Zhuhai

tag: sample type

value: frozen PBMC

value: severe/critical

value: Arbidol hydrochloride, Moxifloxacin, Lopinavir/ ritonavir tablet

tag: neutrophils [g/l]


title: S-S069-1

value: F

tag: covid-19 severity

tag: sample time

value: progression

tag: lymphocytes [g/l]


title: S-S066

value: Wuhan

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

value: unknown

value: Oseltamivir, Lopinavir and Ritonavir Tablets

tag: unpublished


title: S-S067

tag: patient

tag: datasets

value: convalescence

tag: outcome

value: HBV

value: Oseltamivir


title: S-S050

value: Beijing

tag: age

tag: Sex

value: M

value: No

value: Yes

tag: comorbidities

value: Cardiovascular diseases

value: Methylprednisolone, Traditional Chinese medicine


title: S-S064

value: frozen PBMC

value: severe/critical

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

value: hypertension,coronary heart disease

tag: covid-19-related medication and anti-microbials


title: S-S065

tag: city

value: Wuhan

value: F

tag: sample type

value: diabetes

tag: leukocytes [g/l]


title: S-S061

tag: covid-19 severity

tag: sample time

value: progression

value: positive

value: hypertension

value: Ribavirin

tag: neutrophils [g/l]


title: S-S062

value: convalescence

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: unknown

value: Oseltamivir, Arbidol, Ribavirin

tag: lymphocytes [g/l]


title: S-S048

tag: patient

tag: datasets

value: Beijing

value: M

value: No

value: Yes

tag: unpublished


title: S-S060

tag: age

tag: Sex

value: frozen PBMC

value: severe/critical

tag: outcome

value: hypertension,diabetes


title: S-S047

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

tag: comorbidities

value: Cardiovascular diseases

value: Methylprednisolone, Antibiotics


title: S-S059

tag: city

value: Wuhan

value: F

tag: sample type

value: progression

value: deceased

tag: covid-19-related medication and anti-microbials

value: Arbidol, Ribavirin


title: S-S045

tag: covid-19 severity

tag: sample time

value: positive

value: Hypertension, Diabetes

tag: leukocytes [g/l]

value: unknown


title: S-S057

value: Beijing

value: M

value: fresh PBMC

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: hypertension, diabetes, prostate cancer

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, steroids, Human immunoglobulin, antibiotics

tag: neutrophils [g/l]


title: S-S037

tag: patient

tag: datasets

value: frozen PBMC

value: severe/critical

value: No

value: Yes

value: Traditional Chinese medicine

tag: lymphocytes [g/l]


title: S-S054

tag: age

tag: Sex

value: discharged

value: diabetes

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, steroids, Human immunoglobulin, antibiotics, antifungal, MSC(mesenchymal stem cell)

tag: unpublished


title: S-S051

value: progression

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

value: Hypertension

value: Methylprednisolone


title: S-S052

tag: city

value: F

tag: sample type

value: positive

value: deceased

tag: comorbidities

value: Methylprednisolone, Traditional Chinese medicine, Antibiotics

value: unknown


title: S-S053

value: Beijing

tag: covid-19 severity

tag: sample time

tag: covid-19-related medication and anti-microbials

value: Traditional Chinese medicine, Antiviral therapy


title: S-S036-2

value: Hefei

value: M

value: frozen PBMC

value: severe/critical

value: convalescence

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: CHD, hypertension

value: Tocilizumab, antibiotics

tag: leukocytes [g/l]


title: S-S036-1

tag: patient

tag: datasets

value: progression

value: No

value: discharged

tag: neutrophils [g/l]


title: S-S043

tag: age

tag: Sex

value: F

value: Yes

value: Hypertension

value: Methylprednisolone, Traditional Chinese medicine

tag: lymphocytes [g/l]


title: S-S041

value: positive

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: Methylprednisolone, Antibiotics

value: unknown

tag: unpublished


title: S-S044

tag: city

value: Beijing

tag: sample type

tag: outcome

value: Cardiovascular diseases

value: Traditional Chinese medicine


title: S-S039

value: frozen PBMC

tag: covid-19 severity

value: severe/critical

tag: sample time

value: deceased

tag: comorbidities

value: Diuretics, hypoglycemic drugs


title: S-S038

value: M

value: progression

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: covid-19-related medication and anti-microbials


title: S-S040

tag: patient

tag: datasets

value: No

tag: leukocytes [g/l]


title: S-S049

tag: age

tag: Sex

value: discharged

tag: neutrophils [g/l]


title: S-S035-2

value: Hefei

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: steatohepatitis

value: Tocilizumab, antibiotics

tag: lymphocytes [g/l]


title: S-S036-3

tag: city

tag: sample type

value: convalescence

value: positive

value: CHD, hypertension

tag: unpublished


title: S-S035-3

tag: covid-19 severity

tag: sample time

tag: outcome


title: S-S035-4

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: comorbidities


title: S-S042

tag: patient

tag: datasets

value: Beijing

value: F

value: Yes

tag: covid-19-related medication and anti-microbials

value: Methylprednisolone, Traditional Chinese medicine

value: unknown


title: S-S034

value: Chongqing

tag: age

tag: Sex

value: frozen PBMC

value: severe/critical

value: rhIFna1b, Lopinavir Ritonavir tablets, Bicyclic alcohol tablets

tag: leukocytes [g/l]


title: S-S032-3

value: M

value: progression

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: rhIFna1b, Lopinavir Ritonavir tablets, Ribavirin effervescent granules, Estazolam tablets, Potassium Chloride Sustained Release Tablets, L-Amlodipine Besylate Tablets, Moxifloxacin Hydrochloride Tablets

tag: neutrophils [g/l]


title: S-S035-1

tag: city

value: Hefei

tag: sample type

value: No

value: discharged

value: steatohepatitis

tag: lymphocytes [g/l]


title: S-S033

tag: covid-19 severity

tag: sample time

value: convalescence

value: positive

value: rhIFna1b, Lopinavir Ritonavir tablets, Estazolam tablets, Potassium Chloride Sustained Release Tablets, Moxifloxacin Hydrochloride Tablets

tag: unpublished


title: S-S032-1

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Yes

tag: outcome


title: S-S046

tag: patient

tag: datasets

value: Beijing

value: deceased

tag: comorbidities

value: Hypertension

value: Methylprednisolone, Antibiotics


title: S-S031

value: Harbin

tag: age

tag: Sex

value: F

value: fresh PBMC

value: severe/critical

tag: covid-19-related medication and anti-microbials

value: Antibiotics, Traditional Chinese medicine

value: unknown


title: S-S032-2

value: Chongqing

value: M

value: frozen PBMC

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: rhIFna1b, Lopinavir Ritonavir tablets, Ribavirin effervescent granules, Estazolam tablets, Potassium Chloride Sustained Release Tablets, L-Amlodipine Besylate Tablets, Moxifloxacin Hydrochloride Tablets

tag: leukocytes [g/l]


title: S-S029

tag: city

tag: sample type

value: convalescence

value: positive

value: discharged

value: Cardiovascular diseases

value: Antibiotics, Glucocorticoid

tag: neutrophils [g/l]


title: S-S024

value: CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS)

tag: covid-19 severity

tag: sample time

value: Yes

value: diabetes

value: Ribavirin, Interferon alfa2b injection, Moxifloxacin, Methylprednisolone Sodium Succinate for Injection, Lopinavir/ ritonavir

tag: lymphocytes [g/l]


title: S-S025

value: Suihua

value: F

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Moxifloxacin, Lopinavir/ ritonavir, Ribavirin, Xuebijing injection, Lung Cleansing and Detoxifying Decoction, Tereqing Injection

tag: unpublished


title: S-S026

tag: patient

tag: datasets

value: severe/critical

tag: outcome

value: Tereqing Injection, Ganciclovir, Cefmenoxime, Methylprednisolone Sodium Succinate for Injection, Meropenem, Moxifloxacin, Xuebijing injection, Cefoperazone Sodium and Sulbactam Sodium for Injection, Linezolid Tablets, Fluconazole

value: unknown


title: S-S027

tag: age

tag: Sex

tag: comorbidities

value: hypertension

value: Tereqing Injection, Ganciclovir, Cefmenoxime, Methylprednisolone Sodium Succinate for Injection, Meropenem, Moxifloxacin, Xuebijing injection, Piperacillin Sodium/ Tazobactam Sodium, Linezolid Tablets, Chinese medicine decoction, Cefoperazone Sodium and Sulbactam Sodium for Injection


title: S-S022-5

value: Wuhan

value: M

value: B cells sorted from frozen PBMC (MACS, STEMCELL 19054)

value: convalescence

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: No

tag: covid-19-related medication and anti-microbials

value: Methylprednisolone


title: S-S023

tag: city

tag: sample type

value: CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS)

value: positive

value: Yes

value: discharged

value: Moxifloxacin, Lopinavir/ ritonavir, Ribavirin, Xuebijing injection, Fluconazole, Chinese medicine decoction, Methylprednisolone Sodium Succinate for Injection

tag: leukocytes [g/l]


title: S-S022-4

tag: covid-19 severity

tag: sample time

tag: neutrophils [g/l]


title: S-S022-3

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: lymphocytes [g/l]


title: S-S021-4

tag: patient

tag: datasets

tag: unpublished


title: S-S022-2

tag: age

tag: Sex

tag: outcome


title: S-S019

value: frozen PBMC

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: comorbidities

value: Hypertension


title: S-S021-5

tag: city

tag: sample type

value: severe/critical

tag: covid-19-related medication and anti-microbials


title: S-S022-1

tag: covid-19 severity

tag: sample time

value: unknown

tag: leukocytes [g/l]


title: S-S030

value: Harbin

value: fresh PBMC

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Cardiovascular diseases, type 2 diabetes

value: Antibiotics, Glucocorticoid

tag: neutrophils [g/l]


title: S-S021-3

tag: patient

tag: datasets

value: Wuhan

value: M

value: B cells sorted from frozen PBMC (MACS, STEMCELL 19054)

tag: lymphocytes [g/l]


title: S-S021-1

tag: age

tag: Sex

value: convalescence

value: No

tag: unpublished


title: S-S018

value: positive

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

value: Diabetes

value: Methylprednisolone


title: S-S021-2

tag: city

tag: sample type

value: Yes

value: discharged

tag: comorbidities


title: S-S017

value: frozen PBMC

tag: covid-19 severity

tag: sample time

tag: covid-19-related medication and anti-microbials

value: Interferon atomization / Methylprednisolone


title: S-S011-1

source_name: Sputum

value: Guangzhou

value: fresh Sputum

value: severe/critical

value: progression

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: type 2 diabetes,coronary heart disease,type i respiratory failure

value: Human Serum Albumin, Thymosin Alpha1, Diyushengbai tablet, Ribavirin

tag: leukocytes [g/l]


title: S-S016

tag: patient

tag: datasets

value: Wuhan

value: F

value: Hypertension

tag: neutrophils [g/l]


title: S-S015

tag: age

tag: Sex

value: M

value: convalescence

value: No

tag: lymphocytes [g/l]


title: S-S028

value: Harbin

value: fresh PBMC

value: positive

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: Cardiovascular diseases

value: Antibiotics, Glucocorticoid

value: unknown

tag: unpublished


title: S-S014

tag: city

tag: sample type

value: frozen PBMC

tag: outcome

value: discharged

value: Methylprednisolone

value: Yes


title: S-S010-1

value: Guangzhou

value: fresh Sputum

tag: covid-19 severity

value: severe/critical

tag: sample time

value: progression

tag: comorbidities

value: type 2 diabetes,chronic obstructive pulmonary disease,hyperuricemia,acute kidney injury,septic shock,hypertension,mediastinal emphysema

value: Thymosin Alpha1, gama-globulin, Ribavirin


title: S-S009

value: M

value: fresh BALF

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: covid-19-related medication and anti-microbials

value: cefoperazone and tazobactam, voriconazole, Polymyxin B, Azithromycin, Lopinavir/ ritonavir, Arbidol, gama-globulin


title: S-S013

tag: patient

tag: datasets

value: Wuhan

value: convalescence

value: positive

tag: leukocytes [g/l]


title: S-S011-2

tag: age

tag: Sex

value: type 2 diabetes,coronary heart disease,type i respiratory failure

value: Human Serum Albumin, Thymosin Alpha1, Diyushengbai tablet, Ribavirin

tag: neutrophils [g/l]


title: S-S005-2

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

value: type II respiratory failure, septic shock,hypertension, sleep apnea syndrome,chronic hepatitis

value: methylprednisolone, methylprednisolone, Thymosin Alpha1, Ribavirin

tag: lymphocytes [g/l]


title: S-S007-1

tag: city

value: Guangzhou

tag: sample type

value: fresh Sputum

value: hypohepatia (may caused by the anti SARS-CoV-2 drugs)

value: methylprednisolone, Ribavirin

tag: unpublished

value: Yes


title: S-S007-2

value: M

tag: covid-19 severity

value: severe/critical

tag: sample time

value: progression

tag: outcome


title: S-S001-1

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: comorbidities


title: S-S006

tag: patient

tag: datasets

value: fresh BALF

value: Hypertension,Bilateral tonsillectomy

tag: covid-19-related medication and anti-microbials

value: cefoperazone and tazobactam, Meropenem, Teicoplanin, Oseltamivi, glucocorticoid, Mosifloxacin, Lopinavir/ritonavir


title: S-S004-3

tag: age

tag: Sex

value: F

value: positive

value: type 2 diabetes,hypertension,sequel of cerebral infarction,vascular dementia

value: Ribavirin

tag: leukocytes [g/l]


title: S-S004-1

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: discharged

value: type i respiratory failure,sepsis,arhythmia,hypoproteinemia

value: Prednisone, methylprednisolone, gama-globulin, Ribavirin

tag: neutrophils [g/l]


title: S-S020

tag: city

value: Wuhan

tag: sample type

value: frozen PBMC

value: convalescence

value: Diabetes

value: Methylprednisolone

tag: lymphocytes [g/l]


title: S-S005-1

value: Guangzhou

value: M

value: fresh Sputum

tag: covid-19 severity

value: severe/critical

tag: sample time

value: progression

value: type II respiratory failure, septic shock,hypertension, sleep apnea syndrome,chronic hepatitis

value: methylprednisolone, methylprednisolone, Thymosin Alpha1, Ribavirin

tag: unpublished

value: Yes


title: S-S003

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

value: No

tag: outcome

value: type i respiratory failure,sepsis,myocardial damage,brain tumor after therapy

value: Methylprednisolone, Ribavirin


title: S-S012-3

tag: patient

tag: datasets

value: discharged

tag: comorbidities

value: acute kidney injury,myocardial damage, blood coagulation disorders,hypoproteinemia,pulmonary bullous,hepatic cyst,renal cyst

value: Prednisone, methylprednisolone, methylprednisolone, Thymosin Alpha1, Ribavirin


title: S-S004-2

tag: age

tag: Sex

value: F

value: type 2 diabetes,hypertension,sequel of cerebral infarction,vascular dementia

tag: covid-19-related medication and anti-microbials

value: Ribavirin


title: S-S002

value: Guangzhou

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: leukocytes [g/l]


title: S-M063-2

tag: city

value: Wuhan

value: M

tag: sample type

value: CD3+ T cell sorted from fresh PBMC (FACS)

value: mild/moderate

value: convalescence

value: unknown

tag: neutrophils [g/l]


title: S-M063-1

value: CD19+ B cell sorted from fresh PBMC (FACS)

tag: covid-19 severity

tag: sample time

value: positive

tag: lymphocytes [g/l]

value: Yes


title: S-S012-2

value: fresh Sputum

value: severe/critical

value: progression

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: unpublished


title: S-S001-3

source_name: PFMC

tag: patient

tag: datasets

value: fresh PFMC

tag: outcome

value: discharged

value: type 2 diabetes,chronic obstructive pulmonary disease,acute kidney injury,septic shock,hypertension,multiple organ dysfunction syndrome, blood coagulation disorders,myocardial damage

value: methylprednisolone, Ribavirin


title: S-S012-1

value: Guangzhou

tag: age

tag: Sex

tag: comorbidities

value: acute kidney injury,myocardial damage, blood coagulation disorders,hypoproteinemia,pulmonary bullous,hepatic cyst,renal cyst

value: Prednisone, methylprednisolone, methylprednisolone, Thymosin Alpha1, Ribavirin


title: S-S010-2

value: M

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: type 2 diabetes,chronic obstructive pulmonary disease,hyperuricemia,acute kidney injury,septic shock,hypertension,mediastinal emphysema

tag: covid-19-related medication and anti-microbials

value: Thymosin Alpha1, gama-globulin, Ribavirin


title: S-S001-2

tag: city

tag: sample type

value: fresh PBMC

tag: leukocytes [g/l]


title: S-S008

value: F

value: fresh BALF

tag: covid-19 severity

tag: sample time

value: positive

value: unknown

value: Imipenem/cilastatin, Teicoplanin, voriconazole, cefoperazone and tazobactam, Levofloxacin, Caspofungin, Polymyxin B, Meropenem, Lopinavir/ritonavir, Arbidol, gama-globulin

tag: neutrophils [g/l]


title: S-M062-1

value: Wuhan

value: CD19+ B cell sorted from fresh PBMC (FACS)

value: mild/moderate

value: convalescence

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: lymphocytes [g/l]

value: Yes


title: S-M077

tag: patient

tag: datasets

value: Shenzhen

value: progression

value: discharged

value: Interferon atomization, Ribavirin

tag: unpublished


title: S-M078

tag: age

tag: Sex

tag: outcome


title: S-M076-2

value: M

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: comorbidities


title: S-M061-1

tag: city

tag: sample type

tag: covid-19-related medication and anti-microbials


title: S-M074-2

value: fresh PBMC

tag: covid-19 severity

tag: sample time

tag: leukocytes [g/l]


title: S-M075

value: F

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: neutrophils [g/l]


title: S-M062-2

tag: patient

tag: datasets

value: CD3+ T cell sorted from fresh PBMC (FACS)

tag: lymphocytes [g/l]


title: S-M073

value: Huanggang

tag: age

tag: Sex

value: positive

value: Antibiotics

tag: unpublished


title: S-M072

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

value: unknown


title: S-M070

tag: city

tag: sample type

tag: comorbidities


title: S-M069

tag: covid-19 severity

tag: sample time

tag: covid-19-related medication and anti-microbials


title: S-M068

value: Zhuhai

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: leukocytes [g/l]


title: S-M071

tag: patient

tag: datasets

value: mild/moderate

value: Antibiotics, steroids

tag: neutrophils [g/l]


title: S-M066

tag: age

tag: Sex

tag: lymphocytes [g/l]


title: S-M065

value: convalescence

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: unpublished


title: S-M060-2

tag: city

value: Wuhan

tag: sample type

value: No

tag: outcome

value: Yes


title: S-M059-2

tag: covid-19 severity

tag: sample time

value: discharged

tag: comorbidities


title: S-M067

value: progression

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: covid-19-related medication and anti-microbials


title: S-M060-1

tag: patient

tag: datasets

value: CD19+ B cell sorted from fresh PBMC (FACS)

tag: leukocytes [g/l]


title: S-M058-1

tag: age

tag: Sex

tag: neutrophils [g/l]


title: S-M057

value: M

value: frozen PBMC

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: Montelukast sodium Chewable Tablets, IFN-alpha2a

tag: lymphocytes [g/l]


title: S-M061-2

tag: city

value: F

tag: sample type

value: CD3+ T cell sorted from fresh PBMC (FACS)

tag: unpublished


title: S-M056

tag: covid-19 severity

tag: sample time

value: positive

tag: outcome

value: Oseltamivir, IFN-alpha2a


title: S-M059-1

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: comorbidities

value: unknown


title: S-M055

tag: patient

tag: datasets

value: mild/moderate

value: coronary heart disease

tag: covid-19-related medication and anti-microbials

value: Oseltamivir


title: S-M076-1

value: Shenzhen

tag: age

tag: Sex

value: fresh BALF

value: Interferon atomization, Ribavirin

tag: leukocytes [g/l]


title: S-M054

value: Wuhan

value: convalescence

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

value: discharged

value: hypertension,coronary heart disease,HBV

value: Oseltamivir, Lopinavir and Ritonavir Tablets

tag: neutrophils [g/l]


title: S-M074-1

tag: city

value: M

tag: sample type

value: progression

value: No

tag: lymphocytes [g/l]


title: S-M053

value: frozen PBMC

tag: covid-19 severity

tag: sample time

value: positive

value: tumor and gastritis

tag: unpublished


title: S-M052

value: mild/moderate

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: outcome

value: hypertension


title: S-M064

tag: patient

tag: datasets

value: Zhuhai

value: F

value: fresh PBMC

tag: comorbidities

value: unknown


title: S-M050

value: Wuhan

tag: age

tag: Sex

value: convalescence

tag: covid-19-related medication and anti-microbials

value: Arbidol, Interferon


title: S-M049

value: Beijing

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

value: discharged

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, Traditional Chinese medicine

tag: leukocytes [g/l]


title: S-M048

tag: city

value: M

tag: sample type

value: Obesity, type 2 diabetes

value: Interferon alpha 2 b,  Lopinavir/ ritonavir

tag: neutrophils [g/l]


title: S-M047

tag: covid-19 severity

tag: sample time

value: progression

value: positive

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, Arbidol, ribavirin, steroids, Human immunoglobulin

tag: lymphocytes [g/l]


title: S-M046

value: mild/moderate

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: asthma

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, steroids, Human immunoglobulin, antibiotics

tag: unpublished


title: S-M045

tag: patient

tag: datasets

value: fresh PBMC

tag: outcome

value: Hyperthyroidism

value: unknown


title: S-M042-2

tag: age

tag: Sex

value: F

value: convalescence

tag: comorbidities


title: S-M044-1

value: Beijing

tag: bcr single cell sequencing

value: Yes

tag: tcr single cell sequencing

tag: covid-19-related medication and anti-microbials

value: Interferon alpha 2 b,  Lopinavir/ ritonavir, antibiotics


title: S-M044-2

tag: city

tag: sample type

value: discharged

tag: leukocytes [g/l]


title: S-M058-2

value: Wuhan

value: CD3+ T cell sorted from fresh PBMC (FACS)

tag: covid-19 severity

tag: sample time

value: No

tag: neutrophils [g/l]


title: S-M042-1

value: progression

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

value: Interferon alpha 2 b,  Lopinavir/ ritonavir

tag: lymphocytes [g/l]


title: S-M041-2

tag: patient

tag: datasets

value: M

value: mild/moderate

tag: unpublished


title: S-M043-1

tag: age

tag: Sex

value: fresh PBMC

tag: outcome


title: S-M043-2

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: comorbidities


title: S-M037

tag: city

value: Shanghai

tag: sample type

value: frozen PBMC

tag: covid-19-related medication and anti-microbials

value: thymosin, no antibiotics and glucocorticoids


title: S-M039-2

value: F

value: CD19+ B cell sorted from fresh PBMC (MACS)

tag: covid-19 severity

tag: sample time

value: convalescence

tag: leukocytes [g/l]

value: unknown


title: S-M038

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Yes

value: discharged

tag: neutrophils [g/l]


title: S-M039-1

tag: patient

tag: datasets

tag: lymphocytes [g/l]


title: S-M041-1

value: Beijing

tag: age

tag: Sex

tag: unpublished


title: S-M051

value: Wuhan

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome

value: hypertension

value: Oseltamivir


title: S-M040-1

tag: city

tag: sample type

value: positive

tag: comorbidities


title: S-M035-2

value: Shandong

value: M

tag: covid-19 severity

tag: sample time

value: No

tag: covid-19-related medication and anti-microbials


title: S-M035-1

value: fresh PBMC

value: mild/moderate

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: leukocytes [g/l]


title: S-M036-2

tag: patient

tag: datasets

value: Shanghai

value: thymosin, no antibiotics and glucocorticoids

tag: neutrophils [g/l]


title: S-M033

tag: age

tag: Sex

value: CD19+ B cell sorted from fresh PBMC (MACS)

tag: lymphocytes [g/l]


title: S-M034

value: convalescence

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: unpublished


title: S-M036-1

tag: city

tag: sample type

tag: outcome

value: unknown


title: S-M079

value: Shenzhen

value: F

tag: covid-19 severity

tag: sample time

value: progression

value: Yes

tag: comorbidities

value: Interferon atomization


title: S-M031-1

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: discharged

tag: covid-19-related medication and anti-microbials


title: S-M030

tag: patient

tag: datasets

value: frozen PBMC

value: positive

tag: leukocytes [g/l]


title: S-M031-2

value: Shandong

tag: age

tag: Sex

tag: neutrophils [g/l]


title: S-M029

value: Chongqing

value: M

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: rhIFna1b, Ribavirin effervescent granules, Metformin Hydrochloride Tablets, Acarbose Tablets, Bicyclic alcohol tablets

tag: lymphocytes [g/l]


title: S-M027

tag: city

tag: sample type

value: mild/moderate

value: rhIFna1b, Lopinavir Ritonavir tablets,

tag: unpublished


title: S-M026-3

tag: covid-19 severity

tag: sample time

tag: outcome

value: rhIFna1b, Lopinavir Ritonavir tablets, Potassium Chloride Sustained Release Tablets


title: S-M040-2

value: Shanghai

value: CD19+ B cell sorted from fresh PBMC (MACS)

value: convalescence

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: No

tag: comorbidities

value: thymosin, no antibiotics and glucocorticoids


title: S-M026-2

tag: patient

tag: datasets

value: F

value: progression

value: Yes

tag: covid-19-related medication and anti-microbials


title: S-M026-1

tag: age

tag: Sex

value: frozen PBMC

value: discharged

tag: leukocytes [g/l]


title: S-M022

value: Harbin

value: fresh PBMC

value: positive

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: Cardiovascular diseases

value: Antibiotics, Glucocorticoid

value: unknown

tag: neutrophils [g/l]


title: S-M024

tag: city

tag: sample type

value: mild/moderate

tag: lymphocytes [g/l]


title: S-M025

value: Chongqing

value: M

tag: covid-19 severity

tag: sample time

value: rhIFna1b, Lopinavir Ritonavir tablets, PiPa Lu, Metformin Hydrochloride Tablets, Acarbose Tablets,

tag: unpublished


title: S-M021

value: convalescence

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: outcome

value: Antibiotics


title: S-M023

tag: patient

tag: datasets

value: F

tag: comorbidities


title: S-M020

tag: age

tag: Sex

tag: covid-19-related medication and anti-microbials


title: S-M014

value: CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS)

tag: bcr single cell sequencing

tag: tcr single cell sequencing

value: Hypertension, diabetes

value: Hospitalized at Harbin Medical University, no cases

tag: leukocytes [g/l]


title: S-M015

tag: city

tag: sample type

value: Yes

value: discharged

value: Ganciclovir, Xuebijing injection

tag: neutrophils [g/l]


title: S-M017

value: Harbin

value: fresh PBMC

tag: covid-19 severity

tag: sample time

value: positive

value: Antibiotics, Glucocorticoid, Traditional Chinese medicine

tag: lymphocytes [g/l]


title: S-M016

value: Suihua

value: mild/moderate

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

value: Not admitted for treatment

value: unknown

tag: unpublished


title: S-M019

tag: patient

tag: datasets

value: M

value: convalescence

tag: outcome

value: Cardiovascular diseases


title: S-M018

tag: age

tag: Sex

value: F

tag: comorbidities

value: Antibiotics


title: S-M032

value: Shandong

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: covid-19-related medication and anti-microbials


title: S-M013

tag: city

tag: sample type

value: CD3+ T cell and CD19+ B cell sorted from fresh PBMC (FACS)

value: Yes

value: diabetes

value: Ribavirin, Tereqing Injection, Xuebijing injection, Lung Cleansing and Detoxifying Decoction, Lopinavir/ ritonavir

tag: leukocytes [g/l]


title: S-M010-5

value: Wuhan

value: B cells sorted from frozen PBMC (MACS, STEMCELL 19054)

tag: covid-19 severity

tag: sample time

value: No

value: discharged

tag: neutrophils [g/l]


title: S-M010-6

value: mild/moderate

tag: sampling day (days after symptom onset)

value: positive

tag: single cell sequencing platform_id

tag: lymphocytes [g/l]


title: S-M028

tag: patient

tag: datasets

value: Chongqing

value: frozen PBMC

value: rhIFna1b, Benazepril Hydrochloride Tablets, Metoprolol Succinate extended-release tablets, Sodium bicarbonate tablets

value: unknown

tag: unpublished


title: S-M010-4

tag: age

tag: Sex

value: F

value: convalescence

tag: outcome


title: S-M010-3

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: comorbidities


title: S-M011

tag: city

tag: sample type

tag: covid-19-related medication and anti-microbials

value: Interferon atomization / Methylprednisolone


title: S-M010-1

tag: covid-19 severity

tag: sample time

tag: leukocytes [g/l]


title: S-M012

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: neutrophils [g/l]


title: S-M009-6

tag: patient

tag: datasets

tag: lymphocytes [g/l]


title: S-M010-2

tag: age

tag: Sex

tag: unpublished


title: S-M009-4

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: outcome


title: S-M009-5

tag: city

tag: sample type

tag: comorbidities


title: S-M009-3

tag: covid-19 severity

tag: sample time

tag: covid-19-related medication and anti-microbials


title: S-M009-2

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: leukocytes [g/l]


title: S-M008-2

tag: patient

tag: datasets

value: Beijing

value: M

value: Interferon atomization/ Lopinavir/ litonavir

tag: neutrophils [g/l]


title: S-M009-1

tag: age

tag: Sex

tag: lymphocytes [g/l]

value: Yes


title: S-M007-6

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: unpublished


title: S-M008-1

tag: city

tag: sample type

tag: outcome


title: S-M007-5

tag: covid-19 severity

tag: sample time

tag: comorbidities


title: S-M007-4

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: covid-19-related medication and anti-microbials


title: S-M007-2

tag: patient

tag: datasets

value: progression

tag: leukocytes [g/l]


title: S-M007-1

tag: age

tag: Sex

value: B cells sorted from frozen PBMC (MACS, STEMCELL 19054)

tag: neutrophils [g/l]


title: S-M006

value: Wuhan

tag: bcr single cell sequencing

value: No

tag: tcr single cell sequencing

tag: lymphocytes [g/l]


title: S-M005

tag: city

tag: sample type

value: mild/moderate

value: discharged

value: Hypertension, Diabetes

value: Methylprednisolone

tag: unpublished


title: S-M004-4

tag: covid-19 severity

tag: sample time

value: positive

tag: outcome


title: S-M004-2

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: comorbidities

value: unknown


title: S-M004-3

tag: patient

tag: datasets

value: F

tag: covid-19-related medication and anti-microbials


title: S-M004-6

tag: age

tag: Sex

value: convalescence

tag: leukocytes [g/l]


title: S-M004-1

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: neutrophils [g/l]


title: S-M004-5

tag: city

tag: sample type

tag: lymphocytes [g/l]


title: S-M003-3

value: Guangzhou

value: fresh Sputum

tag: covid-19 severity

tag: sample time

value: thalassemia,Anemia due to glucose-6-phosphate dehydrogenase deficiency

value: Ribavirin

tag: unpublished


title: S-M003-2

value: M

tag: sampling day (days after symptom onset)

tag: single cell sequencing platform_id

tag: outcome

value: Yes


title: S-M003-1

tag: patient

tag: datasets

value: progression

tag: comorbidities


title: S-M002-1

tag: age

tag: Sex

tag: covid-19-related medication and anti-microbials


title: S-M002-2

tag: bcr single cell sequencing

tag: tcr single cell sequencing

tag: leukocytes [g/l]


title: S-M007-3

tag: city

value: Beijing

tag: sample type

value: B cells sorted from frozen PBMC (MACS, STEMCELL 19054)

value: Interferon atomization/ Lopinavir/ litonavir

tag: neutrophils [g/l]


title: SM-37_1

status: Public on Jan 11 2021

city: Chandigarh

first: Prabhu

middle: B

last: Patil

state: Chandigarh

address: Sector 39 A

country: India

institute: CSIR Institute of Microbial Technology Chandigarh

description: Total RNA was isolated by growing cells at  37 °C and harvesting cells at mid log phase

data_processing:
Basecalling, demultiplication and adaptor treaming was performed by Illumina MiSeq control software.
Quality of raw reads was assessed by using FastQC toolkit.
Aligning reads to the reference genome of S. maltophilia ATCC 13637 (NZ_CP008838) by using the Bowtie 2 (Langmead and Salzberg, 2012). The aligned SAM files generated by bowtie were sorted using samtools v1.4.1 (Li et al., 2009).  The obtained BAM files were used as input to cufflinks v2.2.1 (Trapnell et al., 2013; Trapnell et al., 2012; Trapnell et al., 2010), which was used to assemble transcripts with FPKM (fragments per kilobase of transcript per million mapped reads) values. The data files for the replicates were merged into single transcript with Cuffmerge and differential gene expression was between both conditions  was performed using the Cuffdiff, a packages of the cufflinks v2.2.1 (Trapnell et al., 2013; Trapnell et al., 2012; Trapnell et al., 2010).
Genome_build: NZ_CP008838
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each condition.

organism: Stenotrophomonas maltophilia

source_name: Bacterial

growth_protocol: S. maltophilia strain MTCC 434T which is equivalent to the ATCC 13637T was grown in the 20 ml Luria Bertani Broth, Miller in 100 ml Erlenmeyer flask at either 37 °C and  28 °C under constant agitation at 200  RPM. Samples were withdrawn at intervals for optical density monitoring at 600 nm (OD600) and cells from both cultures were harvested at the mid log phase.

extract_protocol:
Total RNA was extracted by harvesting the cells and lysis by using TRIzol.  Follwed by phase seperation and Dnase tretemnt using Direct-zol RNA MiniPrep kit (Zymo Research Corporation, Orange, CA, USA).
ScriptSeq complete kit (Epicenter, Illumina, Madison, WI USA) which is combined kit for the ribosomal (rRNA) depletion Ribo-Zero™ Kit (Bacteria) (Epicenter, Illumina, Madison, WI USA) and cDNA library construction kit ScriptSeq™ v2 RNA-Seq library preparation kit (Epicenter, Illumina, Madison, WI USA) was used as per manufacturer's guidlines.

tag: strain

tag: growth phase

value: Mid log

tag: growth temperature

value: 37 °C


title: p753_S18

status: Public on Jan 06 2021

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: 3435 Main Street

department: Oral Biology

country: USA

institute: State University of New York at Buffalo

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ncbi-GRCh38 whole genome using hisat2-2.1.0 with parameters --fr
Reads aligning to the ncbi-GRCh38 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
Counts Normalisation was done to generate Transript per Million reads (TPM) according to the method of Wagner et al., Theory in Bioscience, 2012
Genome_build: ncbi-GRCH38
Supplementary_files_format_and_content: Matrix table with TPM values for all samples

source_name: Salivary Gland

extract_protocol:
Biopsies of minor salivary glands obtained from Sjogren's syndrome patient during routine checkup were embedded in Optimal Cutting Temperature (OCT) media and later process for RNA extraction using Direct-Zol RNA mini-prep kit
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: analysis group

value: Case

tag: disease state

value: Sjogrens Syndome

tag: tissue

value: Salivary Gland


title: SM-28_3

description: Total RNA was isolated by growing cells at  28 °C and harvesting cells at mid log phase

value: 28 °C


title: SM-37_3


title: p909_S17


title: SM-28_2


title: p535_S20


title: SM-28_1


title: p509_S11


title: p613_S14


title: p529_S12


title: p703_S15


title: p325_S19


title: p568_S16


title: EKO Western Diet 22 weeks rep 1

status: Public on Dec 22 2020

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were mapped on the GencodeM annotation of the Mus musculus transcriptome using the bowtie2 program. Estimation of gene expression levels was performed using RSEM. Differential expression analysis was performed applying the quasilikelihood (QL) F-test of the edgeR38 package to RSEM estimated reads counts. Only genes with more than 10 reads in at least 4 different biological replicates were considered. Genes showing a false discovery rate lower than 0.05 were considered differentially expressed
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Aorta

growth_protocol: Eight weeks old mice were randomly divided into 4 groups of 8 mice and fed a regular chow diet (4RF21, Mucedola, Italy) or a Western diet (TD.88137, Envigo, Italy) for 6 or 22 weeks. One week before the end of the dietary treatment, after an overnight fast, mice were anaesthetized with 2% isoflurane (Merial Animal Health, Woking, UK). Blood was collected from the retroorbital plexus into tubes containing 0.1% (w/v) EDTA and centrifuged in a microcentrifuge for 10 minutes at 5900 × g at 4 °C. At the end of the dietary treatments, mice were sacrificed under general anaesthesia with 2% isoflurane (Merial Animal Health, Woking, UK) and blood was removed by perfusion with 1× phosphate-buffered saline (PBS).

extract_protocol:
The aorta was rapidly dissected from the aortic root to the iliac bifurcation and periadventitial fat was removed. Aortas were then snap-frozen in liquid nitrogen for RNA-seq analyses (n=3).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: post natal week 30

tag: genotype

value: EKO


title: EKO Western Diet 22 weeks rep 3


title: EKO Western Diet 22 weeks rep 2


title: EKO chow 22 weeks rep 2


title: 16_IL-4c #6 Male

status: Public on Dec 21 2020

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

description:
sample name:
16

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”
The reads distribution across the genome was assessed using bamutils (from ngsutils)
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10
Quality control of sequencing and mapping results was summarized using MultiQC . Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept
The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow derived macrophages

growth_protocol: Mice we fed high fat diet for 4.5 weeks before 4.5 weeks (injection every other day) of either IL-4complex or PBS (For controls) injection and maintained on HFD throughout. Age matched mice on high fat diet were infected with S. mansoni concurrently.  At 4.5 weeks post injection or 10 weeks post infection, bone marrow was harvested and cultured in M-CSF for 6 days to generate macrophages.

extract_protocol:
cells were harvested, washed in 1X PBS and then RNA was harvested using Trizol reagent. RNA was DNase treated (NEB) and then cleaned with Qiagen MinElute Cleanup kit.
200 nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using KAPA mRNA Hyperprep Kit (Roche)

treatment_protocol: Cells are unstimulated Day 6 bone marrow derived macrophages

tag: cell type

value: bone marrow derived macrophages

value: male

tag: infection status

value: uninfected

tag: treatment

value: IL-4 cpmplex


title: EKO Western Diet 6 weeks rep 1

tag: age

value: post natal week 14


title: EKO chow 22 weeks rep 3


title: EKO Western Diet 6 weeks rep 3


title: SM-37_2


title: EKO chow 6 weeks rep 3


title: EKO chow 22 weeks rep 1


title: EKO chow 6 weeks rep 2


title: EKO chow 6 weeks rep 1


title: EKO Western Diet 6 weeks rep 2


title: 15_IL-4c #5 Male

description:
sample name:
15

tag: Sex


title: 13_IL-4 c #3 Male

description:
sample name:
13


title: 14_IL-4c #4 Male

description:
sample name:
14


title: 10_Infected #5 Male

description:
sample name:
10

value: infected

value: PBS (control)


title: 11_IL-4c #1 Male

description:
sample name:
11


title: 9_Infected #4 Male

description:
sample name:
9


title: 12_IL-4c #2 Male

description:
sample name:
12


title: 6_Infected 1 #Male

description:
sample name:
6

growth_protocol: Mice were fed high fat diet for 4.5 weeks before 4.5 weeks (injection every other day) of either IL-4complex or PBS (For controls) injection and maintained on HFD throughout. Age matched mice on high fat diet were infected with S. mansoni concurrently.  At 4.5 weeks post injection or 10 weeks post infection, bone marrow was harvested and cultured in M-CSF for 6 days to generate macrophages.


title: 7_Infected #2 Male

description:
sample name:
7


title: 3_Uninfected #3 Male

description:
sample name:
3


title: 4_Uninfected #4  Male

description:
sample name:
4


title: 2_Uninfected #2 Male

description:
sample name:
2


title: 1_Uninfected #1 Male

description:
sample name:
1


title: RNA_rep2_120_min

status: Public on Dec 15 2020

city: Durham

first: David

middle: M

last: MacAlpine

state: North Carolina

address: Duke University

department: Department of Pharmacology and Cancer Biology

institute: Duke University Medical Center

description:
RNA at T=120 following Cd addition
gene_expression_TPM_all_times.csv

data_processing:
Reads were aligned using Bowtie 0.12.7 with parameters "-n 2 -l 20 -m 1 -k 1 -X 1000" to release 64 (sacCer3) of the S.cerevisiae genomic sequence obtained from downloads.yeastgenome.org.
Data processing code from github.com/HarteminkLab/cadmium-paper was run against aligned reads. The following steps from this code were performed:
Chromatin replicates were merged and randomly sampled to equivalent proportions for each time point.
For each base pair at each ORF of the genome, chromatin characterization of transcription factors and nucleosomes were computed relative to TSSs obtained from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973313/bin/supp_42_6_3736__index.html
Transcription factor occupancy was characterized using MNase reads shorter than 100 base pairs and within 200 base pairs upstream of TSSs, defined as the "small fragment promoter occupancy" for each ORF.
Nucleosomes were characterized through cross correlating a bivariate Gaussian distribution against MNase reads at high scoring nucleosomes obtained from GEO/GSE36063. An information entropy score was computed using this per base pair cross correlation for first three nucleosomes downstream of each ORF’s TSS, defined as a gene's "gene body nucleosome disorganization".
RNA reads were counted at non-intronic regions inside ORF boundaries. TPM was computed by scaling read counts by ORF length and normalizing to an equivalent sum for each time point.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3)
Supplementary_files_format_and_content: small_fragment_promoter_occupancy_all_times.csv
Supplementary_files_format_and_content: gene_body_nucleosome_disorganization_entropy_all_times.csv
Supplementary_files_format_and_content: gene_expression_TPM_all_times.csv

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Cells were grown in rich medium at 30C to an OD600 0.8.

extract_protocol:
Chromatin were prepared as in Belsky et. al. Genes and Development, 2015
See Belsky et al.

treatment_protocol: Samples were removed for both MNase treatment and RNA-seq as a 0 time point before addition of Cadmium Chloride to a final concentration of 1mM for 120 min.

value: 1 mM Cd

tag: time

value: 120 min


title: RNA_rep2_15_min

description:
RNA at T=15 following Cd addition
gene_expression_TPM_all_times.csv

value: 15 min


title: RNA_rep2_7.5_min

description:
RNA at T=7.5 following Cd addition
gene_expression_TPM_all_times.csv

value: 7.5 min


title: RNA_rep2_30_min

description:
RNA at T=30 following Cd addition
gene_expression_TPM_all_times.csv

value: 30 min


title: RNA_rep2_0_min

description:
RNA at T=0 prior to Cd addition
gene_expression_TPM_all_times.csv

value: 0 mM Cd

value: 0 min


title: K120R_NT (untreated)

status: Public on Dec 02 2020

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University

library_source: genomic

data_processing:
Base-calling was performed onboard the NextSeq 500 using the integrated instrument computer.
FASTQ generation was performed in the Illumina BaseSpace cloud using bcl2fastq with default parameters.
Read alignment was performed using bwa mem with default parameters
samtools rmdup was used to filter duplicate reads
peak calling was performed using macs2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bam file contains aligned reads
Supplementary_files_format_and_content: bed: peak summits locations for every peak
Supplementary_files_format_and_content: narrowPeak: peak locations together with peak summit, pvalue and qvalue
Supplementary_files_format_and_content: peaks excel file: tabular file which contains information about called peaks. Additional information includes pileup and fold enrichment

molecule: genomic DNA

source_name: H1299 cells

growth_protocol: The p53-null human lung cancer cell line H1299 (ATCC) was cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning) supplemented with 10% Fetal Bovine Serum (FBS, GeminiBio) at 37°C and 5% CO2. They were routinly re-plated every 4 days, and used for experimets after no more than 20 passages.

extract_protocol:
Cell lysates were clarified from sonicated nuclei and hp53-DNA complexes were isolated with p53-specific antibody.
Library preparation was done using Swift’s Biosciences Accel-NGS 2S Plus Library Kits for Illumina platforms. 10 ng of DNA was used for library preparation and kit’s protocol was followed for a 200 base pair insert. An additional two sided bead clean up was done after the PCR step using SPRI beads with the formula .6X, then using the supernatant, 1.2x. The library was pooled to 1 nM and the sequenced on a NextSeq 500 using the standard loading protocol.

treatment_protocol: Tet(+) samples were treated with 1 ug/ul of Tetracycle for 24 h before the harvest. Additionally, all samples were cross-linked with the 3% formaldehyde and the reaction was quinched with 7.5% glycine.

tag: stable cell line

value: Tet Repressor expression

value: No treatment

tag: antibody

value: anti-p53 (FL393-x, Santa Cruz)


title: WT_NT (untreated)


title: WT_Tet (treated)

value: Tet treatment


title: 8_Infected #3 Male

description:
sample name:
8

value: bone marrow derived macrophages

value: male


title: K120R_Tet (treated)


title: HTR-8_KD_rep8-1

status: Public on Nov 18 2020

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
aligned to the hg19 genome using HISAT2 (v2.1.0; default paraeters)
transcript abundance was calculated using htseq-count from the HTseq package.
Genome_build: hg19
Supplementary_files_format_and_content: Files contain the number of reads aligning to each gene

growth_protocol: HTR-8/SVneo cells were cultured in RPMI-1640 (ATCC 30-2001) with 5% FBS

extract_protocol:
RNA was extracted 48 hours after transfection using the Qiagen Mini RNA kit
Libraries were prepared using the NEBNext Ultra II Directional library prep kit, unique dual index plate, and poly(A) mRNA magnetic isolation module, following manufacturer’s protocol
Samples were run on the HiSeq 3000, across three lanes using single-end 50bp reads.

treatment_protocol: Cells were seeded at 15 x 10e4 cells/well in a 6-well plate and grown for 48 hours before transfecting. Transfections were carried out with the Lipofectamine RNAiMAX Transfection Reagent (Fisher Scientific 13778150) and with PLAGL1 siRNA(ThermoFisher Scientific 4392420) or a negative control(ThermoFisher Scientific 4390843). We performed a media change 24 hours after transfection.

tag: cell line

value: placental cell line HTR-8/Svneo

value: Plagl1 siRNA

value: PLAGL1 knockdown


title: HTR-8_KD_rep7-3


title: HTR-8_KD_rep6-3


title: HTR-8_KD_rep7-2


title: RNA_rep2_60_min

description:
RNA at T=60 following Cd addition
gene_expression_TPM_all_times.csv

value: 60 min


title: HTR-8_KD_rep5-1


title: HTR-8_KD_rep8-3


title: HTR-8_KD_rep6-2


title: HTR-8_KD_rep6-1


title: HTR-8_KD_rep7-1


title: HTR-8_KD_rep4-3


title: HTR-8_KD_rep4-2


title: HTR-8_KD_rep3-2


title: HTR-8_KD_rep2-3


title: HTR-8_KD_rep3-1


title: HTR-8_KD_rep2-2


title: HTR-8_KD_rep8-2


title: HTR-8_KD_rep2-1


title: HTR-8_KD_rep1-3


title: HTR-8_KD_rep5-3


title: HTR-8_KD_rep1-1


title: HTR-8_KD_rep5-2


title: HTR-8_KD_rep4-1


title: HTR-8_KD_rep3-3


title: HTR-8_Ctrl_rep8-2

value: Negative control siRNA

value: control


title: HTR-8_Ctrl_rep8-1


title: HTR-8_Ctrl_rep8-3


title: HTR-8_Ctrl_rep6-3


title: HTR-8_Ctrl_rep7-3


title: HTR-8_Ctrl_rep7-1


title: HTR-8_Ctrl_rep7-2


title: HTR-8_Ctrl_rep4-3


title: HTR-8_Ctrl_rep5-1


title: HTR-8_Ctrl_rep4-1


title: HTR-8_Ctrl_rep5-3


title: HTR-8_Ctrl_rep3-3


title: HTR-8_Ctrl_rep3-1


title: HTR-8_Ctrl_rep3-2


title: HTR-8_Ctrl_rep6-2


title: HTR-8_Ctrl_rep2-2


title: HTR-8_Ctrl_rep4-2


title: HTR-8_KD_rep1-2


title: HTR-8_Ctrl_rep1-1


title: HTR-8_Ctrl_rep1-2


title: HTR-8_Ctrl_rep1-3


title: HTR-8_Ctrl_rep6-1


title: WT-HEK-3_rnaseq

status: Public on Oct 01 2020

city: Austin

first: Hakan

last: Ozadam

state: TX

address: Department of Molecular Biosciences Moffett Molecular Biology Building 2.122 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas at Austin

description: RNA-Seq from untreated cells

data_processing:
Ribosome profiling and RNA-Seq data were processed using RiboFlow (source code and documentation are available at https://github.com/ribosomeprofiling/riboflow). A detailed description of the data processing steps can be found in https://academic.oup.com/bioinformatics/article/36/9/2929/5701654
Genome_build: Ribosome Profiling and RNA-Seq data were mapped to a transcriptome assembly available in https://github.com/ribosomeprofiling/references_for_riboflow/tree/master/transcriptome/human/v1/riboflow_annot_and_ref
Supplementary_files_format_and_content: Processed data are compiled in a single ribo file (manuscript.HEK293.ribo). The format specification can be found in https://ribopy.readthedocs.io/en/latest/ribo_file_format.html

growth_protocol: HEK293T cell line were obtained from ATCC and maintained in Dulbecco’s modified Eagle’s media (DMEM, GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, GIBCO, Life Technologies) and 1% Penicillin and Streptomycin (GIBCO, Life Technologies) at 37°C in 5% CO2 atmosphere. Cell lines were tested for mycoplasma contamination every six months and were consistently found negative

extract_protocol:
RNA-Seq: Total RNA was extracted with QIAzol and ethanol precipitation from 10% of the lysate volume (see above). Sequencing libraries were generated using the SMARTer Stranded RNA-Seq Kit which uses a template switching reverse transcriptase (Takara Bio 634837). Briefly, 100 ng of total RNA were mixed with 1 µL of a 1:10 dilution of ERCC RNA Spike-In Mix controls (Thermo Fisher 4456740). ERCC mix 1 was added to HEK293T and HEK293T-NSP1 and mix 2 was added to HEK293T-NSP2 samples. RNA hydrolysis was done for 4 min and half of the cDNA was amplified for 10 cycles. Samples were sequenced with NovaSeq 6000 S1 PE 100 (Illumina).
sequencing libraries were generated using the SMARTer Stranded RNA-Seq Kit which uses a template switching reverse transcriptase.

treatment_protocol: pLVX-EF1alpha-SARS-CoV-2-nsp1-2XStrep-IRES-Puro plasmid (Addgene, 141367), pLVXEF1alpha-SARS-CoV-2-nsp2-2XStrep-IRES-Puro plasmid (Addgene, 141368) and pLVXEF1alpha-SARS-CoV-2-N-2XStrep-IRES-Puro (Addgene, 141391) were obtained from Addgene. The IRES-Puro elements in the above plasmids were replaced with IRES-TagBFP from TRE-KRAB-dCAS9-IRES-BFP (Addgene, 85449) to make them compatible with the MeTAFlow assay. Briefly, IRES-Tag BFP was PCR amplified (Fp 5’-TCCGCAGTTTGAAAAGTAAGCCCCTCTCCCTCCCCCCC-3’ and Rp 5’-CAGAGGTTGATTGTTCCAGATTAATTAAGCTTGTGCCCCAGTTTGCTAGGG-3’). The pLVXEF1alpha-SARS-CoV-2-nsp1/nsp2-2XStrep-IRES-Puro plasmids were digested with BamHI (NEB) and MluI (NEB) to remove the IRES-Puromycin fragment followed by gel purification. The purified vector was ligated with the IRES-TagBFP PCR amplified product using Gibson assembly cloning (NEB). For pLVX-EF1alpha-SARS-CoV-2-N-2XStrep-IRES-Puro plasmid, due to presence of internal MluI site in N ORF, a three fragment Gibson cloning was performed. The plasmid was digested with MluI and two PCR amplified products corresponding to a fragment of N ORF and IRES-Tag BFP were PCR amplified using the following oligos. (Fragment 1 Fp 5’ 5’CTCTTGAATAAACACATAGACGCGTATAAGACGTTTCC 3′ and RpGGGAGAGGGGCGGGATCCTTACTTTTCAAAC 3′ and Fragment 2 5’AAGGATCCCGCCCCTCTCCCTCCCCCCC 3′ and Rp 5’CAGAGGTTGATTGTTCCAGATTAATTAAGCTTGTGCCCCAGTTTGCTAGGG3′ The sequences of the resulting plasmid clones were confirmed by Sanger sequencing.

value: no treatment

tag: rna population

value: Total RNA


title: WT-HEK-1_rnaseq

description: RNA-Seq from untreated cells


title: NSP2-HEK-3_rnaseq

description: RNA-Seq from NSP2 expressing cells

value: NSP2 expressing


title: NSP2-HEK-2_rnaseq

description: RNA-Seq from NSP2 expressing cells


title: NSP1-HEK-2_rnaseq

description: RNA-Seq from NSP1 expressing cells

value: NSP1 expressing


title: NSP1-HEK-1_rnaseq

description: RNA-Seq from NSP1 expressing cells


title: HTR-8_Ctrl_rep5-2


title: NSP1-HEK-3_rnaseq

description: RNA-Seq from NSP1 expressing cells


title: WT-HEK-1_ribo

description:
Ribosome profiling from untreated cells
5' Adapter: 12nt UMI followed by NNNN
3' Adapter: AAAAAAAAAACAAAAAAAAAA

data_processing:
Library strategy: Ribosome profiling
Ribosome profiling and RNA-Seq data were processed using RiboFlow (source code and documentation are available at https://github.com/ribosomeprofiling/riboflow). A detailed description of the data processing steps can be found in https://academic.oup.com/bioinformatics/article/36/9/2929/5701654
Genome_build: Ribosome Profiling and RNA-Seq data were mapped to a transcriptome assembly available in https://github.com/ribosomeprofiling/references_for_riboflow/tree/master/transcriptome/human/v1/riboflow_annot_and_ref
Supplementary_files_format_and_content: Processed data are compiled in a single ribo file (manuscript.HEK293.ribo). The format specification can be found in https://ribopy.readthedocs.io/en/latest/ribo_file_format.html

extract_protocol:
Ribosome Profiling: Three million HEK293T cells were plated in a 10 cm2 flask followed by transfection to express SARS-CoV-2 NSP1 and NSP2 (see above). Untransfected and transfected cells (~8 million) were washed twice with 10 mL of ice-cold PBS. The plates were immediately placed on ice and 400 μL of lysis buffer (Tris-Cl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL Cycloheximide, 1% Triton-X) was added to each plate, cells were scraped and transferred to 1.5 ml tubes. Cells were lysed on ice by pipetting up and down ~5 times every five minutes for a total of 10 min. All experiments were done in triplicate. The lysate was clarified by centrifugation at 160 x g for 10 min at 4°C. Ten percent of the clarified lysate by volume was separated, mixed with 700 μl QIAzol and stored at -20°C for RNA-Seq experiments (see below). The rest of the supernatant was immediately processed for ribosome profiling. Briefly, 7 μL of RNaseI (Invitrogen AM2249) was added to the clarified lysates and digestion was done for 1 h at 4 °C. The digestions were stopped with ribonucleoside vanadyl complex (NEB S1402S) at a final concentration of 20 mM. Digested lysates were layered on a 1 M sucrose cushion (Tris, pH 7.4, NaCl 150 mM, MgCl 2 5 mM, DTT 1 mM, 1 M sucrose) and the ribosomes were pelleted by centrifugation in a SW 41 Ti rotor (Beckman Coulter) at 38K rpm and 4°C for 2.5 h. RNA was extracted from the ribosome pellets with the addition of 700 μl QIAzol followed by chloroform and ethanol precipitation. RNA isolated from the pellets were size-selected by running 5 µg of each sample in a 15% polyacrylamide TBEUREA gel. The 21-34 nt RNA fragments were excised and extracted by crushing the gel fragment in 400 µL of RNA extraction buffer (NaOAc [pH 5.5] 300 mM, EDTA 1 mM, SDS 0.25% v/v) followed by a 30 min incubation on dry ice and an overnight incubation at room temperature. The sample was passed through a Spin X filter (Corning 8160) and the flow through was ethanol precipitated in the presence of MgCl2 5 mM and 1 µL of Glycoblue (Invitrogen AM9516). The RNA pellet was resuspended in 10 µL of RNase-free water and immediately processed for library preparation.
Ribosome profiling libraries were prepared with the D-Plex Small RNA-Seq Kit (Diagenode). This method incorporates a 3′ end dephosphorylation step, 5′ unique molecular identifiers (UMI) and a template switching reverse transcriptase that improves the quality of our libraries. Briefly, 25 ng of size-selected ribosome footprints were prepared following the manufacturer’s instructions with some modifications. The cDNA was amplified for 9 cycles and the resulting DNA libraries were pooled in equimolar amounts (~425 nM each). The library pool was cleaned with the AMPure XP beads (Beckman Coulter A63880) and eluted with 30 µL of RNase-free water. To enrich for ~30 bp fragments in the libraries, 3 µg of the cleaned libraries were size-selected in a 3% agarose precast-gel (Sage Science) with the BluePippin system (Sage Science) using 171-203 nt range with tight settings. The resulting size-selected libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent) and sequenced with the NovaSeq 6000 S1 SE 75 (Illumina).

value: RNA from ribosome footprint


title: WT-HEK-2_ribo


title: WT-HEK-3_ribo


title: NSP2-HEK-1_rnaseq

description: RNA-Seq from NSP2 expressing cells


title: WT-HEK-2_rnaseq

description: RNA-Seq from untreated cells


title: HTR-8_Ctrl_rep2-3


title: NSP2-HEK-2_ribo

description:
Ribosome profiling from NSP2 expressing cells
5' Adapter: 12nt UMI followed by NNNN
3' Adapter: AAAAAAAAAACAAAAAAAAAA


title: TS543_DMSO_1%_Input

status: Public on Sep 30 2020

city: New York

first: Junfei Zhao

last: Zhao

address: 1130 St. Nicholas Ave

institute: Columbia University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa mem.
peaks were called using macs2 with the default setting.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated using macs2.

source_name: TS543 glioma cells

extract_protocol: Nuclear extracts were isolated, chromatin fragmented using Covaris sonicator in 1mL tubes for 1min. 10 ug of antibody (TOP2A Abcam TOP2B Abcam) wasc incubated overnight. Washes with RIPA Buffer 4 times and once of TE with 50mM NaCl. Reversed crosslink and DNA purified for sequencing using phenol:chloroform:isoamyl alcohol.

treatment_protocol: 50x10e6 cells were treated with etoposide or DMSO, crosslinked using formaldehyde 1%.

value: TS543 glioma cells

tag: agent

value: DMSO


title: TS543_ICRF_1%_Input

value: ICRF


title: NSP1-HEK-3_ribo

description:
Ribosome profiling from NSP1 expressing cells
5' Adapter: 12nt UMI followed by NNNN
3' Adapter: AAAAAAAAAACAAAAAAAAAA


title: NSP1-HEK-1_ribo


title: NSP2-HEK-1_ribo


title: NSP1-HEK-2_ribo


title: ArabRoot-rep2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
BWA alignment
5',3' coordinate adjustment
MACS2 peak calling
Tn5 integration site intersection with ACRs
binarization
Genome_build: B73 v4/TAIR10
Supplementary_files_format_and_content: binary triplet matrix format of ACRs (column 1), nuclei ID (column 2), and 1/0 binarized counts of Tn5 intregation sites

organism: Arabidopsis thaliana

source_name: embyronic root

extract_protocol:
16,000 nuclei per library  were extracted via FANS
10x Genomics scATAC-seq v1
Paired-end, dual index

value: Fresh


title: NSP2-HEK-3_ribo


title: Leaf2

data_processing:
BWA alignment
5',3' coordinate adjustment
MACS2 peak calling
Tn5 integration site intersection with ACRs
binarization
Genome_build: B73 v4
Supplementary_files_format_and_content: binary triplet matrix format of ACRs (column 1), nuclei ID (column 2), and 1/0 binarized counts of Tn5 intregation sites

molecule: nuclear RNA

organism: Zea mays

source_name: Seedling

extract_protocol:
16,000 nuclei per library  were extracted via FANS
10x Genomics scATAC-seq v1

value: Frozen


title: HTR-8_Ctrl_rep2-1


title: ArabRoot-rep1


title: Crown_root2

source_name: crown root


title: Axillary_bud1

source_name: Axillary bud


title: Axillary_bud2


title: Root2

source_name: Root


title: Tassel

source_name: Tassel


title: Ear

source_name: Ear


title: CR17_CR18

status: Public on Sep 24 2020

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with cellranger
Genome_build: hg38/GRCh38 with SARS-COVID 19 genome MT246667.1
Supplementary_files_format_and_content: count matrix
Supplementary_files_format_and_content: genome.fa, genes.gtf: custom reference
Supplementary_files_format_and_content: RDS files went through ambient RNA removal using SoupX package and basic QC for low quality cells and multiplets.

source_name: Recovered COVID19 Patient

extract_protocol:
10x genomics chromium 3' Next GEM v3.1 single cell RNAseq kit
follow 10x genomics instruction

value: Blood Buffy coat

tag: patient diagnosis

tag: group

value: Recover

tag: type of library

value: expression

tag: subject id

value: sample contains cells from two patients:CR17, CR18


title: Root1


title: b73mo17


title: CR15_CR16

tag: tissue

value: sample contains cells from two patients:CR15, CR16


title: CS11_CS12

source_name: Severe COVID19 Patient

value: Severe

value: sample contains cells from two patients:CS11, CS12


title: CS9_CS10

value: sample contains cells from two patients:CS9, CS10


title: CM3_CM4

source_name: Mild COVID19 Patient

value: Mild

value: sample contains cells from two patients:CM3, CM4


title: CM1_CM2

value: sample contains cells from two patients:CM1, CM2


title: Donor 3 MCSF macrophages

city: London

first: Richard

last: Beatson

address: Innovation Hub, Cancer Centre, Guys Hospital

department: School of Cancer & Pharmaceutical Sciences

institute: King's College London

data_processing:
RNA seq analysis was performed on Partek Flow Software (https://www.partek.com/partek-flow/). All the tools with in the software was run with default settings, unless otherwise indicated.
The quality of the sequencing reads was examined using FastQC (v0.11.4) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw sequencing reads (100-nt, paired-end) were trimmed using Trimgalore (v0.4.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Traces of ribosomal DNA and mitochondrial DNA were removed using the Bowtie2 (v2.2.5)
Reads were aligned to the human reference genome GRCh38 using STAR (v2.5.3a) with two pass mapping Multi- sample setting.
Mapping and alignment quality were examined using FASTQC
Duplicate reads were removed using the MarkDuplicates function of the Picard tools (v2.17.11) (http://broadinstitute.github.io/picard/)
Reads were annotated using the Partek E/M with GENCODE V30 (https://www.gencodegenes.org/human/)
Gene counts were normalised using the Trimmed mean of M-values (TMM)
Genome_build: GENCODE V30
Supplementary_files_format_and_content: tab-delimited text files of raw counts for each Sample available on the series record.

source_name: MCSF monocyte derived macrophages

growth_protocol: Isolated primary human monocytes from healthy volunteers were cultured in AIM-V (serum-free) media at 37C 5% CO2 for 7 days

extract_protocol:
Cells were harvested and FACS sorted (BD FACSAria II Cell Sorter) for live cells after staining with a live/dead dye (ThermoFisher; L23102). Total RNA was isolated from the sorted live cells using the RNeasy Mini Kit (Qiagen; 74104) with DNAse treatment (Sigma; DN25). RNA was quantitated using the Qubit system and the RIN score was assessed using an Agilent bioanalyser 2100 (Agilent RNA 6000 Nano Kit). All samples in this study had RIN scores of 10.
PolyA isolation and library preparation was performed using SureSelect Strand Specific RNA-Seq Library Preparation kit (G9691B) on 335ng of RNA per sample.

treatment_protocol: Cells were treated with recombinant MCSF (50ng/ml every 3 days) or 100ug/ml (day 0) recombinant MUC1-ST.

value: monocyte derived macrophages

tag: sample source

value: Healthy volunteer monocytes

tag: donor id

value: MCSF


title: Donor 2 MCSF macrophages

tag: cell type


title: CM5


title: Donor 1 MUC1-ST macrophages

source_name: MUC1-ST monocyte derived macrophages

tag: treatment


title: Donor 3 MUC1-ST macrophages


title: CS7_CS8

value: sample contains cells from two patients:CS7, CS8


title: sicontrol + IL1β   (sample 9)

status: Public on Sep 19 2020

city: Augusta

first: Xiaochun

last: Long

address: 1460 Laney Walker Blvd, CL-3004

department: Vascular Biology Center

institute: Augusta University

description:
9_sicontrol_IL1B
deSeq2_counts.txt
deSeq2_NormCounts.txt

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRChg38 + Gencode-31 Annotation
Supplementary_files_format_and_content: Raw and normalized counts

source_name: human aortic smooth muscle cells (HASMCs)

growth_protocol: HASMCs were prepared by the department of molecular and cellular physiology at Albany Medical College. Cells were maintained in basal 231 medium supplemented with smooth msucle growth factors (SMG).

extract_protocol: The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample using Illumina’s HiSeq2500v4.

treatment_protocol: Subconfluent HASMCs were transfected with 25 nM siRNA for overnight. Cells were then refreshed with growth medium for 24 hrs. After starvation overnight,cells were treated with IL1b (4 ng/ml) for  24 hrs prior to total RNA extraction for sequencing.

value: Aorta

value: primary human smooth muscle culture

tag: genotype

value: sicontrol


title: siKILN2 + IL1β (sample 10)

description:
10_siKLN2_IL1B
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: Crown_root1

value: Fresh


title: Donor 1 MCSF macrophages


title: siKILN1 + vehicle (sample 2)

description:
2_siKLN1_vehicle
deSeq2_counts.txt
deSeq2_NormCounts.txt

value: vehicle


title: sicontrol + IL1β (sample 4)

description:
4_sicontrol_IL1B
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: siKILN(1+2) + vehicle (sample 3)

description:
3_siKLNmix_vehicle
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: siKILN2 + vehicle (sample 8)

description:
8_siKLN2_vehicle
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: siKILN1 + IL1β (sample 5)

description:
5_siKLN1_IL1B
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: sicontrol + vehicle (sample 7)

description:
7_sicontrol_vehicle
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: sicontrol + vehicle (sample 1)

description:
1_sicontrol_vehicle
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: siKILN(1+2) + IL1β (sample 6)

description:
6_siKLNmix_IL1B
deSeq2_counts.txt
deSeq2_NormCounts.txt


title: CR13_CR14

value: Blood Buffy coat

value: Recover

value: expression

value: sample contains cells from two patients:CR13, CR14


title: TESTGEX_HHT

status: Public on Aug 03 2020

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

institute: Yale University

description: Control Sample

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger mkfastq function from 10X Genomics 2.2.0.
Reads were aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the Cell Ranger count function.
The resulting output was loaded into Seurat v.2.3.4 for analysis.
Cells with less than 50 genes detected, or mitochondrial content above 0.2 of all transcripts were discarded.
Genome_build: GCRhg38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv, features.tsv & genes.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: Peripheral blood

extract_protocol:
B cells were isolated from PBMCs by Human Pan B cell immunomagnetic negative selection kit (StemCell) per manufacturer’s instructions.
Libraries were prepared using the Chromium Single-cell5′ Reagent Kit (10x Genomics) for version 3 chemistry per the manufacturer’s protocol.

value: B-lymphocytes

tag: mgfa class

value: Asymptomatic

tag: isolate


title: MG192B_NOIGHD_HHT

value: Iia


title: MG139B_NOIGHD_HHT

value: IIb


title: SNU719 CLASH 2

status: Public on Aug 01 2020

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

institute: Tulane Health Sciences Center

data_processing:
Library strategy: Crosslinking, Ligation, and Sequencing of Hybrids (CLASH)
Raw sequences were aligned to the combined hg38 and EBV transcriptome using Bowtie2 (version 2.3.3)
Aligned reads were processed using the hyb pipeline (https://github.com/gkudla/hyb)
Counts per million of each microRNA-mRNA hybrid were tallied
Genome_build: hg38_plus_Akata_inverted
Supplementary_files_format_and_content: Counts per million of each microRNA-mRNA hybrid

source_name: Gastric adenocarcinoma

extract_protocol:
Pan-AGO antibody pulldown, followed by intermolecular ligation of hybridized RNAs (see associated text for more details)
Illumina TruSeq Small RNA Sample Prep Kit

value: Gastric adenocarcinoma

tag: virus

value: EBV+


title: SNU719 CLASH 3


title: Akata CLASH 3

source_name: B-cell lymphoma

value: Akata

value: B-Cell lymphoma cell line


title: SNU719 CLASH 1


title: Akata CLASH 2


title: RNA_rep1_60_min

status: Public on Jul 04 2020

description: RNA at T=60 following Cd addition

data_processing:
Reads were aligned using Bowtie 0.12.7 with parameters "-n 2 -l 20 -m 1 -k 1 -X 1000" to release 64 (sacCer3) of the S.cerevisiae genomic sequence obtained from downloads.yeastgenome.org.
Data processing code from github.com/HarteminkLab/cadmium-paper was run against aligned reads. The following steps from this code were performed:
Chromatin replicates were merged and randomly sampled to equivalent proportions for each time point.
For each base pair at each ORF of the genome, chromatin characterization of transcription factors and nucleosomes were computed relative to TSSs obtained from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973313/bin/supp_42_6_3736__index.html
Transcription factor occupancy was characterized using MNase reads shorter than 100 base pairs and within 200 base pairs upstream of TSSs, defined as the "small fragment promoter occupancy" for each ORF.
Nucleosomes were characterized through cross correlating a bivariate Gaussian distribution against MNase reads at high scoring nucleosomes obtained from GEO/GSE36063. An information entropy score was computed using this per base pair cross correlation for first three nucleosomes downstream of each ORF’s TSS, defined as a gene's "gene body nucleosome disorganization".
RNA reads were counted at non-intronic regions inside ORF boundaries. TPM was computed by scaling read counts by ORF length and normalizing to an equivalent sum for each time point.
Genome_build: Saccharomyces cerevisiae S288C reference genome R64-1-1 (sacCer3)

source_name: yeast cells

tag: strain

value: 1 mM Cd

tag: time

value: 60 min


title: Akata CLASH 1

tag: cell line


title: RNA_rep1_7.5_min

description: RNA at T=7.5 following Cd addition

value: 7.5 min


title: RNA_rep1_30_min

description: RNA at T=30 following Cd addition

value: 30 min


title: RNA_rep1_120_min

description: RNA at T=120 following Cd addition

value: 120 min


title: RNA_rep1_0_min

description: RNA at T=0 prior to Cd addition

value: 0 mM Cd

value: 0 min


title: DM507_MNase_rep2_30_min

description: MNase chromatin at T=30 following Cd addition


title: DM506_MNase_rep2_15_min

description: MNase chromatin at T=15 following Cd addition

value: 15 min


title: DM508_MNase_rep2_60_min

description: MNase chromatin at T=60 following Cd addition


title: DM509_MNase_rep2_120_min

description: MNase chromatin at T=120 following Cd addition


title: DM501_MNase_rep1_30_min


title: DM504_MNase_rep2_0_min

description: MNase chromatin at T=0 prior to Cd addition


title: DM505_MNase_rep2_7.5_min

description: MNase chromatin at T=7.5 following Cd addition


title: DM498_MNase_rep1_0_min


title: DM499_MNase_rep1_7.5_min


title: Donor 2 MUC1-ST macrophages

value: monocyte derived macrophages

value: Healthy volunteer monocytes