title: 20_9234-T49_P12

value: M

value: Non-Hispanic


title: 20_9234-T28_P12

status: Public on Mar 25 2022

type: SRA

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Raw data were processed using bcl2fastq Conversion Software (Illumina) to obtain FASTQ files, and the FASTQ files were aligned to the hg38 genome using STAR (Dobin et al., 2013).
Gene expression was quantified with featureCounts (Liao et al., 2014).
Assembly: hg38
Supplementary files format and content: tab delimited file including the counts of reads for all genes and for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: PAXgene blood

growth_protocol: All biosamples were collected in accordance with the guidelines of Institutional Review Boards of Icahn School of Medicine  and  the Naval Medical Research Center (protocol number NMRC.2020.0006) in compliance with all applicable U.S. federal regulations governing the protection of human subjects

extract_protocol:
Total RNA from PAXgene preserved blood was extracted using the Agencourt RNAdvance Blood Kit (Beckman Coulter) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter). Concentration and integrity (RIN) of isolated RNA were determined using Quant-iT™ RiboGreen™ RNA Assay Kit (Thermo Fisher) and an RNA Standard Sensitivity Kit (DNF-471, Agilent Technologies, Santa Clara, CA, USA) on a Fragment Analyzer Automated CE system (Agilent Technologies), respectively.
cDNA libraries were constructed from total RNA using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States) in a Biomek i7 Automated Workstation (Beckman Coulter). Briefly, mRNA was isolated from purified 300 ng total RNA using oligo-dT beads and used to synthesize cDNA following the manufacturer’s instructions. The transcripts for ribosomal RNA (rRNA) and globin were further depleted using the AnyDeplete kit (Tecan Genomics) prior to the amplification of libraries. Library concentration was assessed fluorometrically using the Qubit dsDNA HS Kit (Thermo Fisher), and quality was assessed with the Genomic DNA 50Kb Analysis Kit (DNF-467, Agilent Technologies). Following library preparation, samples were pooled, preliminary sequencing of cDNA libraries (average read depth of 90,000 reads) was performed using a MiSeq system (Illumina) to confirm library quality and concentration. Deep sequencing was subsequently performed using an S4 flow cell in a NovaSeq sequencing system (Illumina) (average read depth ~30 million pairs of 2×100 bp reads). In addition to the 8-base i5 and i7 barcodes, the i7 adaptor contains 8 random bases immediately following the library index. The additional 8 bases are used for duplicate read determination using the Duplicate Marking Tool. To take advantage of this feature, the libraries were sequenced using 16 cycles for the i7 index read.

treatment_protocol: Whole blood was collected in Paxgene blood collection tubes (BD Biosciences) according to the manufacturer's instructions and stored at -80C until RNA extraction.

tag: tissue

value: blood

tag: enrollment batch

value: Later Surveillance

tag: biocollection id

tag: rna-seq plate

tag: participant id

tag: sample collection time point (days since t0)

tag: enrollment date t0

tag: Sex

tag: age

tag: ethnicity

tag: race

value: Black

tag: pcr test for sars-cov-2

value: Not

tag: group

value: Pre


title: 20_9234-T53_P12

value: Post


title: 20_7222-T49_P13

value: Multi-racial

value: Detected

tag: symptom

value: Mid


title: 20_9140-T63_P12

value: F

value: Hispanic

value: White


title: 20_9234-T00_P12

value: Control


title: 20_9140-T56_P12


title: 20_9140-T49_P12


title: 20_9140-T39_P12


title: 20_9140-T35_P12


title: 20_9140-T00_P12


title: 20_9140-T28_P12

value: cough

value: First


title: 20_9056-T46_P12

value: M

value: Asian


title: 20_9056-T42_P12

value: blood


title: 20_9056-T39_P12

value: Later Surveillance


title: 20_9056-T28_P12


title: 20_8991-T00_P12

value: Initial Outbreak

value: Exposed


title: 20_9056-T00_P12

value: Not


title: 20_5513-T00_P13

value: Non-Hispanic


title: 20_8257-T00_P12

value: Mild


title: 20_7451-T53_P12

value: Post


title: 20_7451-T00_P12


title: 20_7451-T91_P12


title: 20_7451-T56_P12


title: 20_7325-T46_P12

value: Detected

value: Mid


title: 20_7451-T28_P12

value: Pre


title: 20_7451-T49_P12

value: White

value: throat


title: 20_7325-T49_P12

value: F


title: 20_7325-T39_P12

value: First


title: 20_7325-T42_P12

value: msk;fatigue;throat;headache;taste


title: 20_7325-T28_P12


title: 20_7325-T00_P12

value: Control


title: 20_5944-T39_P12

value: blood

value: Hispanic

value: Other


title: 20_5944-T42_P12

value: Later Surveillance

value: msk;fatigue;throat


title: 20_5944-T28_P12


title: 20_5944-T32_P12

value: fvr;msk;fatigue;cough;sob;headache


title: 20_5944-T00_P12

value: Not

value: Immune


title: 20_5785-T56_P12

value: M

value: Non-Hispanic

value: Black

value: Post


title: 20_5785-T60_P12

value: msk;fatigue;throat;cough;headache;abd


title: 20_5785-T49_P12

value: msk;throat


title: 20_5785-T10_P12


title: 20_9140-T32_P12

value: F

value: White

value: Detected

value: Mid


title: 20_5288-T49_P12

value: blood

value: throat;cough


title: 20_5513-T00_P12

value: Initial Outbreak

value: Exposed


title: 20_5288-T46_P12

value: Later Surveillance


title: 20_5288-T42_P12


title: 20_5288-T28_P12

value: Not

value: Pre


title: 20_7325-T91_P12


title: 20_5162-T49_P12

value: M

value: Hispanic


title: 20_5162-T28_P12


title: 20_5288-T00_P12

value: Non-Hispanic

value: Control


title: 20_5785-T63_P12

value: Black

value: msk;fatigue;throat;cough;headache;abd

value: Post


title: 20_5162-T53_P12

value: White


title: 20_5162-T00_P12


title: 20_5089-T49_P12

value: F


title: 20_5089-T91_P12


title: 20_5089-T63_P12


title: 20_5089-T46_P12

value: Detected

value: Mid


title: 20_5089-T42_P12

value: blood


title: 20_5089-T35_P12

value: False Negative


title: 20_5089-T39_P12

value: First


title: 20_5089-T28_P12

value: Later Surveillance


title: 20_5089-T00_P12

value: Not


title: 20_5002-T91_P12


title: 20_5002-T56_P12


title: 20_5002-T49_P12


title: 20_5002-T00_P12


title: 20_9862-T28_P11

value: Initial Outbreak

value: Hawaiian/OPI

value: Moderate


title: 20_9837-T28_P11

value: M

value: Non-Hispanic

value: Mild


title: 20_5785-T53_P12

value: Black

value: msk;fatigue;throat;headache


title: 20_5002-T53_P12

value: White

value: Post


title: 20_9356-T28_P11

value: Asymptomatic


title: 20_9640-T28_P11

value: Hispanic


title: 20_9610-T28_P11

value: blood


title: 20_9248-T00_P11


title: 20_9248-T28_P11


title: 20_9194-T28_P11


title: 20_9092-T28_P11


title: 20_9179-T28_P11

value: AI/AN


title: 20_5288-T39_P12

value: Detected

value: Mid


title: 20_8932-T28_P11

value: Not


title: 20_9063-T28_P11

value: Initial Outbreak

value: Asian


title: 20_8849-T28_P11


title: 20_5162-T56_P12

value: Later Surveillance


title: 20_5162-T91_P12

value: M


title: 20_5288-T35_P12

value: Non-Hispanic

value: First


title: 20_8825-T28_P11

value: Exposed


title: 20_8652-T28_P11

value: fatigue

value: Mild


title: 20_8652-T00_P11


title: 20_8440-T28_P11

value: F

value: White

value: headache

value: Moderate


title: 20_8132-T28_P11

value: blood

value: Asymptomatic


title: 20_8136-T00_P11


title: 20_8136-T28_P11


title: 20_8127-T28_P11

value: Hispanic


title: 20_8197-T28_P11

value: Not


title: 20_5002-T28_P12

value: Pre


title: 20_8083-T28_P11

value: Initial Outbreak

value: Black


title: 20_8102-T28_P11

value: M


title: 20_7996-T28_P11

value: Non-Hispanic


title: 20_7865-T28_P11


title: 20_7996-T00_P11


title: 20_7833-T28_P11


title: 20_7766-T28_P11

value: msk;fatigue


title: 20_7656-T28_P11


title: 20_7582-T28_P11


title: 20_7727-T28_P11


title: 20_6939-T28_P11


title: 20_6954-T28_P11


title: 20_7143-T28_P11


title: 20_9262-T28_P11

value: Exposed


title: 20_6600-T28_P11


title: 20_6694-T28_P11


title: 20_9220-T28_P11


title: 20_7458-T28_P11


title: 20_6533-T28_P11

value: diarr


title: 20_6578-T28_P11


title: 20_8991-T00_P11


title: 20_6483-T28_P11


title: 20_6431-T28_P11

value: Mild


title: 20_6367-T28_P11

value: AI/AN


title: 20_6114-T28_P11


title: 20_8552-T28_P11

value: F


title: 20_8585-T28_P11

value: White


title: 20_6107-T28_P11


title: 20_6023-T28_P11

value: Moderate


title: 20_6100-T28_P11

value: blood


title: 20_6092-T28_P11

value: Asymptomatic


title: 20_5985-T28_P11

value: Hispanic


title: 20_5937-T28_P11

value: Not

value: fatigue;throat;sob;nv;headache


title: 20_5738-T28_P11

value: Initial Outbreak


title: 20_5837-T28_P11


title: 20_5864-T28_P11


title: 20_5972-T28_P11


title: 20_5698-T28_P11


title: 20_5662-T28_P11

value: Black


title: 20_5708-T28_P11

value: M


title: 20_5512-T28_P11


title: 20_5513-T00_P11

value: Non-Hispanic


title: 20_5542-T28_P11


title: 20_5342-T28_P11


title: 20_5303-T28_P11


title: 20_5246-T28_P11


title: 20_5285-T28_P11


title: 20_5274-T28_P11


title: 20_5228-T28_P11


title: 20_5218-T28_P11

value: Other


title: 20_5195-T28_P11

value: cough

value: Exposed


title: 20_5135-T28_P11


title: 20_9373-T46_P10

value: Later Surveillance

value: Detected

value: Mid


title: 20_5195-T00_P11

value: White

value: cough;abd;diarr


title: 20_9520-T00_P10

value: blood

value: F

value: fatigue

value: Moderate


title: 20_9373-T56_P10

value: Hispanic

value: Not

value: Post


title: 20_9373-T00_P10

value: M

value: Control


title: 20_9201-T56_P10


title: 20_6212-T28_P11

value: Initial Outbreak

value: Mild


title: 20_9201-T49_P10


title: 20_9201-T46_P10


title: 20_9065-T00_P10

value: Immune +


title: 20_9065-T35_P10

value: Later Surveillance


title: 20_9065-T42_P10


title: 20_8992-T42_P10

value: Detected


title: 20_8992-T35_P10

value: Mid


title: 20_8992-T39_P10

value: White


title: 20_8991-T00_P10

value: Exposed


title: 20_8876-T56_P10

value: blood

value: Non-Hispanic


title: 20_8876-T46_P10

value: fatigue;taste


title: 20_8992-T00_P10

value: nv


title: 20_8876-T49_P10


title: 20_8876-T00_P10


title: 20_8860-T56_P10

value: Asian


title: 20_8800-T49_P10


title: 20_8800-T46_P10


title: 20_8017-T49_P10

value: Hispanic

value: Not


title: 20_8860-T39_P10

value: M

value: First


title: 20_8257-T00_P10

value: Initial Outbreak


title: 20_8017-T46_P10


title: 20_8017-T56_P10


title: 20_8800-T00_P10

value: Control


title: 20_7700-T49_P10

value: Other


title: 20_8860-T00_P10

value: Later Surveillance


title: 20_7583-T49_P10

value: msk;fatigue;throat;sob;headache

value: Pre


title: 20_7247-T49_P10

value: Multi-racial

value: Detected

value: Mid


title: 20_7247-T46_P10

value: blood

value: Non-Hispanic


title: 20_7247-T42_P10


title: 20_7247-T00_P10


title: 20_7700-T56_P10


title: 20_8017-T00_P10


title: 20_7700-T42_P10


title: 20_9201-T00_P10

value: White


title: 20_7583-T53_P10


title: 20_7583-T28_P10


title: 20_7193-T42_P10

value: F


title: 20_7247-T56_P10

value: Post


title: 20_8860-T46_P10

value: Asian

value: Not

value: taste


title: 20_7700-T00_P10

value: M

value: Hispanic


title: 20_7193-T63_P10

value: Control


title: 20_8800-T56_P10

value: Later Surveillance


title: 20_7084-T56_P10


title: 20_7193-T56_P10


title: 20_7030-T46_P10


title: 20_7084-T46_P10


title: 20_7084-T49_P10


title: 20_6956-T56_P10


title: 20_7084-T00_P10


title: 20_7030-T56_P10


title: 20_7030-T00_P10


title: 20_7916-T56_P10


title: 20_6956-T49_P10


title: 20_7700-T46_P10

value: Other


title: 20_6956-T00_P10


title: 20_6911-T56_P10


title: 20_6956-T46_P10


title: 20_6911-T42_P10


title: 20_6911-T39_P10


title: 20_7583-T56_P10


title: 20_6132-T56_P10


title: 20_6911-T00_P10


title: 20_7247-T35_P10


title: 20_6132-T42_P10

value: chill;msk;fatigue;headache


title: 20_6132-T00_P10


title: 20_5910-T56_P10

value: Black


title: 20_5910-T00_P10


title: 20_5910-T49_P10

value: Detected


title: 20_5890-T56_P10

value: Mid


title: 20_5910-T46_P10

value: blood


title: 20_5890-T49_P10


title: 20_5890-T46_P10


title: 20_5890-T00_P10


title: 20_5322-T56_P10


title: 20_5513-T00_P10

value: Initial Outbreak

value: Non-Hispanic

value: Exposed


title: 20_5322-T49_P10

value: White


title: 20_5322-T00_P10


title: 20_5322-T46_P10


title: 20_9914-T42_P9

value: AI/AN

value: Post


title: 20_9914-T56_P9

value: Reinfection


title: 20_9914-T00_P9

value: M

value: Not


title: 20_9914-T35_P9


title: 20_9914-T39_P9


title: 20_9719-T46_P9


title: 20_9719-T49_P9


title: 20_9719-T00_P9

value: Control


title: 20_6911-T35_P10

value: Later Surveillance

value: Hispanic

value: Multi-racial


title: 20_9511-T56_P9


title: 20_9511-T49_P9


title: 20_9511-T00_P9


title: 20_6132-T46_P10


title: 20_6132-T49_P10


title: 20_9500-T46_P9


title: 20_6132-T39_P10

value: First


title: 20_9500-T49_P9

value: Detected


title: 20_9500-T00_P9


title: 20_9235-T56_P9


title: 20_9235-T46_P9

value: Mid


title: 20_9235-T49_P9

value: blood


title: 20_9235-T00_P9


title: 20_8629-T56_P9


title: 20_8991-T00_P9

value: Initial Outbreak


title: 20_8629-T00_P9

value: Non-Hispanic


title: 20_8629-T53_P9


title: 20_9511-T46_P9


title: 20_8378-T56_P9


title: 20_8528-T49_P9


title: 20_8349-T56_P9

value: Black


title: 20_8528-T00_P9

value: White

value: throat;headache


title: 20_8378-T42_P9

value: chill;msk;fatigue;throat;cough;headache


title: 20_8528-T46_P9


title: 20_8378-T00_P9


title: 20_9719-T56_P9

value: Post


title: 20_8349-T46_P9

value: M


title: 20_7981-T56_P9

value: Not


title: 20_8349-T00_P9

value: Control


title: 20_7981-T49_P9

value: Later Surveillance


title: 20_9520-T00_P9

value: F

value: Hispanic

value: fatigue

value: Moderate


title: 20_7981-T46_P9

value: Detected

value: Mid


title: 20_7981-T00_P9

value: blood


title: 20_7733-T49_P9


title: 20_7733-T46_P9


title: 20_7733-T42_P9

value: msk;throat;cough


title: 20_7733-T39_P9


title: 20_7733-T35_P9


title: 20_7733-T56_P9


title: 20_7733-T00_P9


title: 20_7711-T49_P9


title: 20_9500-T56_P9

value: Non-Hispanic


title: 20_7711-T00_P9

value: White


title: 20_7683-T46_P9


title: 20_7683-T49_P9


title: 20_7683-T00_P9


title: 20_7611-T56_P9

value: taste


title: 20_7611-T53_P9


title: 20_7611-T00_P9


title: 20_7037-T56_P9

value: Black


title: 20_7037-T49_P9


title: 20_7037-T00_P9


title: 20_6016-T42_P9

value: Post


title: 20_6016-T39_P9

value: M


title: 20_6016-T00_P9

value: Not


title: 20_6016-T35_P9


title: 20_5988-T49_P9


title: 20_5988-T00_P9

value: Control


title: 20_5988-T56_P9

value: Later Surveillance


title: 20_5988-T46_P9


title: 20_5743-T39_P9


title: 20_5743-T56_P9


title: 20_5903-T00_P9


title: 20_5765-T00_P9


title: 20_5765-T46_P9


title: 20_5743-T00_P9


title: 20_5513-T00_P9

value: Initial Outbreak

value: F

value: Exposed


title: 20_5189-T56_P9

value: Reinfection


title: 20_7683-T56_P9


title: 20_5189-T39_P9


title: 20_5189-T42_P9


title: 20_5189-T35_P9


title: 20_5189-T00_P9


title: 20_5038-T49_P9

value: Hispanic

value: Detected


title: 20_5743-T35_P9

value: blood

value: Mid


title: 20_9808-T14_P8

value: Non-Hispanic


title: 20_5038-T00_P9

value: White


title: 20_9808-T07_P8


title: 20_5038-T46_P9


title: 20_9749-T28_P8

value: Pre


title: 20_9749-T56_P8


title: 20_9568-T00_P8


title: 20_9568-T28_P8


title: 20_9520-T00_P8

value: fatigue

value: Moderate


title: 20_9469-T00_P8


title: 20_7037-T46_P9

value: M

value: Black


title: 20_9252-T53_P8

value: Not

value: Post


title: 20_9252-T49_P8

value: Later Surveillance


title: 20_9317-T00_P8

value: Control


title: 20_9302-T00_P8

value: Other


title: 20_9302-T28_P8


title: 20_9252-T28_P8


title: 20_9315-T00_P8


title: 20_9247-T56_P8

value: F


title: 20_9247-T49_P8

value: Hispanic


title: 20_9237-T56_P8


title: 20_5743-T42_P9

value: Detected


title: 20_9234-T56_P8

value: blood


title: 20_9234-T53_P8


title: 20_9234-T49_P8

value: Mid


title: 20_9153-T53_P8

value: Non-Hispanic


title: 20_9153-T56_P8

value: White


title: 20_9140-T56_P8


title: 20_9140-T49_P8


title: 20_8991-T00_P8

value: Initial Outbreak

value: Exposed


title: 20_8586-T56_P8

value: Problems:Inconclusive ran twice. New sample required


title: 20_9007-T00_P8

value: M


title: 20_9007-T28_P8


title: 20_8586-T53_P8


title: 20_8122-T53_P8


title: 20_7728-T14_P8


title: 20_8257-T00_P8

value: Mild


title: 20_7776-T53_P8


title: 20_7728-T10_P8

value: Not


title: 20_7692-T00_P8

value: Hawaiian/OPI


title: 20_7683-T35_P8

value: Later Surveillance


title: 20_7451-T53_P8

value: Post


title: 20_7711-T46_P9


title: 20_7438-T56_P8

value: Other


title: 20_9385-T56_P8

value: F


title: 20_7683-T42_P8

value: fatigue;sob


title: 20_7728-T07_P8

value: Hispanic


title: 20_7438-T53_P8

value: blood


title: 20_7451-T49_P8

value: Detected

value: throat

value: Mid


title: 20_7252-T56_P8

value: AI/AN


title: 20_7392-T00_P8

value: White

value: Control


title: 20_7246-T00_P8


title: 20_7252-T49_P8

value: cough


title: 20_7191-T14_P8

value: Non-Hispanic


title: 20_7213-T53_P8

value: M

value: Not


title: 20_6985-T53_P8

value: Later Surveillance

value: Black


title: 20_6542-T00_P8


title: 20_6059-T28_P8

value: Pre


title: 20_6323-T00_P8

value: Asian


title: 20_5948-T00_P8

value: F


title: 20_5944-T28_P8

value: Hispanic

value: Other

value: First


title: 20_5914-T00_P8

value: blood


title: 20_5849-T28_P8


title: 20_5849-T00_P8


title: 20_5893-T56_P8

value: Post


title: 20_5737-T00_P8


title: 20_5846-T49_P8


title: 20_5513-T00_P8

value: Initial Outbreak

value: Exposed


title: 20_5632-T56_P8

value: White

value: Detected

value: Mid


title: 20_5632-T49_P8


title: 20_5846-T56_P8

value: Non-Hispanic

value: fvr;fatigue;sob


title: 20_5405-T21_P8

value: Later Surveillance

value: M

value: Not


title: 20_5237-T56_P8


title: 20_5455-T56_P8


title: 20_7438-T49_P8


title: 20_5237-T53_P8


title: 20_5162-T56_P8


title: 20_5162-T53_P8


title: 20_5068-T56_P8

value: Black


title: 20_6985-T56_P8


title: 20_5012-T00_P8

value: F

value: Control


title: 20_6636-T56_P8

value: msk;fatigue;abd


title: 20_5068-T28_P8

value: Pre


title: 20_5068-T53_P8

value: blood


title: 20_5002-T53_P8

value: Post


title: 20_5002-T56_P8


title: 20_9749-T46_P7

value: Hispanic


title: 20_9940-T42_P7

value: msk;fatigue;cough;sob;taste

value: First


title: 20_9940-T28_P7

value: White

value: Problems:Inconclusive ran twice. New sample required


title: 20_9749-T49_P7


title: 20_9634-T28_P7

value: Asian

value: Detected


title: 20_9749-T39_P7

value: Later Surveillance


title: 20_9385-T35_P7

value: Mid


title: 20_5408-T56_P8

value: Non-Hispanic

value: Not


title: 20_9385-T39_P7

value: F


title: 20_9634-T00_P7

value: M

value: Control


title: 20_9385-T49_P7


title: 20_9520-T00_P7

value: Initial Outbreak

value: fatigue

value: Moderate


title: 20_5455-T49_P8

value: blood

value: Hispanic

value: Other

value: Post


title: 20_9157-T49_P7

value: White

value: sob;nv


title: 20_9244-T00_P7


title: 20_9157-T46_P7


title: 20_9153-T49_P7

value: Detected


title: 20_9157-T28_P7

value: Later Surveillance

value: Pre


title: 20_9157-T39_P7

value: Non-Hispanic

value: First


title: 20_9153-T42_P7


title: 20_9153-T28_P7

value: Not


title: 20_5162-T49_P8

value: M

value: Mid


title: 20_9127-T49_P7

value: F

value: cough;headache


title: 20_9940-T49_P7


title: 20_8702-T00_P7

value: Control


title: 20_8702-T28_P7

value: blood


title: 20_8991-T00_P7

value: Initial Outbreak

value: Hispanic

value: Exposed


title: 20_8586-T49_P7

value: White


title: 20_8586-T46_P7


title: 20_8426-T46_P7


title: 20_9634-T49_P7

value: Asian


title: 20_8586-T28_P7


title: 20_8122-T49_P7

value: Detected


title: 20_8426-T49_P7

value: Later Surveillance


title: 20_8586-T00_P7


title: 20_7869-T28_P7

value: Other

value: Pre


title: 20_8257-T00_P7

value: Non-Hispanic

value: Mild


title: 20_8426-T42_P7

value: M

value: fvr;msk;fatigue;throat;cough

value: First


title: 20_8167-T00_P7

value: Black

value: Not


title: 20_8426-T28_P7

value: blood


title: 20_8167-T28_P7


title: 20_7577-T39_P7

value: F

value: Mid


title: 20_8122-T00_P7

value: Control


title: 20_7325-T49_P7

value: White


title: 20_7577-T46_P7

value: Post


title: 20_7325-T46_P7

value: Detected


title: 20_8426-T00_P7

value: Later Surveillance


title: 20_8167-T49_P7

value: Hispanic


title: 20_7776-T46_P7


title: 20_7869-T00_P7

value: Other


title: 20_7309-T00_P7


title: 20_7776-T28_P7

value: Non-Hispanic

value: Pre


title: 20_7222-T46_P7

value: M

value: Multi-racial


title: 20_7160-T46_P7


title: 20_9127-T46_P7


title: 20_9244-T28_P7


title: 20_7776-T49_P7


title: 20_7149-T28_P7


title: 20_7149-T49_P7


title: 20_7309-T28_P7

value: First


title: 20_6985-T46_P7

value: Black


title: 20_6985-T42_P7


title: 20_7149-T00_P7

value: Not

value: Immune


title: 20_6985-T49_P7

value: blood


title: 20_6636-T46_P7

value: F


title: 20_6228-T00_P7

value: Control


title: 20_6241-T28_P7

value: White


title: 20_6228-T28_P7

value: msk;sob;headache


title: 20_7577-T49_P7

value: Post


title: 20_6096-T28_P7

value: Later Surveillance


title: 20_5408-T49_P7

value: Detected

value: Mid


title: 20_6096-T42_P7

value: Hispanic

value: fvr


title: 20_6636-T49_P7

value: Non-Hispanic


title: 20_5513-T00_P7

value: Initial Outbreak

value: Exposed


title: 20_5893-T49_P7


title: 20_5237-T49_P7

value: M


title: 20_6096-T00_P7

value: Not


title: 20_5011-T49_P7


title: 20_5621-T49_P7

value: AI/AN


title: 20_5408-T42_P7

value: blood

value: First


title: 20_5893-T42_P7

value: F

value: msk;throat


title: 20_6241-T49_P7

value: White


title: 20_5089-T49_P7

value: Post


title: 20_5011-T28_P7

value: Later Surveillance

value: throat

value: Pre


title: 20_5002-T49_P7


title: 20_5237-T46_P7

value: Detected

value: Mid


title: 20_9449-T14_P6

value: Hispanic


title: 20_9859-T00_P6

value: Black


title: 20_9449-T07_P6


title: 20_5011-T00_P7

value: Non-Hispanic

value: Control


title: 20_5089-T46_P7


title: 20_9449-T03_P6

value: M

value: Not


title: 20_9449-T00_P6

value: blood


title: 20_9365-T35_P6


title: 20_9385-T39_P6


title: 20_9365-T39_P6


title: 20_9247-T35_P6

value: chill;cough


title: 20_9247-T32_P6

value: F

value: First


title: 20_9140-T39_P6

value: White


title: 20_9127-T42_P6

value: cough;headache


title: 20_9247-T39_P6

value: Later Surveillance


title: 20_8586-T39_P6


title: 20_9056-T39_P6

value: Asian


title: 20_8522-T14_P6


title: 20_9001-T00_P6

value: AI/AN


title: 20_9140-T35_P6

value: Detected


title: 20_9127-T35_P6

value: fatigue;throat;cough;headache;abd;diarr


title: 20_9056-T42_P6

value: Mid


title: 20_8387-T03_P6

value: Hispanic


title: 20_8586-T42_P6

value: Non-Hispanic


title: 20_8387-T07_P6


title: 20_8522-T07_P6


title: 20_7776-T42_P6


title: 20_7776-T39_P6


title: 20_8359-T39_P6

value: Other


title: 20_7620-T28_P6

value: M


title: 20_9581-T07_P6


title: 20_7488-T07_P6

value: Not


title: 20_7620-T24_P6

value: blood


title: 20_9385-T35_P6


title: 20_9140-T32_P6


title: 20_7222-T42_P6

value: Multi-racial


title: 20_9001-T03_P6

value: F


title: 20_7252-T42_P6

value: msk;cough


title: 20_7325-T42_P6

value: White

value: msk;fatigue;throat;headache;taste


title: 20_9127-T39_P6

value: Later Surveillance


title: 20_7325-T39_P6

value: First


title: 20_7160-T42_P6


title: 20_7325-T28_P6

value: Pre


title: 20_7160-T39_P6

value: Detected


title: 20_7222-T35_P6


title: 20_7191-T07_P6


title: 20_8359-T42_P6


title: 20_6313-T10_P6


title: 20_7191-T00_P6

value: msk;fatigue


title: 20_7252-T39_P6

value: AI/AN

value: Mid


title: 20_7325-T00_P6

value: Non-Hispanic

value: Control


title: 20_6845-T03_P6

value: Black


title: 20_5944-T32_P6

value: Hispanic

value: Other

value: fvr;msk;fatigue;cough;sob;headache


title: 20_6636-T39_P6

value: blood

value: F


title: 20_9001-T07_P6

value: Not


title: 20_5944-T42_P6

value: msk;fatigue;throat


title: 20_6313-T14_P6

value: Later Surveillance

value: M

value: White


title: 20_5944-T39_P6


title: 20_8387-T00_P6

value: Detected

value: First


title: 20_5632-T39_P6


title: 20_5540-T03_P6


title: 20_5632-T28_P6

value: chill;msk

value: Pre


title: 20_5540-T07_P6

value: Non-Hispanic

value: Mid


title: 20_5540-T00_P6

value: Black

value: fatigue;throat;cough


title: 20_5288-T35_P6


title: 20_6845-T07_P6


title: 20_5089-T42_P6


title: 20_5237-T42_P6


title: 20_5288-T39_P6


title: 20_5288-T42_P6


title: 20_6845-T00_P6


title: 20_5089-T39_P6


title: 20_5237-T28_P6


title: 20_6636-T35_P6

value: chill;msk;throat;cough;headache


title: 20_5217-T07_P6

value: Hispanic


title: 20_9808-T03_P5

value: blood


title: 20_9581-T03_P5

value: F

value: Asian


title: 20_9385-T32_P5


title: 20_9385-T28_P5

value: Not


title: 20_5237-T39_P6

value: Later Surveillance


title: 20_9808-T00_P5


title: 20_9247-T00_P5

value: Control


title: 20_9336-T03_P5


title: 20_5632-T42_P6

value: White


title: 20_9365-T00_P5


title: 20_9247-T28_P5


title: 20_9234-T28_P5

value: M


title: 20_9237-T35_P5

value: Detected

value: First


title: 20_9237-T28_P5

value: Pre


title: 20_9234-T00_P5

value: Non-Hispanic


title: 20_9127-T28_P5


title: 20_9140-T28_P5

value: cough


title: 20_9005-T14_P5

value: Post


title: 20_9005-T10_P5


title: 20_8416-T28_P5


title: 20_9056-T28_P5


title: 20_8522-T03_P5

value: Mid


title: 20_8522-T00_P5


title: 20_8359-T35_P5

value: Other


title: 20_8359-T28_P5

value: Hispanic


title: 20_8359-T32_P5

value: blood


title: 20_7620-T17_P5


title: 20_7910-T00_P5


title: 20_7577-T32_P5

value: F


title: 20_7577-T35_P5


title: 20_8364-T00_P5


title: 20_5089-T35_P6

value: False Negative


title: 20_9336-T00_P5


title: 20_7910-T10_P5

value: Problems:QNS/Leaked in Transit

value: headache


title: 20_9581-T00_P5

value: Later Surveillance

value: Asian


title: 20_7488-T03_P5

value: White


title: 20_7577-T28_P5

value: Detected


title: 20_7451-T28_P5

value: M

value: Not


title: 20_7488-T00_P5

value: Non-Hispanic

value: First


title: 20_7451-T00_P5

value: Control


title: 20_7434-T28_P5


title: 20_7434-T00_P5


title: 20_7389-T28_P5

value: nv


title: 20_7389-T00_P5


title: 20_7252-T35_P5

value: AI/AN

value: Mid


title: 20_7252-T32_P5

value: blood

value: Hispanic


title: 20_7252-T28_P5

value: F


title: 20_7160-T35_P5


title: 20_7193-T28_P5


title: 20_9056-T00_P5


title: 20_7193-T35_P5


title: 20_7160-T28_P5

value: Pre


title: 20_7160-T00_P5


title: 20_7005-T00_P5

value: taste

value: Post


title: 20_7005-T07_P5

value: Later Surveillance


title: 20_6403-T28_P5

value: Black


title: 20_7005-T10_P5

value: White


title: 20_6944-T28_P5

value: M


title: 20_6944-T00_P5

value: Not


title: 20_6636-T32_P5

value: Non-Hispanic

value: Detected


title: 20_6728-T28_P5

value: Initial Outbreak

value: Multi-racial

value: Mild


title: 20_6636-T28_P5


title: 20_5893-T28_P5


title: 20_5810-T00_P5

value: Control


title: 20_5697-T00_P5

value: blood

value: Asian


title: 20_5693-T35_P5

value: F

value: Hispanic

value: cough


title: 20_5893-T35_P5

value: throat

value: First


title: 20_5693-T00_P5

value: Later Surveillance


title: 20_5693-T28_P5

value: White


title: 20_5619-T28_P5

value: M

value: Immune +


title: 20_5405-T07_P5

value: Black

value: Not

value: Post


title: 20_7340-T28_P5


title: 20_5408-T35_P5

value: Non-Hispanic

value: Pre


title: 20_5455-T28_P5

value: Other


title: 20_5288-T28_P5

value: blood


title: 20_5405-T03_P5


title: 20_5217-T03_P5

value: Detected

value: Mid


title: 20_5162-T00_P5

value: Hispanic

value: Control


title: 20_5217-T00_P5

value: F


title: 20_5089-T28_P5


title: 20_5162-T28_P5


title: 20_9131-T28_P4

value: Initial Outbreak

value: Moderate


title: 20_9445-T28_P4

value: White

value: Asymptomatic


title: 20_9512-T28_P4

value: M


title: 20_9005-T00_P4

value: Later Surveillance

value: First


title: 20_5002-T00_P5

value: Not


title: 20_5002-T28_P5

value: Non-Hispanic


title: 20_8991-T28_P4

value: Exposed


title: 20_5288-T00_P5


title: 20_9641-T28_P4


title: 20_9005-T03_P4

value: Post


title: 20_8014-T28_P4

value: blood


title: 20_8257-T28_P4

value: Mild


title: 20_8245-T28_P4

value: msk;fatigue;throat;cough;sob;headache


title: 20_5089-T00_P5


title: 20_7910-T03_P4

value: headache


title: 20_7910-T07_P4


title: 20_9005-T07_P4


title: 20_7728-T00_P4

value: Hispanic


title: 20_7910-T00_P4

value: Detected


title: 20_7728-T03_P4


title: 20_5405-T10_P5

value: Black


title: 20_7620-T14_P4

value: Mid


title: 20_7620-T00_P4

value: White


title: 20_7620-T10_P4


title: 20_7327-T00_P4

value: F

value: Immune +


title: 20_7466-T28_P4

value: Initial Outbreak

value: M


title: 20_7327-T03_P4

value: Later Surveillance

value: Not


title: 20_7057-T20_P4


title: 20_9835-T28_P4

value: Asymptomatic


title: 20_7057-T00_P4

value: Immune


title: 20_7033-T20_P4

value: blood

value: Post


title: 20_7033-T00_P4


title: 20_6943-T20_P4

value: Non-Hispanic

value: Multi-racial


title: 20_6991-T28_P4


title: 20_7005-T00_P4

value: taste


title: 20_6634-T28_P4

value: Hispanic

value: Moderate


title: 20_6875-T28_P4

value: Black

value: msk;headache

value: Mild


title: 20_6320-T28_P4

value: F


title: 20_6872-T28_P4

value: Initial Outbreak

value: White


title: 20_6067-T28_P4


title: 20_6001-T28_P4

value: M

value: Exposed


title: 20_5653-T28_P4

value: Not


title: 20_6449-T28_P4

value: Asymptomatic


title: 20_5674-T20_P4

value: blood

value: Later Surveillance


title: 20_5615-T28_P4

value: Non-Hispanic


title: 20_5658-T28_P4


title: 20_5844-T28_P4


title: 20_5568-T28_P4

value: Asian

value: throat


title: 20_7005-T03_P4

value: taste

value: Post


title: 20_5411-T28_P4


title: 20_6634-T00_P4

value: Hispanic

value: Moderate


title: 20_7432-T28_P4

value: Multi-racial

value: headache;abd


title: 20_5420-T28_P4

value: Initial Outbreak

value: F

value: Mild


title: 20_5405-T03_P4

value: M

value: Black


title: 20_5405-T00_P4

value: Detected

value: First


title: 20_5139-T00_P4

value: blood

value: Later Surveillance

value: Not

value: Control


title: 20_5326-T28_P4

value: White


title: 20_5134-T28_P4

value: Asymptomatic


title: 20_9990-T00_P3

value: Non-Hispanic


title: 20_9940-T00_P3

value: Hispanic


title: 20_9853-T00_P3


title: 20_9419-T00_P3


title: 20_6943-T00_P4

value: Multi-racial

value: Pre


title: 20_9279-T00_P3

value: AI/AN


title: 20_9140-T00_P3

value: F


title: 20_9145-T00_P3


title: 20_9041-T00_P3


title: 20_9036-T00_P3


title: 20_9127-T00_P3


title: 20_9005-T00_P3


title: 20_8946-T00_P3


title: 20_8769-T00_P3


title: 20_8359-T00_P3

value: Other


title: 20_8269-T00_P3

value: M

value: headache


title: 20_8585-T00_P3

value: Initial Outbreak


title: 20_7741-T00_P3


title: 20_7812-T00_P3


title: 20_7630-T00_P3

value: Black


title: 20_7577-T00_P3

value: blood


title: 20_7620-T00_P3

value: Later Surveillance

value: Detected

value: First


title: 20_7583-T00_P3

value: White

value: Not

value: Control


title: 20_7327-T00_P3

value: Hispanic

value: Immune +


title: 20_7193-T00_P3

value: Non-Hispanic


title: 20_7438-T00_P3


title: 20_7160-T00_P3


title: 20_9252-T00_P3


title: 20_7099-T00_P3

value: Exposed


title: 20_5063-T28_P4

value: F

value: msk;fatigue

value: Moderate


title: 20_9356-T00_P3

value: M

value: Asymptomatic


title: 20_7284-T00_P3

value: Immune


title: 20_9153-T00_P3

value: blood


title: 20_7057-T14_P3

value: Later Surveillance

value: Post


title: 20_7057-T00_P3


title: 20_7057-T17_P3


title: 20_8416-T00_P3


title: 20_7053-T00_P3


title: 20_7033-T17_P3

value: Detected

value: Mid


title: 20_7033-T14_P3

value: Problems:New Sample Required


title: 20_9021-T00_P3

value: White

value: Not

value: Control


title: 20_7033-T10_P3

value: Hispanic


title: 20_7776-T00_P3

value: Non-Hispanic

value: throat


title: 20_7033-T00_P3


title: 20_6985-T00_P3

value: Black


title: 20_6943-T17_P3

value: F

value: Multi-racial


title: 20_6943-T14_P3


title: 20_6943-T10_P3


title: 20_6943-T00_P3

value: Pre


title: 20_6939-T00_P3

value: Initial Outbreak

value: Moderate


title: 20_6636-T00_P3

value: blood

value: Later Surveillance


title: 20_7222-T00_P3

value: M


title: 20_6059-T00_P3


title: 20_5937-T00_P3

value: sob;headache;abd

value: Exposed


title: 20_5893-T00_P3

value: White


title: 20_5876-T00_P3

value: Not


title: 20_5837-T00_P3

value: Asymptomatic


title: 20_5840-T00_P3

value: Control


title: 20_5846-T00_P3

value: Non-Hispanic


title: 20_7057-T10_P3

value: Hispanic

value: Detected

value: Mid


title: 20_5785-T10_P3

value: Black

value: Post


title: 20_5693-T00_P3

value: F


title: 20_5674-T17_P3

value: Multi-racial


title: 20_5674-T07_P3

value: blood

value: sob


title: 20_5608-T00_P3

value: Initial Outbreak

value: M

value: Mild


title: 20_5632-T00_P3

value: Later Surveillance

value: White


title: 20_5455-T00_P3

value: Other

value: Immune +


title: 20_5674-T14_P3

value: Not


title: 20_9992-T00_P2R

value: Hispanic

value: chill;msk


title: 20_5270-T00_P3

value: Control


title: 20_5068-T00_P3

value: Non-Hispanic

value: Black


title: 20_5466-T00_P3

value: F


title: 20_5674-T00_P3

value: Multi-racial

value: Detected

value: First


title: 20_9836-T00_P2R

value: blood

value: Initial Outbreak

value: Asymptomatic


title: 20_9749-T00_P2R

value: Later Surveillance


title: 20_5237-T00_P3

value: M

value: White


title: 20_9640-T00_P2R


title: 20_9711-T00_P2R

value: taste

value: Immune


title: 20_6634-T00_P3

value: Hispanic

value: Moderate


title: 20_9651-T00_P2R

value: Immune +


title: 20_9520-T00_P2R

value: fatigue


title: 20_5944-T00_P3

value: Other

value: Not


title: 20_9512-T00_P2R

value: Black


title: 20_9373-T42_P2R

value: Detected

value: headache

value: Mid


title: 20_9373-T39_P2R

value: blood


title: 20_9373-T35_P2R


title: 20_9262-T00_P2R

value: Initial Outbreak

value: Non-Hispanic

value: Exposed


title: 20_9194-T00_P2R

value: M

value: White

value: Asymptomatic


title: 20_9179-T00_P2R

value: AI/AN


title: 20_9220-T00_P2R


title: 20_9157-T00_P2R

value: Later Surveillance

value: F

value: Control


title: 20_9092-T00_P2R


title: 20_8991-T00_P2R

value: Hispanic


title: 20_8932-T00_P2R


title: 20_8939-T00_P2R


title: 20_5655-T00_P3

value: Not


title: 20_8747-T00_P2R


title: 20_8552-T00_P2R

value: Black

value: Mild


title: 20_8825-T00_P2R


title: 20_8440-T00_P2R

value: Moderate


title: 20_8278-T00_P2R


title: 20_8420-T00_P2R

value: Immune +


title: 20_8257-T00_P2R

value: blood


title: 20_8197-T00_P2R

value: Initial Outbreak


title: 20_8132-T00_P2R

value: Non-Hispanic


title: 20_8127-T00_P2R


title: 20_7725-T00_P2R


title: 20_7582-T00_P2R


title: 20_7458-T00_P2R


title: 20_7865-T00_P2R


title: 20_7766-T00_P2R

value: msk

value: Exposed


title: 20_7727-T00_P2R

value: M

value: White


title: 20_7030-T35_P2R

value: Mid


title: 20_7030-T42_P2R

value: Later Surveillance

value: Detected


title: 20_6811-T00_P2R

value: F

value: chill;msk;throat


title: 20_6933-T00_P2R


title: 20_7340-T00_P2R

value: Hispanic


title: 20_7143-T00_P2R

value: Asymptomatic


title: 20_6694-T00_P2R


title: 20_6578-T00_P2R


title: 20_6600-T00_P2R


title: 20_6537-T28_P2R

value: Not

value: Mild


title: 20_6537-T00_P2R


title: 20_6533-T00_P2R

value: Moderate


title: 20_6483-T00_P2R

value: blood


title: 20_6403-T00_P2R

value: Black

value: Immune +


title: 20_6431-T00_P2R

value: Initial Outbreak

value: Non-Hispanic


title: 20_6114-T00_P2R

value: M


title: 20_6455-T00_P2R

value: White


title: 20_6100-T00_P2R


title: 20_6107-T00_P2R


title: 20_6092-T00_P2R


title: 20_5864-T00_P2R


title: 20_5720-T00_P2R


title: 20_7252-T00_P2R

value: AI/AN

value: Control


title: 20_5738-T00_P2R

value: Exposed


title: 20_5698-T00_P2R


title: 20_5619-T56_P2R

value: Later Surveillance


title: 20_5513-T00_P2R

value: F


title: 20_5619-T49_P2R

value: Hispanic


title: 20_7451-T56_P2R

value: Post


title: 20_5619-T53_P2R

value: Not


title: 20_5613-T00_P2R


title: 20_5473-T00_P2R


title: 20_5619-T00_P2R


title: 20_5303-T00_P2R

value: Asymptomatic


title: 20_5285-T00_P2R


title: 20_5228-T00_P2R

value: Moderate


title: 20_5135-T00_P2R

value: blood


title: 20_9966-T00_P1


title: 20_6212-T00_P2R

value: fatigue

value: Mild


title: 20_9520-T00_P1

value: Initial Outbreak


title: 20_9610-T00_P1


title: 20_9835-T00_P1


title: 20_9862-T00_P1

value: Hawaiian/OPI


title: 20_5972-T00_P2R


title: 20_9445-T00_P1

value: M


title: 20_5621-T00_P2R


title: 20_9248-T00_P1

value: Non-Hispanic

value: White


title: 20_9215-T00_P1

value: cough;abd


title: 20_9063-T00_P1

value: Asian


title: 20_9131-T00_P1

value: throat;cough;sob


title: 20_8892-T00_P1

value: F

value: Black

value: Exposed


title: 20_8257-T00_P1


title: 20_8566-T00_P1


title: 20_8991-T00_P1

value: Hispanic


title: 20_5512-T00_P2R


title: 20_8370-T00_P1


title: 20_8245-T00_P1


title: 20_8102-T00_P1


title: 20_8083-T00_P1


title: 20_8014-T00_P1

value: Asymptomatic


title: 20_9939-T00_P1


title: 20_5185-T00_P2R

value: Later Surveillance

value: Control


title: 20_7432-T00_P1

value: blood

value: Multi-racial


title: 20_7656-T00_P1

value: Initial Outbreak

value: fatigue


title: 20_7466-T00_P1

value: M

value: Mild


title: 20_9837-T00_P1

value: Non-Hispanic

value: White


title: 20_9641-T00_P1


title: 20_6954-T00_P1

value: taste


title: 20_6991-T00_P1


title: 20_6449-T00_P1


title: 20_6367-T00_P1

value: AI/AN


title: 20_6872-T00_P1

value: F

value: Moderate


title: 20_6320-T00_P1


title: 20_6067-T00_P1


title: 20_6023-T00_P1


title: 20_5844-T00_P1


title: 20_5662-T00_P1

value: Black


title: 20_5653-T00_P1

value: Exposed


title: 20_5708-T00_P1


title: 20_5568-T00_P1

value: Hispanic

value: Asian

value: Asymptomatic


title: 20_6001-T00_P1

value: blood


title: 20_5615-T00_P1


title: 20_5513-T00_P1


title: 20_5542-T00_P1


title: 20_5658-T00_P1


title: 20_5420-T00_P1


title: 20_7833-T00_P1


title: 20_5326-T00_P1


title: 20_5342-T00_P1


title: 20_5411-T00_P1


title: 20_5246-T00_P1


title: 20_6537-T00_P1


title: 20_5063-T00_P1


title: HN30_NC_cells_time2

city: Fuzhou

first: Ting

last: Lan

state: Fujian

address: NO.88,Jiaotong Road,Fuzhou City,Fujian Prov

country: China

institute: Fujian Medical University

description:
Transfected with a scrambled siRNA
rep2

data_processing:
After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: counts.txt: Matrix table with raw gene counts for every gene and every sample.

molecule: total RNA

source_name: HNSCC cells

growth_protocol: Before transfection, we seeded HN6 and HN30 cells in 6-well plates.

extract_protocol:
After transfection for 24h, cells were harvested to be extracted total RNA using NucleoZol Reagent (TaKaRa, Dalian, China) according to the manufacturer’s protocol.
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
RNA library for RNA-seq was prepared as follows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double- strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: HN6 and HN30 cells were transfected with 2 siRNA logos against human FAT1 and a scrambled siRNA respectively with Lipofectamine RNAiMAX according to the manufacturer's instructions. On the following day, cells were harvested to be extracted total RNA using NucleoZol Reagent according to the manufacturer’s protocol.

tag: cell line

tag: sirna

value: NC


title: HN30_FAT1-sh2_cells_time1

description:
Transfected with siRNA-2 logos against FAT1
rep1


title: HN30_FAT1-sh1_cells_time2

description:
Transfected with siRNA-1 logos against FAT1
rep2


title: HN30_FAT1-sh2_cells_time2

description:
Transfected with siRNA-2 logos against FAT1
rep2


title: HN30_NC_cells_time1

description:
Transfected with a scrambled siRNA
rep1


title: HN6_FAT1-sh2_cells_time2


title: HN30_FAT1-sh1_cells_time1

description:
Transfected with siRNA-1 logos against FAT1
rep1


title: 1162V1

city: Changzhou

first: Xia

last: Yi

address: 21 Gehu Middle Road

institute: Changzhou University

data_processing:
RNA-Seq sequencing assays were carried out by CapitalBio Technology Co., Ltd, Beijing, China, using the Illumina NovaSeq 6000 platform and long-read MinION sequencer.
HTSeq was used to calculate the gene count of mRNA.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: Z. mobilis ZM4

growth_protocol: Z. mobilis ZM4 was incubated in RM medium containing 20 g/L glucose, 2 g/L KH2PO4, and 10 g/L yeast extract at 30 oC without shaking .

extract_protocol:
We used TRIzol reagent (Invitrogen, Carlsbad, CA, USA) to isolate the total RNA from the freshly harvested recombinant Z. mobilis ZM4 samples.
A KAPA kit (Cat no.KK4602) was used to develop a further absolute quantification of the prepared library

treatment_protocol: Three replicates were carried out under the stress of 4-hydroxybenzaldehyde, syringaldehyde, and vanillin.

tag: strain

value: Z. mobilis ZM4::pHW20a-ZMO1162

tag: treatment

value: under the stress of vanillin


title: 1162V3


title: HN6_FAT1-sh1_cells_time2


title: 1162S3

value: under the stress of syringaldehyde


title: HN6_NC_cells_time2

description:
Transfected with a scrambled siRNA
rep2


title: 1162S2


title: 1162S1


title: 1162H3

value: under the stress of 4-hydroxybenzaldehyde


title: HN6_FAT1-sh1_cells_time1


title: HN6_FAT1-sh2_cells_time1


title: HN6_NC_cells_time1

description:
Transfected with a scrambled siRNA
rep1


title: 1162H2


title: 1162H1


title: 20_5218-T00_P1

tag: tissue

tag: enrollment batch

value: Initial Outbreak

value: M

value: Other


title: 20aV3

value: Z. mobilis ZM4::pHW20a


title: 20_5134-T00_P1

tag: biocollection id

tag: rna-seq plate

value: White


title: 20aV2


title: lupus non-lesional skin 5

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were  sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired end reads.
Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10X Cell Ranger software.
The samples were then merged into a single expression matrix using the cellranger aggr pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: raw expression values for each library in sparse matrix format

source_name: skin

extract_protocol:
7 patients with active CLE were recruited for this study, all of whom contributed lesional and non-lesional (sun-protected skin of the buttock) 6mm punch skin biopsies. A diagnosis of SLE was confirmed for 6 of 7 patients via the European League Against Rheumatism/American College of Rheumatology criteria. 14 healthy controls were recruited for skin biopsy. The study was approved by the University of Michigan Institutional Review Board (IRB), and all patients were consented. The study was conducted according to the Declaration of Helsinki Principles.
Generation of single-cell suspensions for scRNA-seq was performed as follows: Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70μM mesh. Epidermal and dermal cells were combined in 1:1 ratio, and libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system with chemistry v3.

tag: disease

value: lupus non-lesional


title: lupus non-lesional skin 4


title: lupus non-lesional skin 6


title: 20aV1


title: 20aS1


title: 1162V2


title: lupus non-lesional skin 3


title: 20aS3


title: lupus lesional skin 6

value: lupus lesional


title: lupus lesional skin 7


title: lupus non-lesional skin 2


title: 20aS2


title: lupus non-lesional skin 1


title: 20aH3


title: 20aH1


title: lupus lesional skin 5


title: 20aH2


title: lupus lesional skin 4


title: lupus lesional skin 2


title: lupus lesional skin 3


title: lupus non-lesional skin 7


title: N610M-2

city: Shanghai

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

institute: Fudan university

data_processing:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The sequencing libraries were sequenced on an Illumina Hiseq2500/X platform. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Cuffquant and cuffnorm (v2.2.1) was used to calculate FPKMs of genes in each sample.
Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group.
Assembly: mm9
Supplementary files format and content: Raw gene counts and fpkm for every gene and every sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease state

value: Normal


title: N610M-3


title: N610C-7

value: NAFL


title: N610M-4


title: lupus lesional skin 1


title: N610C-8


title: Healthy normal skin 14

value: healthy


title: MICB-iso-NK-3

city: Boston

first: Soumya

last: Badrinath

state: MA

address: 1 jimmy fund way

department: Cancer Immunology and Virology

institute: DFCI

description:
Sample 24
Group G
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells

data_processing:
Samples were sequenced on an Illumina HiSeq with a 2x150 Paired End (PE) configuration to generate FASTQ files  FASTQ files were aligned to mm10 using STAR (2.5.2a) with quantMode = GeneCounts
The unstranded genecounts for each sample were analyzed for differential gene expression using the R (3.6.3) package DESeq2 (1.26.0).  DESeq2 model was built with the design (~CellType) where “CellType” refers to the different sorted populations, with all CellTypes included in the model, and Raw gene count data, DESeq2 normalized gene count data, and RLD (regularized log transformed data) were extracted from the resulting DeSeq2 object
Genome_build: mm10
Supplementary_files_format_and_content: hit counts for the genes, raw gene hit counts, normalized gene hit counts, r log transformed gene hit counts, log2 fold change and (adjusted) p-value table,log2 fold change and (adjusted) p-value table for significantly DE genes, GO enrichment analysis results

source_name: NK cells from tdln of B16F10 (MICB-dox) tumor bearing mice

growth_protocol: C57BL/6J mice immunized and boosted with MICB-vax or Ctrl-vax were injected subcutaneously with 0.3x106 B16F10 (MICB-dox) tumors. Once the tumors were palpable (~50mm2), treatment was initiated

extract_protocol:
tumor draining lymph nodes were minced and placed into digestion medium  and placed at 37C with constant agitation at 200 rpm. migratory DCs and NK cells were sorted as decribed in the manuscript. Cells were sorted directly into 250uL of Trizol LS (Invitrogen) and RNA was purified by phenol chloroform extraction.
RNA was quantified using Qubit and TapeStation. RNA sequencing libraries were made using the SMART-Seq v4 Ultra Low Input Kit. This library prep uses Poly(A) selection to target mRNA, with enrichment for full length transcripts."

treatment_protocol: mice immunized with MICB-vax or Ctrl-vax were injected intraperitonially with 100µl of dox (5mg/kg in PBS) without or with CD4 depletion initiated 2 days prior to dox induction

value: B16F10 (MICB-dox)

tag: vaccine group

value: MICB vaccine

tag: treatment group

value: doxyclycine


title: MICB-iso-NK-2

description:
Sample 23
Group G
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 13


title: MICB-iso-NK-1

description:
Sample 22
Group G
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: N610C-4


title: MICB-iso-mDC-1

description:
Sample 19
Group C
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells

source_name: migratory DCs from tdln of B16F10 (MICB-dox) tumor bearing mice


title: MICB-iso-mDC-2

description:
Sample 20
Group C
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 12 hours after exposure, Replicate 2

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

data_processing:
De-multiplexing sequenced raw files with bcl2fastq (Illumina), and quality was checked with FastQC.
Kallisto was used to quantify gene expression with 100 bootstraps.
RNA-Seq reads were mapped to the coding sequences with BWA and conducted statistical test with DESeq2
Genome_build: Ramazzottius variornatus genome from Yoshida et al., PLoS Biology 2019 (http://ensembl.tardigrades.org/index.html)
Supplementary_files_format_and_content: merged_kallisto.txt : Quantified TPM values of each sample.

organism: Ramazzottius varieornatus

source_name: Whole body

growth_protocol: The animals were reared in environments established by Horikawa (29), and were maintained in 90 mm petrish plates. About 600 animals were placed on 2.0% bacto-agar layered dishes and fed with Chlorella vulgaris mixed in Volvic. The petrish plates were lidded and placed in a dark incubator, set at 22 ˚C. The animals were transferred to new plates every 7 days.

extract_protocol:
Tardigrades were immersed in 100µL of Trizol reagent in a PCR tube (30 animals per sample) and preserved at -80˚C. Biomasher II was used for the homogenization of tardigrades and added 200µL of TRIzol reagent to the preservation PCR tube for total RNA extraction with Direct-Zol.
We have used NEBNext Oligo d(T)25 beads for mRNA Isolation, and RNA fragmentation, and NEBNext Ultra RNA Library Prep Kit for cDNA synthesis, adapter ligation and PCR enrichment.

treatment_protocol: Irradiation of the tardigrades was conducted using a UV-C lamp of a drying rack following the protocol by Horikawa et al. (2). Tardigrades were set on a volvic gel layered in a plastic plate, and excess water was removed. This procedure does not induce anhydrobiosis and is required since UV-C does not penetrate a layer of water. The plates were then set on for irradiation by the UV-C lamp. At these distances, the average dosage was 0.54 mW/cm2 (0.0054kJ/m2). Water was added to the plates immediately after irradiation and was set to incubate in a dark chamber set at 22˚C until sampling.


title: Healthy normal skin 12


title: Healthy normal skin 11


title: MICB-aCD4-NK-3

description:
Sample 18
Group H
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: MICB-aCD4-NK-1

description:
Sample 16
Group H
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 09 hours after exposure, Replicate 3


title: Healthy normal skin 10


title: MICB-iso-mDC-3

description:
Sample 21
Group C
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 9


title: Short time-course, 12 hours after exposure, Replicate 1


title: MICB-aCD4-NK-2

description:
Sample 17
Group H
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 5


title: Healthy normal skin 7


title: Short time-course, 06 hours after exposure, Replicate 3


title: Healthy normal skin 6


title: Short time-course, 06 hours after exposure, Replicate 2


title: Ferritin-iso-mDC-3

description:
Sample 9
Group A
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells

value: control vaccine


title: Ferritin-iso-mDC-2

description:
Sample 8
Group A
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: MICB-aCD4-mDC-3

description:
Sample 15
Group D
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 8


title: Ferritin-iso-mDC-1

description:
Sample 7
Group A
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: MICB-aCD4-mDC-2

description:
Sample 14
Group D
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: MICB-aCD4-mDC-1

description:
Sample 13
Group D
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Ferritin-iso-NK-2

description:
Sample 11
Group E
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 09 hours after exposure, Replicate 1


title: Short time-course, 09 hours after exposure, Replicate 2


title: Ferritin-iso-NK-3

description:
Sample 12
Group E
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 05 hours after exposure, Replicate 3


title: Ferritin-iso-NK-1

description:
Sample 10
Group E
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells,isotype control antibody was injected intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 3


title: Control_rep3

city: Berlin

first: Katrin

last: Kreuzer

address: Max-Dohrn-Str. 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
De-multipltiplexing of sequencing reads was accomplished using Illumina bcl2fastq (version 2.20)
Adapter trimming was performed with Skewer (version 0.2.2)
Data quality was assessed by FastQC version 0.11.5.
In the reference, the pseudoautosomal regions (PAR) on chromosome Y were masked (chrY:10001-2649520, chrY:59034050-59363566). Reads from these regions are located in the corresponding section on chromosome X.
Alignment to the human genome (hg 19) was performed using STAR (version 2.7.3)
After removing genes with low expression (sum of reads across all samples below two), 35324 genes were retained and analyzed by the R-package DESeq2 version 1.30.1 using default settings estimation of size factors and dispersion.
Negative Binomial GLM fitting and Wald statistics were applied to test for differential gene expression between each treatment and control conditions, respectively. False discovery rate (FDR) was used to control for multiple testing. Only genes with a q-value ≤ 0.05 and absolute log2 fold change > log2(1.5) were included in the further analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Counted reads per gene as raw counts and normalized counts. Normalized counts contain all genes which sum of mapped reads across all samples is greater than one. Normalizing was performed with DESeq2.

source_name: TK6 cell line

growth_protocol: The human lymphoblastoid cell line TK6 (CLS, Eppelheim, Germany) was cultured in RPMI 1640 Medium with L-glutamine and 2.0 g/l NaHCO3 (PAN-Biotech, Aidenbach, Germany) supplemented with 10% fetal bovine serum (Biochrom, Berlin, Germany) and 100 U/mL penicillin, and 100 µg/mL streptomycin (Capricorn Scientific, Ebsdorfergrund, Germany). The cells were maintained in culture between 0.5 × 105 and 1 × 106 cells/ml. For all studies, cells were seeded at a density of 1 × 105 cells/ml and cultured for 48 h prior to treatment commencement at 37 °C and 5% CO2

extract_protocol:
RNA isolation was performed with the RNeasy Mini Kit (Qiagen) according to the manufactures' protocol.
Libraries were prepared from 100 ng of RNA using the TruSeq Stranded Total RNA kit (Illumina)

treatment_protocol: Stock solutions of Aflatoxin B1 (50 µM stock solution), Benzo[a]pyrene (5 mM), Lasiocarpine (1 mM), Methyleugenol (250 mM), Nitrosopyrrolidine (undiluted, liquid form), 3-MCPD (1 M), PFOA (250 mM), PFOS (50 mM) and Methapyrilene HCL (40 mM) were added 1:1000 to TK6 cells (final cell concentration 0.4x10^6) including rat S9 mix plus cofactors as external metabolic activating system. After 4 hours, TK6 cells were washed three times with PBS (centrifugation step at 400xg for 5 min), resuspended in RPMI medium (+10% FCS +1% Peniciline/Streptomycine) and recovered until 24 hours of incubation were completed.

value: Control

tag: concentration


title: Ferritin-aCD4-NK-3

description:
Sample 6
Group F
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Healthy normal skin 4


title: Healthy normal skin 2


title: Short time-course, 06 hours after exposure, Replicate 1


title: Short time-course, 12 hours after exposure, Replicate 3


title: SB3 [TCR]

description: CD45+ lymphoctyes sorted from B16F10 (MICB-dox) tumors 7 days following MICB induction on tumor cells

data_processing:
10x Genomics' cellranger was run to demultiplex BCL files, and fastq files were generated using cellranger mkfastq
Single cell gene expression quantification was performed using cellranger count
V(D)J sequences and annotations were generated by running cellranger vdj
Genome_build: mm10
Supplementary_files_format_and_content: UMI count matrix of gene expression per cell, with cell barcodes and gene names provided in separate files

source_name: B16F10 (MICB-dox) subcutaneous tumors

extract_protocol:
Tumors were harvested 7 days lfollowing MICB induction, single cell suspensions were prepared and stained with antibodies. Briefly, dead cells were excluded by staining with Zombie Green viability dye (Biolegend) and Fc receptors were blocked prior to the addition of PE-conjugated anti-mouse CD45 (clone 30-F11, Biolegend) antibody. 5,000 CD45+ live cells were sorted from each tumor sample using a FACSAria IIIu instrument. Equal numbers of sorted CD45+ cells from 5 mice per group were pooled, pelleted and resuspended at 1x103 cells/µl in PBS containing 0.04% RNase-free BSA.
For each of the four groups, 5,000 cells were used for the 10X Genomics 5’ v2 single cell assay. Reverse transcription, cDNA amplification and library preparation were performed according to the manufacturer’s protocol. Completed libraries were sequenced on the Illumina HiSeq 2500 instrument with rapid-run mode, yielding >40,000 reads per cell.  Amplified cDNA was also used for TCR V(D)J targeted enrichment using the using Chromium Single Cell Mouse TCR Amplification Kit. TCR V(D)J libraries were sequenced on the Illumina HiSeq 2500 platform with a 150bp paired-end configuration.

treatment_protocol: mice immunized with MICB-vax or Ctrl-vax were injected intraperitonially with either 100µl of dox (5mg/kg in PBS) or PBS, resulting in four groups, three control groups (Ctrl-vax + PBS, Ctrl-vax + dox, MICB-vax + PBS) and one experimental group (MICB-vax + dox).

value: B16F10 (MICB)

value: PBS


title: Control_rep2


title: Short time-course, 04 hours after exposure, Replicate 3


title: Healthy normal skin 1


title: Control_rep1


title: Ferritin-aCD4-NK-2

description:
Sample 5
Group F
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Ferritin-aCD4-NK-1

description:
Sample 4
Group F
NK cells sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: SB2


title: Ferritin-aCD4-mDC-3

description:
Sample 3
Group B
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Ferritin-aCD4-mDC-2

description:
Sample 2
Group B
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 04 hours after exposure, Replicate 1


title: Control_rep4


title: Ferritin-aCD4-mDC-1

description:
Sample 1
Group B
migratory DCs sorted from tdLN of B16F10 (MICB-dox)tumor bearing mice 2 days following MICB induction on tumor cells, CD4 T cells were depleted by injecting aCD4 ab intraperitoneally 2 days prior to dox induction on tumor cells


title: Short time-course, 05 hours after exposure, Replicate 2


title: SB4 [TCR]


title: Short time-course, 05 hours after exposure, Replicate 1


title: PRDM14_AID_Venus_Naive_Plus_IAA_Rep3_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Standard Illumina base-calling pipeline.
Reads were trimmed using trim galore v0.6.5 using default parameters to remove the standard Illumina adaptor sequence. Reads were mapped to the human GRCh38 genome assembly using HISAT 2.1.0 guided by the gene models from the Ensembl v70 release. Samtools was used to convert to BAM files that were imported to Seqmonk v45.0.
Genome_build: GRCh38
RNA-seq report: A comma separated report of transprictps (log2 RPM).

source_name: H9 PRDM14-AID-Venus line

growth_protocol: Naive cells were cultured in in PXGL conditions in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2-supplement, 0.5x B27-supplement, 2mM L-Glutamine, 50 U/ml Penicillin-Streptomycin, 0.1mM beta-mercaptoethanol, 1 µM PD0325901, 2 µM XAV939, 20ng/ml human LIF and 2 µM Go6983 on a MEF-layer seeded at a density of 2 million cells per 6-well plate. For feeder-free culture, PXGL naive PSCs were cultured on Matrigel–coated plates. Naïve cell reprogramming of PRDM14-AID-Venus cells was performed by Chemical Resetting.

extract_protocol:
Total RNA was extracted in TRIzol Reagent.
Indexed libraries were constructed from 500ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina with the Poly(A) mRNA Magnetic Isolation Module. Library fragment size and concentration was determined using an Agilent Bioanalyzer 2100 and KAPA Library Quantification Kit.

value: H9 PRDM14-AID-Venus line

tag: cell type

value: Naive human pluripotent stem cells

value: Addition of 100 um Indole acetic acid (IAA) for 24 h


title: SB2 [TCR]


title: SB1 [TCR]


title: SB4


title: Short time-course, 04 hours after exposure, Replicate 2


title: PRDM14_AID_Venus_Naive_Plus_IAA_Rep1_RNAseq


title: SB1


title: 3T3L1, Par-4 ChIP-seq_rep1

city: LEXINGTON

first: Vivek

middle: M.

last: Rangnekar

state: KY

address: 789 s limestone

institute: University of Kentucky

library_source: genomic

data_processing:
Bowtie2 was used to map the reads.
MACS2 was used for peak assignment
peak annotation was done using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: .xlsx contains peak scores

molecule: genomic DNA

source_name: preadipocyte cell line

growth_protocol: 3T3-L1 cells were maintained in DMEM+10% FBS (passages no higher than 10) in hydrophilic  polystyrene T-75 flasks

extract_protocol:
3T3-L1 cultured cells (~80% confluency) were fixed in a formaldehyde-containing buffer that would also fix any DNA-binding protein complexes to the chromatin.
Library preparation was performed using the MicroPlex Library Preparation Ki v2 (Diagenode) according manufacturer’s instructions.

treatment_protocol: No treatment was performed

value: committed undifferentiated preadipocyte cell line

tag: chip antibody

value: Antibodies for Par-4 N-terminal (R-334, sc-1807)

value: no treatment


title: SB3


title: 3T3L1, Par-4 ChIP-seq_rep2


title: Methapyrilene HCL_rep3

value: Methapyrilene HCL

value: 40 µM


title: 3-MCPD_rep3

value: 1 mM


title: PFOS_rep3

value: PFOS

value: 50 µM


title: PRDM14_AID_Venus_Naive_No_IAA_Rep3_RNAseq


title: 3T3L1, Par-4 ChIP-seq_rep3


title: Short time-course, 03 hours after exposure, Replicate 3


title: Short time-course, 03 hours after exposure, Replicate 2


title: PRDM14_AID_Venus_Naive_Plus_IAA_Rep2_RNAseq


title: Short time-course, 03 hours after exposure, Replicate 1


title: PFOA_rep3

value: PFOA


title: Nitrosopyrrolidin_rep3

value: Nitrosopyrrolidin

value: 20 mM


title: PRDM14_AID_Venus_Naive_No_IAA_Rep1_RNAseq


title: Short time-course, 02 hours after exposure, Replicate 3


title: WT_Day10_Rep3_RNAseq

description: log2_RPM_values_for_Collier_Bendall_RNA-seq_GEO_submission.txt

data_processing:
Standard Illumina base-calling pipeline.
ChIP-seq: Reads were trimmed using trim galore v0.6.5 using default parameters to remove the standard Illumina adapter sequence, and mapped to the human genome GRCh38 using Bowtie2. BAM files imported to Seqmonk.
RNA-seq: Reads were trimmed using trim galore v0.6.5 using default parameters to remove the standard Illumina adaptor sequence. Reads were mapped to the human GRCh38 genome assembly using HISAT 2.1.0 guided by the gene models from the Ensembl v70 release. Samtools was used to convert to BAM files that were imported to Seqmonk v45.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: A tab-separated file of log2RPM read counts per 500bp. The file is a SeqMonk annotated probe report, which includes fields chomosome, start, end, log2 RPM values for each sample.
Supplementary_files_format_and_content: A tab-separated file with the following fields: mRNA name (Ensembl); Chromosome; Start; End; Strand; mRNA ID (Ensembl); Description (Ensembl); log2 RPM values.

source_name: Human embryonic stem cells (ESCs)

growth_protocol: Primed cells were cultured in either feeder-dependent or feeder-free conditions. Feeder-dependent conditions were grown in 80% Advanced DMEM, 20% Knockout Serum Replacement, 2mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.1 mM beta-mercaptoethanol, and 4 ng/ml basic fibroblast growth factor on irradiated mouse embryonic fibroblasts (MEF). For feeder-independent conditions, cells were transferred onto Vitronectin-coated plates (0.5mg/cm2) in complete TeSR-E8 or mTeSR1 medium. Cells were passaged by 5 min incubation at room temperature with 0.5 mM EDTA in PBS. Naive cells were cultured in in t2i/L+PKCi conditions in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2-supplement, 0.5x B27-supplement, 2mM L-Glutamine, 50 U/ml Penicillin-Streptomycin, 0.1mM beta-mercaptoethanol, 1 µM PD0325901, 1 µM CHIR99021, 20ng/ml human LIF and 2 µM Go6983 on a MEF-layer seeded at a density of 2 million cells per 6-well plate. For feeder-free culture, t2i/L+PKCi naive PSCs were cultured on Matrigel–coated plates. Primed to naïve cell reprogramming was performed in 5i/LA conditions and by Chemical Resetting.

extract_protocol:
ChIP-seq: Cells were dissociated with Accutase and washed with PBS. Cells were cross-linked with 2 mM Di(N-succinimidyl) glutarate in PBS for 45 min at room temperature with shaking and then with 1% methanol-free paraformaldehyde for 12.5 min at room temperature with shaking. Fixation was quenched with 0.125 M Glycine for 5 min at room temperature with shaking. Chromatin was fragmented by sonication on a Microson ultrasonic cell disruptor XL Misonix wand sonicator with output setting of 10W using 30 or 34 sonication cycles (15s on, 30s off) for primed and naïve cell chromatin respectively. Fragmented chromatin was incubated with 10 µg of antibody overnight at 4C. Chromatin-antibodies complexes were isolated using Magnetic Protein A or G dynabeads and washed. Eluted chromatin was de-crosslinked and DNA was purified using AMPure XP beads.
RNA-seq: Total RNA was extracted in TRIzol Reagent.
ChIP-Seq libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina using the manufacturer’s protocol, with libraries indexed using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2). Library fragment size and concentration were determined using the Qubit fluorometer double stranded DNA high sensitivity assay kit, using an Agilent Bioanalyzer 2100 and by KAPA Library Quantification Kit. Samples were sequenced on an Illumina NextSeq500 instrument as HighOutput 75 bp single-end reads at the Babraham Institute Next Generation Sequencing Facility.
RNA-seq: Indexed libraries were constructed from 500ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina with the Poly(A) mRNA Magnetic Isolation Module. Library fragment size and concentration was determined using an Agilent Bioanalyzer 2100 and KAPA Library Quantification Kit.

value: Day 10 reprogramming cells


title: PRDM14_AID_Venus_Naive_No_IAA_Rep2_RNAseq


title: Lasiocarpin_rep3

value: Lasiocarpin

value: 1 µM


title: WT_Day10_Rep2_RNAseq


title: WT_Day0_Rep3_RNAseq

value: Primed ESCs


title: WT_Day0_Rep2_RNAseq


title: WT_Day0_Rep1_RNAseq


title: Short time-course, 01 hours after exposure, Replicate 1


title: Short time-course, 01 hours after exposure, Replicate 2


title: Aflatoxin B1_rep3

value: Aflatoxin B1


title: RING1B_Primed_Rep1_ChIPseq

value: RING1B (Atsuta et al., 2001)


title: RING1B_Naive_Rep2_ChIPseq

value: Naive ESCs (NK2 H9 line)


title: Methapyrilene HCL_rep2


title: PFOS_rep2


title: RING1B_Primed_Rep2_ChIPseq


title: RING1B_Naive_Rep1_ChIPseq


title: PO-N3 rep3

city: Shijiazhuang

first: Caili

last: Bi

state: Hebei

address: No.20 Road East. 2nd Ring South, Yuhua District

department: College of life sciences

institute: Hebei Normal University

data_processing:
illumina Bcl2fastq (v2.17.1.14) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  polymerase chain reaction (PCR) primers, or fragments thereof, and low-quality sequence (quality of bases lower than 20) using Cutadapt(version 1.9.1)software, then the high quality clean data were mapped to Arabidopsis thaliana genome (TAIR10) using Hisat2 (v2.0.1) with default parameters.
Hisat2 (v2.0.1) was used to index reference genome sequence.
Fragments Per Kilo bases per Million reads（FPKM）were calculated using a protocol from Mortazavi et al., Nature methods, 2008.
Assembly: TAIR10
Supplementary files format and content: excel file include FPKM values for all samples

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings harbour pTaF5H1:TaF5H1

growth_protocol: all the Arabidopsis seedlings were normally grown for two weeks before salt treatments.

extract_protocol:
all the samples were frozen in liquid nitrogen and then were delivered to GENEWIZ company in dry ice, and RNAs was harvested using TRIzol Reagent/RNeasy Mini Kit (Qiagen) kits. 1 ug of total RNA was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Arabidopsis seedlings of wild-type(Col-0) and seedlings harbour pTaF5H1:TaF5H1 were either grown in nutrient solutions for 6 hours (as control) or NaCl (200 mM) treated for 6 hours

tag: development stage

value: 2-week old seedlings

value: leaves

value: treated by 200 mM NaCl for 6 hours

tag: genotype

value: harbour pTaF5H1:TaF5H1


title: Short time-course, Non-exposed, Replicate 3


title: PFOA_rep2


title: PO-N2 rep2


title: PCGF3_Primed_Rep2_ChIPseq

tag: cell line


title: PO-N1 rep1


title: Short time-course, 02 hours after exposure, Replicate 2


title: 3-MCPD_rep2

value: 1 mM


title: Methyleugenol_rep3

value: Methyleugenol


title: WT-N3 rep3

source_name: Arabidopsis seedlings of wild-type (Col-0)

value: wild-type (Col-0)


title: Nitrosopyrrolidin_rep2


title: Short time-course, 02 hours after exposure, Replicate 1


title: PCGF3_Naive_Rep2_ChIPseq


title: Long time-course, 72 hours after exposure, Replicate 3


title: WT-N2 rep2


title: Benzo[a]pyren_rep3

value: Benzo[a]pyren

value: 5 µM


title: Methyleugenol_rep2


title: Short time-course, 01 hours after exposure, Replicate 3


title: PCGF3_Naive_Rep1_ChIPseq


title: WT-N1 rep1


title: Long time-course, 72 hours after exposure, Replicate 1


title: Benzo[a]pyren_rep2


title: Lasiocarpin_rep2


title: PO-3 rep3

value: untreated, normally grown for 6 hours


title: PCGF3_5_DKO_Rep2_ChIPseq


title: Long time-course, 48 hours after exposure, Replicate 3


title: PCGF3_5_DKO_Rep1_ChIPseq


title: PO-2 rep2


title: Aflatoxin B1_rep2


title: Input_Primed_Rep2_ChIPseq


title: Long time-course, 48 hours after exposure, Replicate 2


title: Methapyrilene HCL_rep1

value: Methapyrilene HCL

value: 40 µM


title: Input_Primed_Rep1_ChIPseq


title: Short time-course, Non-exposed, Replicate 2


title: Short time-course, Non-exposed, Replicate 1


title: PO-1 rep1


title: WT-3 rep3


title: PCGF3_Primed_Rep1_ChIPseq


title: PFOS_rep1

value: PFOS

value: 50 µM


title: Long time-course, 36 hours after exposure, Replicate 3


title: Long time-course, 48 hours after exposure, Replicate 1


title: WT-2 rep2


title: Input_Naive_Rep2_ChIPseq


title: Input_Naive_Rep1_ChIPseq


title: PFOA_rep1

value: PFOA


title: Long time-course, 36 hours after exposure, Replicate 2


title: 3-MCPD_rep1


title: WT-1 rep1


title: Long time-course, 36 hours after exposure, Replicate 1


title: H8_KO_Day10_Rep3_RNAseq

value: Day 10 reprogramming cells


title: Long time-course, 72 hours after exposure, Replicate 2


title: Nitrosopyrrolidin_rep1

value: Nitrosopyrrolidin

value: 20 mM


title: Methyleugenol_rep1


title: H8_KO_Day10_Rep2_RNAseq


title: WUS-GR  DEX1 small RNA-seq

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

description: small RNA

data_processing:
Basecalls performed using CASAVA version 1.4
3' and 5' adaptor were removed by home perl scripts
uniq reads number were count
reads great than 18 nt were kept for small RNA analysis
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample

source_name: 4-week adult plant

growth_protocol: Seeds pretreated for 2 days at 4°C were grown in soil in the greenhouse for another 4-weeks  (22°C, 16 h light /8 h dark photoperiod).

extract_protocol:
The shoot apexes were flash frozen in liquid nitrogen, and total RNA were isolated using the mirVana™ miRNA Isolation Kit (lif tetechnology).Total RNA was fractionated by electrophoresis. RNA from 10 to 60 nt was sliced and recovered.
The 10-60 nt small RNA were selected for library building.The purified small RNA was subjected to adapter ligation, reverse transcription, PCR amplification with NEXTflex Small RNA Sequencing Kit (Bioo Scientific), and the resulting libraries sent for deep sequencing by Illumina HiSeq2000.

treatment_protocol: The 4-week-old pUBI10:mCherry-GR-linker-WUS plants were sprayed with or without DEX (15μM) for 2 days. The shoot apices were collected and removing older flowers.

tag: developmental stage

value: 4-week adult plant

value: shoot apexes

tag: genotype beckground


title: Long time-course, 24 hours after exposure, Replicate 2

tag: strain


title: WUS-GR MOCK 2 small RNA-seq

description: small RNA

tag: tissue


title: H8_KO_Day10_Rep1_RNAseq


title: Lasiocarpin_rep1

tag: treatment

value: Lasiocarpin

value: 1 µM


title: Long time-course, 24 hours after exposure, Replicate 1


title: H8_KO_Day0_Rep3_RNAseq

value: Primed ESCs


title: Benzo[a]pyren_rep1


title: H8_KO_Day0_Rep2_RNAseq


title: Long time-course, 18 hours after exposure, Replicate 3


title: WUS-GR MOCK 1 small RNA-seq

description: small RNA


title: Aflatoxin B1_rep1

value: Aflatoxin B1


title: H8_KO_Day0_Rep1_RNAseq


title: Long time-course, 18 hours after exposure, Replicate 2


title: PITT-86

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to mouse reference genome hg38 by STAR aligner (version 2.7.5a) and gene counts were quantified by --quant  Mode GeneCounts option
Genome_build: hg38
Supplementary_files_format_and_content: txt file for gene read counts

source_name: liver

extract_protocol:
Liver biopsies were isolated using Total RNeasy Mini Kit (QIAGEN Inc.). RNA-seq libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Normal

tag: gender

value: F

tag: nas

tag: age


title: WUS-GR DEX2 small RNA-seq

description: small RNA


title: FSPS13B_reset_RNAseq

source_name: Hman induced pluripotent stem cells (iPSCs)

value: Day 10 reprogramming cells (FSPS13B line)


title: PITT-85

tag: disease


title: Long time-course, 18 hours after exposure, Replicate 1


title: Long time-course, 24 hours after exposure, Replicate 3


title: FSPS13B_refractory_RNAseq


title: Long time-course, 12 hours after exposure, Replicate 3


title: Long time-course, 12 hours after exposure, Replicate 2


title: PITT-04


title: D7_KO_Day10_Rep3_RNAseq


title: MS-38


title: D7_KO_Day10_Rep2_RNAseq


title: Long time-course, 12 hours after exposure, Replicate 1


title: R6/2 mice at symptomatic stage of 9 weeks of age rep3

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from mouse eyeball

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Mouse Gene 2.1 ST ArrayStrip (20 h, 292 48 °C)

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: eyeball

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: All animals had unlimited access to water and breeding chow (Special Diet Services, Witham, UK), and housing conditions and environmental enrichment.

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: All animals were cull at specific time-points by cervical dislocation. Eye tissues were harvested and snap-frozen in liquid nitrogen. Next, they were kept at -80C till further analysis.

value: eyeball

value: 9 weeks of age


title: R6/2 mice at symptomatic stage of 9 weeks of age rep4

description: Gene expression data from mouse eyeball


title: Long time-course, Non-exposed, Replicate 3


title: Long time-course, Non-exposed, Replicate 2


title: ctrl-Thermo

description: ctrl-Thermo


title: LB-53

value: NAFLD disease

value: Borderline


title: R6/2 mice at symptomatic stage of 9 weeks of age rep2

description: Gene expression data from mouse eyeball


title: D7_KO_Day0_Rep2_RNAseq


title: LB-52

value: M


title: D7_KO_Day0_Rep3_RNAseq


title: Long time-course, Non-exposed, Replicate 1


title: wild type 9 weeks of age rep4

description: Gene expression data from mouse eyeball

value: wild type


title: wild type 9 weeks of age rep2

description: Gene expression data from mouse eyeball


title: LB-51


title: LB-50


title: wild type 9 weeks of age rep3

description: Gene expression data from mouse eyeball


title: mRNA_H_Pylori_rep65 [GP178UT1AC1]

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Data was processed with using Bowtie 2 and RSEM softwares.
Genome_build: hg19
Supplementary_files_format_and_content: rsem files were generated using RSEM; Scores represent Transcripts Per Million and Fragments Per Kilobase Million.

source_name: mRNA from H Pylori negative gastric tumor tissue

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
illumina True Seq RNA Access sample Preparation Kit

value: female

tag: age range

tag: tissue type

value: tumor

tag: h. pylori infection

value: negative


title: T3 (treated 3)

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.8.4)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of  expression gene

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Synchronized young adults were cultured on NGM plates with or without 0.1 µM VK2 and incubated at 20°C for seven days. The worms were transferred to new NGM plates with or without VK2 every day to get rid of the progeny and then collected.

extract_protocol:
Monarch RNA Total Miniprep Kit
Library preparation was performed using a KAPA Stranded RNA-Seq Library Prep Kit (Illumina), and the quality was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Paired-end sequencing was performed on an Illumina NovaSeq 6000.

value: adult

value: whole body


title: T2 (treated 2)


title: LB-49


title: T1 (treated 1)


title: mRNA_H_Pylori_rep64 [2S035T1AC1]


title: C3 (control 3)


title: LB-48


title: wild type 6 months of age rep4

description: Gene expression data from mouse eyeball

value: 6 months of age


title: mRNA_H_Pylori_rep62 [2S072T1AC1]

value: male


title: mRNA_H_Pylori_rep63 [2S052T1AC1]


title: D7_KO_Day10_Rep1_RNAseq

tag: cell type

value: Day 10 reprogramming cells


title: C2 (control 2)


title: LB-46

value: Steatosis


title: C1 (control 1)


title: R6/2 mice at symptomatic stage of 9 weeks of age rep1

description: Gene expression data from mouse eyeball


title: mRNA_H_Pylori_rep60 [2S051T1AC1]


title: LB-45


title: R6/1 mice at symptomatic stage 6 months rep3

description: Gene expression data from mouse eyeball


title: R6/1 mice at symptomatic stage 6 months rep1

description: Gene expression data from mouse eyeball


title: wild type 6 months of age rep3

description: Gene expression data from mouse eyeball


title: (nlrc5) CT26 H3K36me2 NLRC5 KD

city: shanghai

first: jiale

middle: jia

last: ren

state: shanghai

address: yueyang road 320

department: shanghai institute of nutrition and health

institute: CAS

data_processing:
The 75-nt sequence reads generated by Illumina sequencing  were mapped to the genome using the GALAXY Map with BWA(map short reads(<100bp) against reference genome)
Examine aligned records in BAM datasets to locate duplicate molecules to produce a MarkDuplicates BAM  file
Generates coverage bigWig file from a MarkDuplicates BAM  file
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607).

treatment_protocol: no treatment

value: BALB/c

tag: antibody

tag: genotype/variation

value: Nlrc5 KO


title: wild type 9 weeks of age rep1

description: Gene expression data from mouse eyeball

value: eyeball

tag: genotype


title: Case2 Tumor CD45 cells

city: Suita

first: Masatoshi

last: Kitakaze

state: Osaka

address: Yamadanishi, 4-2-88-703

institute: Osaka University

data_processing:
BD Targeted Rhapsody Analysis Pipeline Version 1.8
Genome_build: hg19

source_name: Immune cells in colorectal cancer

extract_protocol:
CD45+ cells were targeted for single-cell RNA-seq analysis using the BD Rhapsody Single-Cell Analysis System (BD Biosciences; Fan et al., 2015). Briefly, the single-cell suspension was loaded into a BD Rhapsody cartridge with >200,000 microwells, and single-cell capture was achieved by random distribution and gravity precipitation. Next, the bead library was loaded into the microwell cartridge to saturation so that the bead was paired with a cell in a microwell. The cells were lysed in a microwell cartridge to hybridize mRNA molecules onto bar-coded capture oligos on the beads. These beads were then retrieved from the microwell cartridge into a single tube for subsequent cDNA synthesis, exonuclease I digestion, and multiplex-PCR–based library construction. The Illumina library was converted to the library for DNBSEQ using the MGIEasy Universal Library Conversion Kit (App-A). Sequencing was performed on a DNBSEQ-G400RS (MGI) in a 100-base paired-end mode. The BD Rhapsody Analysis Pipeline was used to process the sequencing data (fastq files), and output result files were analyzed and visualized using BD Data View software v.1.2.2 (BD Biosciences).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Rectum cancer

value: CD45 immune cells

tag: disease state

value: colorectal cancer


title: R6/1 mice at symptomatic stage 6 months rep2

description: Gene expression data from mouse eyeball


title: D7_KO_Day0_Rep1_RNAseq

tag: cell line

value: Primed ESCs


title: wild type 6 months of age rep2

description: Gene expression data from mouse eyeball

value: wild type


title: LB-44

value: NAFLD disease

value: M

value: Borderline


title: (nlrc5) CT26 H3K36me2 P

value: WT


title: Case1 Normal CD45 cells

source_name: Immune cells in colon tissue

value: Assending colon

value: normal colon


title: LB-43


title: (nlrc5) CT26 H3K36me2 input

value: input


title: mRNA_H_Pylori_rep57 [2S019T1AC1]

value: female

value: tumor

value: negative


title: Case1 Tumor CD45 cells

value: Assending colon cancer


title: (whsc1) CT26 H3K36me2 WHSC1 KO

value: BALB/c

value: Whsc1 KO


title: mRNA_H_Pylori_rep56 [2S016T1AC1]


title: LB-42


title: LB-47

value: F


title: (whsc1) CT26 H3K36me2 P


title: LB-41

value: NASH


title: Hepatic stellate cells - WT_3

city: Nanjing

first: Wen-Song

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM and count valus for each Sample

source_name: Wild type mice (C57BL/6J background)

growth_protocol: HSCs were isolated from WT or S100a16+/- mice and cultured in FBS-containing medium for 7 days for full differentiation

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: HSCs were cultured in FBS-containing medium for 7 days

value: hepatic stellate cells

value: cultured in FBS-containing medium for fully activation

value: Wild type


title: mRNA_H_Pylori_rep61 [2S060T1AC1]


title: LB-07

value: NAFLD disease

value: M

value: Steatosis


title: Hepatic stellate cells - WT_2


title: mRNA_H_Pylori_rep55 [1S996T1AC1]


title: (whsc1) CT26 H3K36me2 input

value: WT


title: mRNA_H_Pylori_rep54 [1S947T1AC1]

value: male


title: LB-40


title: Hepatic stellate cells - WT_1


title: LB-39

value: Borderline


title: mRNA_H_Pylori_rep53 [1S976T1AC1]