title: 4797-023-60

description: Gene expression data from bronchial brushing 4797-023-60.


title: 4797-043-60

status: Public on Oct 25 2022

type: SRA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Gene expression data from bronchial brushing 4797-043-60.

library_source: transcriptomic

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_bronchial_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_bronchial_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

molecule: total RNA

organism: Homo sapiens

source_name: Brushing of bronchial epithelium

extract_protocol:
Total RNA was isolated from nasal and bronchial brushings using the miRNeasy Mini Kit [QIAGEN].
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit.

tag: tissue

value: Brushing of bronchial epithelium

tag: subject

tag: Sex

value: Male

tag: age

tag: smoking status

value: Former smoker

tag: fev1 %_predicted


title: 4202-003-55

description: Gene expression data from nasal brushing 4202-003-55.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_nasal_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_nasal_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

source_name: Brushing of nasal epithelium

value: Brushing of nasal epithelium

value: Current smoker


title: 4797-022-60

description: Gene expression data from bronchial brushing 4797-022-60.

value: Female


title: 4797-026-60

description: Gene expression data from bronchial brushing 4797-026-60.


title: 4797-045-60

description: Gene expression data from bronchial brushing 4797-045-60.


title: 4797-028-60

description: Gene expression data from bronchial brushing 4797-028-60.


title: 4797-020-60

description: Gene expression data from bronchial brushing 4797-020-60.


title: 4238-018-55

description: Gene expression data from nasal brushing 4238-018-55.


title: 4797-029-60

description: Gene expression data from bronchial brushing 4797-029-60.


title: 4797-027-60

description: Gene expression data from bronchial brushing 4797-027-60.


title: 4797-014-63

description: Gene expression data from bronchial brushing 4797-014-63.


title: 4797-011-60

description: Gene expression data from bronchial brushing 4797-011-60.


title: 4797-012-60

description: Gene expression data from bronchial brushing 4797-012-60.


title: 4797-008-60

description: Gene expression data from bronchial brushing 4797-008-60.


title: 4797-002-60

description: Gene expression data from bronchial brushing 4797-002-60.


title: 4797-010-60

description: Gene expression data from bronchial brushing 4797-010-60.


title: 4797-005-60

description: Gene expression data from bronchial brushing 4797-005-60.


title: 4797-007-60

description: Gene expression data from bronchial brushing 4797-007-60.


title: 4797-009-60

description: Gene expression data from bronchial brushing 4797-009-60.


title: 4797-006-60

description: Gene expression data from bronchial brushing 4797-006-60.


title: 4796-107-60

description: Gene expression data from bronchial brushing 4796-107-60.


title: 4796-099-60

description: Gene expression data from bronchial brushing 4796-099-60.


title: 4796-103-60

description: Gene expression data from bronchial brushing 4796-103-60.


title: 4796-088-60

description: Gene expression data from bronchial brushing 4796-088-60.


title: 4796-110-60

description: Gene expression data from bronchial brushing 4796-110-60.


title: 4796-085-60

description: Gene expression data from bronchial brushing 4796-085-60.


title: 4796-117-60

description: Gene expression data from bronchial brushing 4796-117-60.


title: 4796-106-60

description: Gene expression data from bronchial brushing 4796-106-60.


title: 4796-094-60

description: Gene expression data from bronchial brushing 4796-094-60.


title: 4796-111-60

description: Gene expression data from bronchial brushing 4796-111-60.


title: 4796-108-60

description: Gene expression data from bronchial brushing 4796-108-60.


title: 4796-095-60

description: Gene expression data from bronchial brushing 4796-095-60.


title: 4796-093-60

description: Gene expression data from bronchial brushing 4796-093-60.


title: 4796-112-60

description: Gene expression data from bronchial brushing 4796-112-60.


title: 4796-102-60

description: Gene expression data from bronchial brushing 4796-102-60.


title: 4796-091-60

description: Gene expression data from bronchial brushing 4796-091-60.


title: 4796-090-60

description: Gene expression data from bronchial brushing 4796-090-60.


title: 4796-084-60

description: Gene expression data from bronchial brushing 4796-084-60.


title: 4797-003-60

description: Gene expression data from bronchial brushing 4797-003-60.


title: 4796-076-60

description: Gene expression data from bronchial brushing 4796-076-60.


title: 4796-074-60

description: Gene expression data from bronchial brushing 4796-074-60.


title: 4796-073-60

description: Gene expression data from bronchial brushing 4796-073-60.


title: 4796-080-60

description: Gene expression data from bronchial brushing 4796-080-60.


title: 4796-071-60

description: Gene expression data from bronchial brushing 4796-071-60.


title: 4796-070-60

description: Gene expression data from bronchial brushing 4796-070-60.


title: 4796-069-60

description: Gene expression data from bronchial brushing 4796-069-60.


title: 4796-065-60

description: Gene expression data from bronchial brushing 4796-065-60.


title: 4796-067-60

description: Gene expression data from bronchial brushing 4796-067-60.


title: 4796-066-60

description: Gene expression data from bronchial brushing 4796-066-60.


title: 4796-064-60

description: Gene expression data from bronchial brushing 4796-064-60.


title: 4796-060-60

description: Gene expression data from bronchial brushing 4796-060-60.


title: 4796-058-60

description: Gene expression data from bronchial brushing 4796-058-60.


title: 4796-053-60

description: Gene expression data from bronchial brushing 4796-053-60.


title: 4796-056-60

description: Gene expression data from bronchial brushing 4796-056-60.


title: 4796-051-60

description: Gene expression data from bronchial brushing 4796-051-60.


title: 4796-052-60

description: Gene expression data from bronchial brushing 4796-052-60.


title: 4796-059-60

description: Gene expression data from bronchial brushing 4796-059-60.


title: 4796-047-60

description: Gene expression data from bronchial brushing 4796-047-60.


title: 4796-046-60

description: Gene expression data from bronchial brushing 4796-046-60.


title: 4796-045-60

description: Gene expression data from bronchial brushing 4796-045-60.


title: 4796-055-60

description: Gene expression data from bronchial brushing 4796-055-60.


title: 4796-054-60

description: Gene expression data from bronchial brushing 4796-054-60.


title: 4796-050-60

description: Gene expression data from bronchial brushing 4796-050-60.


title: 4796-041-60

description: Gene expression data from bronchial brushing 4796-041-60.


title: 4796-043-60

description: Gene expression data from bronchial brushing 4796-043-60.


title: 4796-039-60

description: Gene expression data from bronchial brushing 4796-039-60.


title: 4796-037-60

description: Gene expression data from bronchial brushing 4796-037-60.


title: 4796-072-60

description: Gene expression data from bronchial brushing 4796-072-60.


title: 4796-036-60

description: Gene expression data from bronchial brushing 4796-036-60.


title: 4796-032-60

description: Gene expression data from bronchial brushing 4796-032-60.


title: 4796-034-60

description: Gene expression data from bronchial brushing 4796-034-60.


title: 4796-033-60

description: Gene expression data from bronchial brushing 4796-033-60.


title: 4796-030-60

description: Gene expression data from bronchial brushing 4796-030-60.


title: 4796-057-60

description: Gene expression data from bronchial brushing 4796-057-60.


title: 4796-023-60

description: Gene expression data from bronchial brushing 4796-023-60.


title: 4796-027-60

description: Gene expression data from bronchial brushing 4796-027-60.


title: 4796-029-60

description: Gene expression data from bronchial brushing 4796-029-60.


title: 4796-024-60

description: Gene expression data from bronchial brushing 4796-024-60.


title: 4796-025-60

description: Gene expression data from bronchial brushing 4796-025-60.


title: 4796-044-60

description: Gene expression data from bronchial brushing 4796-044-60.


title: 4796-014-60

description: Gene expression data from bronchial brushing 4796-014-60.


title: 4796-015-60

description: Gene expression data from bronchial brushing 4796-015-60.


title: 4796-001-60

description: Gene expression data from bronchial brushing 4796-001-60.


title: 4796-016-60

description: Gene expression data from bronchial brushing 4796-016-60.


title: 4796-004-60

description: Gene expression data from bronchial brushing 4796-004-60.


title: 4795-143-60

description: Gene expression data from bronchial brushing 4795-143-60.


title: 4796-009-60

description: Gene expression data from bronchial brushing 4796-009-60.


title: 4796-008-60

description: Gene expression data from bronchial brushing 4796-008-60.


title: 4796-018-60

description: Gene expression data from bronchial brushing 4796-018-60.


title: 4795-144-60

description: Gene expression data from bronchial brushing 4795-144-60.


title: 4795-123-60

description: Gene expression data from bronchial brushing 4795-123-60.


title: 4795-141-60

description: Gene expression data from bronchial brushing 4795-141-60.


title: 4796-035-60

description: Gene expression data from bronchial brushing 4796-035-60.


title: 4795-125-60

description: Gene expression data from bronchial brushing 4795-125-60.


title: 4795-124-60

description: Gene expression data from bronchial brushing 4795-124-60.


title: 4796-031-60

description: Gene expression data from bronchial brushing 4796-031-60.


title: 4795-120-60

description: Gene expression data from bronchial brushing 4795-120-60.


title: 4795-112-60

description: Gene expression data from bronchial brushing 4795-112-60.


title: 4795-110-60

description: Gene expression data from bronchial brushing 4795-110-60.


title: 4795-108-60

description: Gene expression data from bronchial brushing 4795-108-60.


title: 4796-013-60

description: Gene expression data from bronchial brushing 4796-013-60.


title: 4795-103-60

description: Gene expression data from bronchial brushing 4795-103-60.


title: 4795-101-60

description: Gene expression data from bronchial brushing 4795-101-60.


title: 4795-098-60

description: Gene expression data from bronchial brushing 4795-098-60.


title: 4795-097-60

description: Gene expression data from bronchial brushing 4795-097-60.


title: 4795-096-60

description: Gene expression data from bronchial brushing 4795-096-60.


title: 4795-100-60

description: Gene expression data from bronchial brushing 4795-100-60.


title: 4795-092-60

description: Gene expression data from bronchial brushing 4795-092-60.


title: 4795-087-60

description: Gene expression data from bronchial brushing 4795-087-60.


title: 4795-094-60

description: Gene expression data from bronchial brushing 4795-094-60.


title: 4795-091-60

description: Gene expression data from bronchial brushing 4795-091-60.


title: 4795-082-60

description: Gene expression data from bronchial brushing 4795-082-60.


title: 4795-072-60

description: Gene expression data from bronchial brushing 4795-072-60.


title: 4795-080-60

description: Gene expression data from bronchial brushing 4795-080-60.


title: 4795-119-60

description: Gene expression data from bronchial brushing 4795-119-60.


title: 4795-070-60

description: Gene expression data from bronchial brushing 4795-070-60.


title: 4795-071-60

description: Gene expression data from bronchial brushing 4795-071-60.


title: 4795-074-60

description: Gene expression data from bronchial brushing 4795-074-60.


title: 4795-089-60

description: Gene expression data from bronchial brushing 4795-089-60.


title: 4795-066-60

description: Gene expression data from bronchial brushing 4795-066-60.


title: 4795-114-60

description: Gene expression data from bronchial brushing 4795-114-60.


title: 4795-069-60

description: Gene expression data from bronchial brushing 4795-069-60.


title: 4795-065-60

description: Gene expression data from bronchial brushing 4795-065-60.


title: 4795-064-60

description: Gene expression data from bronchial brushing 4795-064-60.


title: 4795-062-60

description: Gene expression data from bronchial brushing 4795-062-60.


title: 4795-099-60

description: Gene expression data from bronchial brushing 4795-099-60.


title: 4795-059-60

description: Gene expression data from bronchial brushing 4795-059-60.


title: 4795-095-60

description: Gene expression data from bronchial brushing 4795-095-60.


title: 4795-056-60

description: Gene expression data from bronchial brushing 4795-056-60.


title: 4795-086-60

description: Gene expression data from bronchial brushing 4795-086-60.


title: 4795-081-60

description: Gene expression data from bronchial brushing 4795-081-60.


title: 4795-058-60

description: Gene expression data from bronchial brushing 4795-058-60.


title: 4795-054-60

description: Gene expression data from bronchial brushing 4795-054-60.


title: 4795-051-60

description: Gene expression data from bronchial brushing 4795-051-60.


title: 4795-042-60

description: Gene expression data from bronchial brushing 4795-042-60.


title: 4795-053-60

description: Gene expression data from bronchial brushing 4795-053-60.


title: 4795-041-60

description: Gene expression data from bronchial brushing 4795-041-60.


title: 4795-044-60

description: Gene expression data from bronchial brushing 4795-044-60.


title: 4795-040-60

description: Gene expression data from bronchial brushing 4795-040-60.


title: 4795-039-60

description: Gene expression data from bronchial brushing 4795-039-60.


title: 4795-038-60

description: Gene expression data from bronchial brushing 4795-038-60.


title: 4795-037-60

description: Gene expression data from bronchial brushing 4795-037-60.


title: 4795-035-60

description: Gene expression data from bronchial brushing 4795-035-60.


title: 4795-026-60

description: Gene expression data from bronchial brushing 4795-026-60.


title: 4795-036-60

description: Gene expression data from bronchial brushing 4795-036-60.


title: 4795-031-60

description: Gene expression data from bronchial brushing 4795-031-60.


title: 4795-024-60

description: Gene expression data from bronchial brushing 4795-024-60.


title: 4795-030-60

description: Gene expression data from bronchial brushing 4795-030-60.


title: 4795-060-60

description: Gene expression data from bronchial brushing 4795-060-60.


title: 4795-032-60

description: Gene expression data from bronchial brushing 4795-032-60.


title: 4795-019-60

description: Gene expression data from bronchial brushing 4795-019-60.


title: 4795-023-60

description: Gene expression data from bronchial brushing 4795-023-60.


title: 4795-017-60

description: Gene expression data from bronchial brushing 4795-017-60.


title: 4795-055-60

description: Gene expression data from bronchial brushing 4795-055-60.


title: 4795-014-60

description: Gene expression data from bronchial brushing 4795-014-60.


title: 4795-021-60

description: Gene expression data from bronchial brushing 4795-021-60.


title: 4795-018-60

description: Gene expression data from bronchial brushing 4795-018-60.


title: 4795-013-60

description: Gene expression data from bronchial brushing 4795-013-60.


title: 4795-046-60

description: Gene expression data from bronchial brushing 4795-046-60.


title: 4795-012-60

description: Gene expression data from bronchial brushing 4795-012-60.


title: 4795-011-60

description: Gene expression data from bronchial brushing 4795-011-60.


title: 4795-045-60

description: Gene expression data from bronchial brushing 4795-045-60.


title: 4795-004-60

description: Gene expression data from bronchial brushing 4795-004-60.


title: 4795-005-60

description: Gene expression data from bronchial brushing 4795-005-60.


title: 4795-008-60

description: Gene expression data from bronchial brushing 4795-008-60.


title: 4794-002-60

description: Gene expression data from bronchial brushing 4794-002-60.


title: 4795-007-60

description: Gene expression data from bronchial brushing 4795-007-60.


title: 4793-042-60

description: Gene expression data from bronchial brushing 4793-042-60.


title: 4793-035-60

description: Gene expression data from bronchial brushing 4793-035-60.


title: 4793-039-60

description: Gene expression data from bronchial brushing 4793-039-60.


title: 4793-033-60

description: Gene expression data from bronchial brushing 4793-033-60.


title: 4793-032-60

description: Gene expression data from bronchial brushing 4793-032-60.


title: 4793-028-60

description: Gene expression data from bronchial brushing 4793-028-60.


title: 4793-025-60

description: Gene expression data from bronchial brushing 4793-025-60.


title: 4793-017-60

description: Gene expression data from bronchial brushing 4793-017-60.


title: 4793-027-60

description: Gene expression data from bronchial brushing 4793-027-60.


title: 4793-016-60

description: Gene expression data from bronchial brushing 4793-016-60.


title: 4793-021-60

description: Gene expression data from bronchial brushing 4793-021-60.


title: 4795-010-60

description: Gene expression data from bronchial brushing 4795-010-60.


title: 4793-013-60

description: Gene expression data from bronchial brushing 4793-013-60.


title: 4793-015-60

description: Gene expression data from bronchial brushing 4793-015-60.


title: 4793-011-60

description: Gene expression data from bronchial brushing 4793-011-60.


title: 4793-007-60

description: Gene expression data from bronchial brushing 4793-007-60.


title: 4792-036-60

description: Gene expression data from bronchial brushing 4792-036-60.


title: 4793-012-60

description: Gene expression data from bronchial brushing 4793-012-60.


title: 4793-005-60

description: Gene expression data from bronchial brushing 4793-005-60.


title: 4795-002-60

description: Gene expression data from bronchial brushing 4795-002-60.


title: 4792-031-60

description: Gene expression data from bronchial brushing 4792-031-60.


title: 4794-001-60

description: Gene expression data from bronchial brushing 4794-001-60.


title: 4792-030-60

description: Gene expression data from bronchial brushing 4792-030-60.


title: 4793-006-60

description: Gene expression data from bronchial brushing 4793-006-60.


title: 4792-020-60

description: Gene expression data from bronchial brushing 4792-020-60.


title: 4792-029-60

description: Gene expression data from bronchial brushing 4792-029-60.


title: 4792-017-60

description: Gene expression data from bronchial brushing 4792-017-60.


title: 4792-024-60

description: Gene expression data from bronchial brushing 4792-024-60.


title: 4792-018-60

description: Gene expression data from bronchial brushing 4792-018-60.


title: 4792-009-60

description: Gene expression data from bronchial brushing 4792-009-60.


title: 4792-010-60

description: Gene expression data from bronchial brushing 4792-010-60.


title: 4792-015-60

description: Gene expression data from bronchial brushing 4792-015-60.


title: 4792-005-60

description: Gene expression data from bronchial brushing 4792-005-60.


title: 4791-006-60

description: Gene expression data from bronchial brushing 4791-006-60.


title: 4791-003-60

description: Gene expression data from bronchial brushing 4791-003-60.


title: 4792-007-60

description: Gene expression data from bronchial brushing 4792-007-60.


title: 4792-001-60

description: Gene expression data from bronchial brushing 4792-001-60.


title: 4792-013-60

description: Gene expression data from bronchial brushing 4792-013-60.


title: 4791-002-60

description: Gene expression data from bronchial brushing 4791-002-60.


title: 4791-004-60

description: Gene expression data from bronchial brushing 4791-004-60.


title: 4790-090-60

description: Gene expression data from bronchial brushing 4790-090-60.


title: 4790-089-60

description: Gene expression data from bronchial brushing 4790-089-60.


title: 4790-084-60

description: Gene expression data from bronchial brushing 4790-084-60.


title: 4790-080-60

description: Gene expression data from bronchial brushing 4790-080-60.


title: 4790-081-60

description: Gene expression data from bronchial brushing 4790-081-60.


title: 4790-073-60

description: Gene expression data from bronchial brushing 4790-073-60.


title: 4790-077-60

description: Gene expression data from bronchial brushing 4790-077-60.


title: 4790-074-60

description: Gene expression data from bronchial brushing 4790-074-60.


title: 4790-078-60

description: Gene expression data from bronchial brushing 4790-078-60.


title: 4790-072-60

description: Gene expression data from bronchial brushing 4790-072-60.


title: 4790-070-60

description: Gene expression data from bronchial brushing 4790-070-60.


title: 4790-059-60

description: Gene expression data from bronchial brushing 4790-059-60.


title: 4790-061-60

description: Gene expression data from bronchial brushing 4790-061-60.


title: 4790-056-60

description: Gene expression data from bronchial brushing 4790-056-60.


title: 4790-069-60

description: Gene expression data from bronchial brushing 4790-069-60.


title: 4790-063-60

description: Gene expression data from bronchial brushing 4790-063-60.


title: 4790-060-60

description: Gene expression data from bronchial brushing 4790-060-60.


title: 4790-057-60

description: Gene expression data from bronchial brushing 4790-057-60.


title: 4790-055-60

description: Gene expression data from bronchial brushing 4790-055-60.


title: 4790-052-60

description: Gene expression data from bronchial brushing 4790-052-60.


title: 4790-051-60

description: Gene expression data from bronchial brushing 4790-051-60.


title: 4790-050-60

description: Gene expression data from bronchial brushing 4790-050-60.


title: 4790-053-60

description: Gene expression data from bronchial brushing 4790-053-60.


title: 4790-046-60

description: Gene expression data from bronchial brushing 4790-046-60.


title: 4790-045-60

description: Gene expression data from bronchial brushing 4790-045-60.


title: 4790-044-60

description: Gene expression data from bronchial brushing 4790-044-60.


title: 4790-054-60

description: Gene expression data from bronchial brushing 4790-054-60.


title: 4790-041-60

description: Gene expression data from bronchial brushing 4790-041-60.


title: 4790-040-60

description: Gene expression data from bronchial brushing 4790-040-60.


title: 4790-039-60

description: Gene expression data from bronchial brushing 4790-039-60.


title: 4790-043-60

description: Gene expression data from bronchial brushing 4790-043-60.


title: 4790-038-60

description: Gene expression data from bronchial brushing 4790-038-60.


title: 4790-037-60

description: Gene expression data from bronchial brushing 4790-037-60.


title: 4790-035-60

description: Gene expression data from bronchial brushing 4790-035-60.


title: 4790-031-60

description: Gene expression data from bronchial brushing 4790-031-60.


title: 4790-032-60

description: Gene expression data from bronchial brushing 4790-032-60.


title: 4790-034-60

description: Gene expression data from bronchial brushing 4790-034-60.


title: 4790-029-60

description: Gene expression data from bronchial brushing 4790-029-60.


title: 4790-028-60

description: Gene expression data from bronchial brushing 4790-028-60.


title: 4790-027-60

description: Gene expression data from bronchial brushing 4790-027-60.


title: 4790-024-60

description: Gene expression data from bronchial brushing 4790-024-60.


title: 4790-023-60

description: Gene expression data from bronchial brushing 4790-023-60.


title: 4790-022-60

description: Gene expression data from bronchial brushing 4790-022-60.


title: 4790-015-60

description: Gene expression data from bronchial brushing 4790-015-60.


title: 4790-026-60

description: Gene expression data from bronchial brushing 4790-026-60.


title: 4790-016-60

description: Gene expression data from bronchial brushing 4790-016-60.


title: 4790-014-60

description: Gene expression data from bronchial brushing 4790-014-60.


title: 4790-011-60

description: Gene expression data from bronchial brushing 4790-011-60.


title: 4790-019-60

description: Gene expression data from bronchial brushing 4790-019-60.


title: 4790-009-60

description: Gene expression data from bronchial brushing 4790-009-60.


title: 4790-012-60

description: Gene expression data from bronchial brushing 4790-012-60.


title: 4790-013-60

description: Gene expression data from bronchial brushing 4790-013-60.


title: 4790-002-60

description: Gene expression data from bronchial brushing 4790-002-60.


title: 4790-001-60

description: Gene expression data from bronchial brushing 4790-001-60.


title: 4790-003-60

description: Gene expression data from bronchial brushing 4790-003-60.


title: 4790-030-60

description: Gene expression data from bronchial brushing 4790-030-60.


title: 4714-013-60

description: Gene expression data from bronchial brushing 4714-013-60.


title: 4790-005-60

description: Gene expression data from bronchial brushing 4790-005-60.


title: 4714-009-60

description: Gene expression data from bronchial brushing 4714-009-60.


title: 4714-012-60

description: Gene expression data from bronchial brushing 4714-012-60.


title: 4714-008-60

description: Gene expression data from bronchial brushing 4714-008-60.


title: 4714-007-60

description: Gene expression data from bronchial brushing 4714-007-60.


title: 4790-025-60

description: Gene expression data from bronchial brushing 4790-025-60.


title: 4714-005-60

description: Gene expression data from bronchial brushing 4714-005-60.


title: 4790-021-60

description: Gene expression data from bronchial brushing 4790-021-60.


title: 4790-076-60

description: Gene expression data from bronchial brushing 4790-076-60.


title: 4438-091-60

description: Gene expression data from bronchial brushing 4438-091-60.


title: 4714-001-60

description: Gene expression data from bronchial brushing 4714-001-60.


title: 4438-076-60

description: Gene expression data from bronchial brushing 4438-076-60.


title: 4438-085-60

description: Gene expression data from bronchial brushing 4438-085-60.


title: 4438-073-60

description: Gene expression data from bronchial brushing 4438-073-60.


title: 4790-006-60

description: Gene expression data from bronchial brushing 4790-006-60.


title: 4438-068-60

description: Gene expression data from bronchial brushing 4438-068-60.


title: 4438-056-60

description: Gene expression data from bronchial brushing 4438-056-60.


title: 4438-067-60

description: Gene expression data from bronchial brushing 4438-067-60.


title: 4438-066-60

description: Gene expression data from bronchial brushing 4438-066-60.


title: 4438-055-60

description: Gene expression data from bronchial brushing 4438-055-60.


title: 4438-059-60

description: Gene expression data from bronchial brushing 4438-059-60.


title: 4714-023-60

description: Gene expression data from bronchial brushing 4714-023-60.


title: 4438-052-60

description: Gene expression data from bronchial brushing 4438-052-60.


title: 4438-051-60

description: Gene expression data from bronchial brushing 4438-051-60.


title: 4790-008-60

description: Gene expression data from bronchial brushing 4790-008-60.


title: 4438-045-60

description: Gene expression data from bronchial brushing 4438-045-60.


title: 4438-041-60

description: Gene expression data from bronchial brushing 4438-041-60.


title: 4438-036-60

description: Gene expression data from bronchial brushing 4438-036-60.


title: 4438-032-60

description: Gene expression data from bronchial brushing 4438-032-60.


title: 4438-035-60

description: Gene expression data from bronchial brushing 4438-035-60.


title: 4438-034-60

description: Gene expression data from bronchial brushing 4438-034-60.


title: 4438-030-60

description: Gene expression data from bronchial brushing 4438-030-60.


title: 4438-037-60

description: Gene expression data from bronchial brushing 4438-037-60.


title: 4438-031-60

description: Gene expression data from bronchial brushing 4438-031-60.


title: 4438-054-60

description: Gene expression data from bronchial brushing 4438-054-60.


title: 4438-028-60

description: Gene expression data from bronchial brushing 4438-028-60.


title: 4438-029-60

description: Gene expression data from bronchial brushing 4438-029-60.


title: 4438-058-60

description: Gene expression data from bronchial brushing 4438-058-60.


title: 4438-027-60

description: Gene expression data from bronchial brushing 4438-027-60.


title: 4438-024-60

description: Gene expression data from bronchial brushing 4438-024-60.


title: 4438-026-60

description: Gene expression data from bronchial brushing 4438-026-60.


title: 4438-023-60

description: Gene expression data from bronchial brushing 4438-023-60.


title: 4438-021-60

description: Gene expression data from bronchial brushing 4438-021-60.


title: 4438-019-60

description: Gene expression data from bronchial brushing 4438-019-60.


title: 4438-022-60

description: Gene expression data from bronchial brushing 4438-022-60.


title: 4438-017-60

description: Gene expression data from bronchial brushing 4438-017-60.


title: 4438-016-60

description: Gene expression data from bronchial brushing 4438-016-60.


title: 4438-015-60

description: Gene expression data from bronchial brushing 4438-015-60.


title: 4438-018-60

description: Gene expression data from bronchial brushing 4438-018-60.


title: 4438-014-60

description: Gene expression data from bronchial brushing 4438-014-60.


title: 4438-005-60

description: Gene expression data from bronchial brushing 4438-005-60.


title: 4438-009-60

description: Gene expression data from bronchial brushing 4438-009-60.


title: 4438-004-60

description: Gene expression data from bronchial brushing 4438-004-60.


title: 4438-012-60

description: Gene expression data from bronchial brushing 4438-012-60.


title: 4438-013-60

description: Gene expression data from bronchial brushing 4438-013-60.


title: 4238-038-60

description: Gene expression data from bronchial brushing 4238-038-60.


title: 4438-003-60

description: Gene expression data from bronchial brushing 4438-003-60.


title: 4278-003-60

description: Gene expression data from bronchial brushing 4278-003-60.


title: 4438-010-60

description: Gene expression data from bronchial brushing 4438-010-60.


title: 4238-037-60

description: Gene expression data from bronchial brushing 4238-037-60.


title: 4238-029-60

description: Gene expression data from bronchial brushing 4238-029-60.


title: 4278-002-60

description: Gene expression data from bronchial brushing 4278-002-60.


title: 4238-027-60

description: Gene expression data from bronchial brushing 4238-027-60.


title: 4238-025-60

description: Gene expression data from bronchial brushing 4238-025-60.


title: 4438-025-60

description: Gene expression data from bronchial brushing 4438-025-60.


title: 4238-022-60

description: Gene expression data from bronchial brushing 4238-022-60.


title: 4238-016-60

description: Gene expression data from bronchial brushing 4238-016-60.


title: 4238-019-60

description: Gene expression data from bronchial brushing 4238-019-60.


title: 4238-018-60

description: Gene expression data from bronchial brushing 4238-018-60.


title: 4238-017-60

description: Gene expression data from bronchial brushing 4238-017-60.


title: 4238-008-60

description: Gene expression data from bronchial brushing 4238-008-60.


title: 4238-012-60

description: Gene expression data from bronchial brushing 4238-012-60.


title: 4238-004-60

description: Gene expression data from bronchial brushing 4238-004-60.


title: 4238-002-60

description: Gene expression data from bronchial brushing 4238-002-60.


title: 4202-033-63

description: Gene expression data from bronchial brushing 4202-033-63.


title: 4202-023-60

description: Gene expression data from bronchial brushing 4202-023-60.


title: 4202-022-60

description: Gene expression data from bronchial brushing 4202-022-60.


title: 4202-015-60

description: Gene expression data from bronchial brushing 4202-015-60.


title: 4202-016-60

description: Gene expression data from bronchial brushing 4202-016-60.


title: 4202-021-60

description: Gene expression data from bronchial brushing 4202-021-60.


title: 4238-030-60

description: Gene expression data from bronchial brushing 4238-030-60.


title: 4202-003-60

description: Gene expression data from bronchial brushing 4202-003-60.


title: 4202-017-60

description: Gene expression data from bronchial brushing 4202-017-60.


title: 4202-019-60

description: Gene expression data from bronchial brushing 4202-019-60.


title: 4238-028-60

description: Gene expression data from bronchial brushing 4238-028-60.


title: 4202-012-60

description: Gene expression data from bronchial brushing 4202-012-60.


title: 4202-002-60

description: Gene expression data from bronchial brushing 4202-002-60.


title: 4202-006-60

description: Gene expression data from bronchial brushing 4202-006-60.


title: 4202-004-60

description: Gene expression data from bronchial brushing 4202-004-60.


title: A.I_m7

city: CIUDAD DE MEXICO

first: Abrahan

last: Hernandez-Hernandez

state: CIUDAD DE MEXICO

address: Dr.Márquez No.162, Col. Doctores, Delegación: Cuauhtémoc

country: Mexico

institute: Hospital Infantil de México Federico Gómez

data_processing:
Quality control of raw data files was performed (fastq) with FastQC v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://multiqc.info)
The reads were aligned to the human reference genome, ribosomal RNA and Non chromosomal RNA (e.g., mitochondrial genome, sequence contigs not yet mapped on chromosomes) with STAR 2.7.9a
Sorting of SAM files BAM files were done using Samtools 1.13
BAM files were used to generate the read summarization and a count table, in which the number of reads assigned to each feature in each library is recorded, using featureCounts from the subread 2.0.3 package
The count table was used to perform trimmed mean of M values (TMM) normalization and gene differential expression in Empirical Analysis of Digital Gene Expression Data in R (EdgeR) from Bioconductor
Functional analysis of the mis regulated genes was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Simultaneous purification of RNA and DNA from tumor and healthy (control) biopsies with the AllPrep DNA/RNA/miRNA Universal kit (QIAGEN) was done
Purified RNA with an acceptable RIN value of 5.5 to 7.6 was used to perform sequencing libraries with the TruSeq Stranded total RNA with Illumina Ribo-Zero Plus rRNA depletion kit (Illumina)

value: Cerebellum

tag: histological grade

tag: molecular classification

tag: pathology


title: A.I_m8


title: C_m94

source_name: Cerebellum

value: Control


title: A.IV_m49

source_name: Glioblastoma

value: Cerebrum

value: Glioblastoma


title: A.III_m69


title: A.III_m29


title: A.I_m20


title: B_m102

source_name: Cerebrum


title: A.IV_m10

source_name: Gliosarcoma

value: Gliosarcoma


title: A.IV_cm8


title: A.II_cm75


title: A.I_cm71


title: 4202-025-60

description: Gene expression data from bronchial brushing 4202-025-60.


title: A.III_cm54


title: A.I_m46


title: A.I_cm30


title: A.II_cm15


title: C_a12b


title: B_a12a


title: B_a10a


title: D14 post-injury FDL, biol rep 2

city: Rochester

first: Jessica

last: Ackerman

state: NY

address: 605 Elmwood Ave

institute: University of Rochester

data_processing:
Demultiplexing: spaceranger-1.3.1/spaceranger mkfastq --run=. --samplesheet=spaceRanger.csv --output-dir ./spaceRanger --nopreflight --jobmode=slurm --localcores=24 --localmem=120
Counting: spaceranger-1.3.1/spaceranger count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --slide=${SLIDE} --area=${AREA} --image=${IMAGE}
Assembly: combined cellranger provided “refdata-gex-mm10 2020-A” and user provided tdTomato sequence
Supplementary files format and content: feature barcode matrix data (.tsv, .mtx)

organism: Mus musculus

source_name: murine hindpaw

extract_protocol:
Whole hindpaws from experimental mice were collected and fresh frozen prior to sectioning onto gene expression slides (10X Visium)
RNA extraction, cDNA amplification, and library construction were carried out according to the 10X Genomics Visium user guide, rev F

treatment_protocol: Experimental mice were given tamoxifen D-7 to -4 prior to complete transection and repair of the FDL tendon in the hindpaw to label resident Scx-lin+ cells and visualize their contribution

value: murine hindpaw

value: 10-12 weeks

tag: strain

value: Scx-CreER; Ai9 F/+

tag: time

value: Day 14


title: D14 post-injury FDL, biol rep 1


title: D28 post-injury FDL, biol rep 1

value: Day 28


title: D28 post-injury FDL, biol rep 2


title: D21 post-injury FDL, biol rep 1

value: Day 21


title: Uninjured FDL control, D0 biol rep 1

value: Day 0


title: D21 post-injury FDL, biol rep 2


title: Uninjured FDL control, D0 biol rep 2


title: A.II_cm39

value: Brain stem


title: drosophila Kc167 MgR rep3

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

description:
total RNA, remove rRNA
Discover the 3'-end Nm of RNA

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads
First, Cutadapt (v2.8) was used to cut the adapters of the paired-end reads with the following parameters: cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 15 -e 0.15. Then reads were subsequently mapped to the reference genome (mm10 or dm6) and transcriptome with STAR software with the following parameters: --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 30 --outFilterMismatchNmax 15 --outFilterMismatchNoverLmax 0.1 --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 15 --outFilterMatchNminOverLread 0.8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --seedSearchLmax 0 --seedMultimapNmax 20000 --seedPerReadNmax 1000 --seedPerWindowNmax 100 --seedNoneLociPerWindow 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
To identify significantly enriched 3’end-Nm sites,  we first call significant 3’-end singal with following criteria: (1) upFC=endCov/upCov≥2; (2) downFC=endCov/downCov≥2; (3) p value≤-5; (4) read count≥5. A candidate 3’-end Nm site was required to bear a significant 3'-end singal in all nine samples under three conditions (i.e. inupt, MgR-treated, MgR+OED-treated).
Assembly: mm10, dm6
Supplementary files format and content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (RPM).

organism: Drosophila melanogaster

source_name: disaggregated 8–12h Drosophila embryos

growth_protocol: KC167 cells were cultivated at 26℃ in serum-free medium containing 1% penicillin and streptomycin (Gibco) without CO2. Mouse testes were isolated from 3 pieces of 8 weeks sexual mature C57BL/6J mouse (GuangDong Medical Laboratory Animal Center)

extract_protocol:
RNA was collected using RNAzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MgR exoribonuclease digestion reaction: RNA samples from the previous step were firstly denatured at 65℃ for 5min and put it on ice immediately. MgR exoribonuclease (Synbio Tech) digestion reaction was conducted by using 4ug enzyme for 1μg RNA samples with MgR Reaction buffer (20mM Tris ph=8.5, 10μM Zncl2, 100mM KCl) at 37℃ for 1 hour. Purify small RNA using RNA Clean&Concentration-5 kit (Zymoresearch; R1017), according to the manufacturer’s instructions. NaIO4 oxidation-elimination-dephosphorylation (OED): MgR treatment RNA was oxidized with 20mM NaIO4 (Thermo, PI20504) under 200mM lysine-HCl buffer (ph=8.5) incubated at 37℃ for 30min with shaking in the darkness and the β-elimination reacting automatically. Quench the reaction by adding thylene glycol (Thermo, 29810). Dephosphorylate was followed by adding rSAP enzyme (NEB, M0371L) to incubate at 37℃ for 30min with shaking in the darkness. The RNA was purified using RNA Clean&Concentration-5 kit (Zymoresearch; R1017), according to the manufacturer’s instructions. Then another OED cycle was conducted for the previous purified RNA, followed by purification. Finally, the RNA samples were subjected to periodate oxidation followed β-elimination reacting automatically without the subsequent dephosphorylation step, purifying with Rnasefree water.

tag: treatment

value: MgR-treated

tag: treatment label

tag: genotype

value: wild type


title: drosophila Kc167 input rep2

value: non-treated


title: chip111

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

library_source: genomic

data_processing:
Library strategy: Chem-seq
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0 with parameters -p 40 -m 1 -S -q
peaks were called using MACS2 version 2.1.1 with parameters callpeak -g hs -B --SPMR
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were converted from bdg files generated by MACS2 version 2.1.1; Scores reprsent signal per million reads for fragment pileup profiles

molecule: genomic DNA

source_name: Human osteosarcoma U2OS cells

growth_protocol: U2OS cells (passage 15-20) were routinely grown till confluence (10% FBS with 1% Pen+Str antibiotics in DMEM), released to serum-free DMEM medium and continued for 36 h

extract_protocol:
Cells were fixed by formadehyde for 10min and washed twice with cold PBS, trypsinized and normalized cell numbers; extract genomic DNA and sonicate. Strepavidin agarose beads (50ul) were incubated for at least 2 h, wash with PBS+0.1% BSA, and extract beads captured DNA with MiniElute DNA kit (QIAGEN).
Libraries were prepared according to Illumina's instructions

treatment_protocol: When Per2-dLuc reached the peak of Per2-dLuc, cells were treated with biotin-DRB (40uM) for 0.5 h

tag: cell line

tag: labeling compound

value: Biotinylated DRB

tag: pull-down beads

value: Strepavidin agarose (Thermo Fisher #SA10004)


title: input16

source_name: Human osteosarcoma U3OS cells


title: drosophila Kc167 MgR rep1


title: drosophila Kc167 input rep3


title: drosophila Kc167 MgR+OED rep2

value: MgR+OED-treated

value: exoribonuclease RNase R treated


title: drosophila Kc167 MgR rep2


title: drosophila Kc167 MgR+OED rep3


title: drosophila Kc167 MgR+OED rep1


title: drosophila Kc167 input rep1


title: 1698

type: RNA

description:
Gene expression data from bronchial brushing of subject 1698.
reanalysis of GSM912432

hyb_protocol: The labeled fragmented cDNA was hybridized to Affymetrix Human Gene ST v1.0 microarrays for 16-18 hours in the GeneChip Hybridization Oven 640 (45C, 60rpm rotation). The hybridized samples were washed. Using Affymetrix Fluidics Station 450 (Hybridization Washing and Staining Kit, Affymetrix), the samples were first stained with streptavidin (SAPE). This was followed by signal amplification with a biotinylated goat anti-streptavidin antibody and a second SAPE stain.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

label: biotin

label_protocol: High molecular weight RNA was processed and hybridized to Affymetrix Human Gene Arrays ST v1.0 as described in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). Briefly, 200ng of high molecular weight RNA was reverse transcribed (Whole Transcript cDNA Synthesis Kit, Affymetrix). The resulting cDNA was used as a template for in vitro transcription (IVT) (Whole Transcript cDNA Amplification Kit, Affymetrix). The resulting antisense cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix) and then reverse transcribed with dUTP incorporation (Whole Transcript cDNA Synthesis Kit, Affymetrix, Santa Clara, CA). The resulting single-stranded sense DNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1). The fragmented DNA was labeled using DNA Labeling Reagent which is covalently linked to biotin with terminal deoxynucleotidyl transferase (TdT) (Whole Transcript Terminal Labeling Kit, Affymetrix).

extract_protocol: Isolation of high molecular weight RNA was performed using the miRNeasy mini kit (Qiagen) as per the manufacturer's instructions. Briefly, bronchial epithelial cells were lysed and homogenized in QIAzol Lysis Reagent. After chloroform extraction, the aqueous phase containing RNA was mixed with ethanol. This was applied to an RNeasy Mini Spin Column to retain high molecular weight RNA (>200 nt). After washing, high molecular weight RNA was eluted.

tag: original geo accession

value: Female

value: Current smoker

tag: fev1 % predicted

tag: cancer status


title: 8000250

description:
Gene expression data from bronchial brushing of subject 8000250.
reanalysis of GSM912429

tag: Sex

value: Male

tag: age

value: Former smoker


title: 1957

description:
Gene expression data from bronchial brushing of subject 1957.
reanalysis of GSM912442

tag: smoking status


title: 8000355

description:
Gene expression data from bronchial brushing of subject 8000355.
reanalysis of GSM912418


title: 5000730

description:
Gene expression data from bronchial brushing of subject 5000730.
reanalysis of GSM912422


title: 1322

description:
Gene expression data from bronchial brushing of subject 1322.
reanalysis of GSM912430


title: 9000045

description:
Gene expression data from bronchial brushing of subject 9000045.
reanalysis of GSM912446


title: 4000350

description:
Gene expression data from bronchial brushing of subject 4000350.
reanalysis of GSM912426


title: 8000566

description:
Gene expression data from bronchial brushing of subject 8000566.
reanalysis of GSM912440


title: 1977

description:
Gene expression data from bronchial brushing of subject 1977.
reanalysis of GSM912419


title: 4000816

description:
Gene expression data from bronchial brushing of subject 4000816.
reanalysis of GSM912417


title: 9000273

description:
Gene expression data from bronchial brushing of subject 9000273.
reanalysis of GSM912438


title: 8000208

description:
Gene expression data from bronchial brushing of subject 8000208.
reanalysis of GSM912444


title: 6000070

description:
Gene expression data from bronchial brushing of subject 6000070.
reanalysis of GSM912427


title: 8000588

description:
Gene expression data from bronchial brushing of subject 8000588.
reanalysis of GSM912424


title: 6000022

description:
Gene expression data from bronchial brushing of subject 6000022.
reanalysis of GSM912434


title: 9000217

description:
Gene expression data from bronchial brushing of subject 9000217.
reanalysis of GSM912414


title: 1293

description:
Gene expression data from bronchial brushing of subject 1293.
reanalysis of GSM912409


title: 4000447

description:
Gene expression data from bronchial brushing of subject 4000447.
reanalysis of GSM912410


title: 8000592

description:
Gene expression data from bronchial brushing of subject 8000592.
reanalysis of GSM912413


title: 9000277

description:
Gene expression data from bronchial brushing of subject 9000277.
reanalysis of GSM912415


title: 8000492

description:
Gene expression data from bronchial brushing of subject 8000492.
reanalysis of GSM912412


title: 6000145

description:
Gene expression data from bronchial brushing of subject 6000145.
reanalysis of GSM912436


title: 5000550

description:
Gene expression data from bronchial brushing of subject 5000550.
reanalysis of GSM912421


title: 8000282

description:
Gene expression data from bronchial brushing of subject 8000282.
reanalysis of GSM912411


title: 1279

description:
Gene expression data from bronchial brushing of subject 1279.
reanalysis of GSM912408


title: 4000794

description:
Gene expression data from bronchial brushing of subject 4000794.
reanalysis of GSM912416


title: 1155

description:
Gene expression data from bronchial brushing of subject 1155.
reanalysis of GSM912407


title: 9000109

description:
Gene expression data from bronchial brushing of subject 9000109.
reanalysis of GSM912406


title: 1992

description:
Gene expression data from bronchial brushing of subject 1992.
reanalysis of GSM912405


title: 9000073

description:
Gene expression data from bronchial brushing of subject 9000073.
reanalysis of GSM912404


title: 8000540

description:
Gene expression data from bronchial brushing of subject 8000540.
reanalysis of GSM912403


title: 5000396

description:
Gene expression data from bronchial brushing of subject 5000396.
reanalysis of GSM912398


title: 9000377

description:
Gene expression data from bronchial brushing of subject 9000377.
reanalysis of GSM912394


title: 4000111

description:
Gene expression data from bronchial brushing of subject 4000111.
reanalysis of GSM912397


title: 6000151

description:
Gene expression data from bronchial brushing of subject 6000151.
reanalysis of GSM912400


title: 8000471

description:
Gene expression data from bronchial brushing of subject 8000471.
reanalysis of GSM912391


title: 8000562

description:
Gene expression data from bronchial brushing of subject 8000562.
reanalysis of GSM912392


title: 8000246

description:
Gene expression data from bronchial brushing of subject 8000246.
reanalysis of GSM912401


title: 8000290

description:
Gene expression data from bronchial brushing of subject 8000290.
reanalysis of GSM912402


title: 9000289

description:
Gene expression data from bronchial brushing of subject 9000289.
reanalysis of GSM912393


title: 1273

description:
Gene expression data from bronchial brushing of subject 1273.
reanalysis of GSM912395


title: 1751

description:
Gene expression data from bronchial brushing of subject 1751.
reanalysis of GSM912388


title: 1656

description:
Gene expression data from bronchial brushing of subject 1656.
reanalysis of GSM912387


title: 5000264

description:
Gene expression data from bronchial brushing of subject 5000264.
reanalysis of GSM912384


title: 6000043

description:
Gene expression data from bronchial brushing of subject 6000043.
reanalysis of GSM912399


title: 6000228

description:
Gene expression data from bronchial brushing of subject 6000228.
reanalysis of GSM912390


title: 9000233

description:
Gene expression data from bronchial brushing of subject 9000233.
reanalysis of GSM912396


title: 9000213

description:
Gene expression data from bronchial brushing of subject 9000213.
reanalysis of GSM912383


title: 4000572

description:
Gene expression data from bronchial brushing of subject 4000572.
reanalysis of GSM912389


title: 9000101

description:
Gene expression data from bronchial brushing of subject 9000101.
reanalysis of GSM912380


title: 8000568

description:
Gene expression data from bronchial brushing of subject 8000568.
reanalysis of GSM912378


title: 8000403

description:
Gene expression data from bronchial brushing of subject 8000403.
reanalysis of GSM912376


title: 8000524

description:
Gene expression data from bronchial brushing of subject 8000524.
reanalysis of GSM912377


title: 9000005

description:
Gene expression data from bronchial brushing of subject 9000005.
reanalysis of GSM912386


title: 9000173

description:
Gene expression data from bronchial brushing of subject 9000173.
reanalysis of GSM912382


title: 8000576

description:
Gene expression data from bronchial brushing of subject 8000576.
reanalysis of GSM912379


title: 5000311

description:
Gene expression data from bronchial brushing of subject 5000311.
reanalysis of GSM912375


title: 8000243

description:
Gene expression data from bronchial brushing of subject 8000243.
reanalysis of GSM912385


title: 4000141

description:
Gene expression data from bronchial brushing of subject 4000141.
reanalysis of GSM912371


title: 5000061

description:
Gene expression data from bronchial brushing of subject 5000061.
reanalysis of GSM912374


title: 1915

description:
Gene expression data from bronchial brushing of subject 1915.
reanalysis of GSM912368


title: 5000019

description:
Gene expression data from bronchial brushing of subject 5000019.
reanalysis of GSM912373


title: 2035

description:
Gene expression data from bronchial brushing of subject 2035.
reanalysis of GSM912369


title: 876

description:
Gene expression data from bronchial brushing of subject 876.
reanalysis of GSM912367


title: 9000229

description:
Gene expression data from bronchial brushing of subject 9000229.
reanalysis of GSM912365


title: 9000113

description:
Gene expression data from bronchial brushing of subject 9000113.
reanalysis of GSM912381


title: 4000179

description:
Gene expression data from bronchial brushing of subject 4000179.
reanalysis of GSM912372


title: 8000459

description:
Gene expression data from bronchial brushing of subject 8000459.
reanalysis of GSM912361


title: 8000504

description:
Gene expression data from bronchial brushing of subject 8000504.
reanalysis of GSM912363


title: 9000237

description:
Gene expression data from bronchial brushing of subject 9000237.
reanalysis of GSM912366


title: 8000580

description:
Gene expression data from bronchial brushing of subject 8000580.
reanalysis of GSM912364


title: 5000568

description:
Gene expression data from bronchial brushing of subject 5000568.
reanalysis of GSM912358


title: 2081

description:
Gene expression data from bronchial brushing of subject 2081.
reanalysis of GSM912370


title: 4000012

description:
Gene expression data from bronchial brushing of subject 4000012.
reanalysis of GSM912357


title: 6000358

description:
Gene expression data from bronchial brushing of subject 6000358.
reanalysis of GSM912359


title: 4000438

description:
Gene expression data from bronchial brushing of subject 4000438.
reanalysis of GSM912353


title: 8000451

description:
Gene expression data from bronchial brushing of subject 8000451.
reanalysis of GSM912354


title: 9000157

description:
Gene expression data from bronchial brushing of subject 9000157.
reanalysis of GSM912349


title: 9000262

description:
Gene expression data from bronchial brushing of subject 9000262.
reanalysis of GSM912350


title: 9000049

description:
Gene expression data from bronchial brushing of subject 9000049.
reanalysis of GSM912355


title: 9000473

description:
Gene expression data from bronchial brushing of subject 9000473.
reanalysis of GSM912351


title: 8000502

description:
Gene expression data from bronchial brushing of subject 8000502.
reanalysis of GSM912362


title: 1227

description:
Gene expression data from bronchial brushing of subject 1227.
reanalysis of GSM912356


title: 1241

description:
Gene expression data from bronchial brushing of subject 1241.
reanalysis of GSM912352


title: 9000069

description:
Gene expression data from bronchial brushing of subject 9000069.
reanalysis of GSM912348


title: 8000272

description:
Gene expression data from bronchial brushing of subject 8000272.
reanalysis of GSM912360


title: 8000298

description:
Gene expression data from bronchial brushing of subject 8000298.
reanalysis of GSM912346


title: 4000789

description:
Gene expression data from bronchial brushing of subject 4000789.
reanalysis of GSM912344


title: 9000193

description:
Gene expression data from bronchial brushing of subject 9000193.
reanalysis of GSM912339


title: 8000439

description:
Gene expression data from bronchial brushing of subject 8000439.
reanalysis of GSM912336


title: 4000727

description:
Gene expression data from bronchial brushing of subject 4000727.
reanalysis of GSM912335


title: 8000508

description:
Gene expression data from bronchial brushing of subject 8000508.
reanalysis of GSM912330


title: 9000206

description:
Gene expression data from bronchial brushing of subject 9000206.
reanalysis of GSM912340


title: 8000435

description:
Gene expression data from bronchial brushing of subject 8000435.
reanalysis of GSM912347


title: 1684

description:
Gene expression data from bronchial brushing of subject 1684.
reanalysis of GSM912331


title: 9000225

description:
Gene expression data from bronchial brushing of subject 9000225.
reanalysis of GSM912341


title: 1051

description:
Gene expression data from bronchial brushing of subject 1051.
reanalysis of GSM912343


title: 5000721

description:
Gene expression data from bronchial brushing of subject 5000721.
reanalysis of GSM912345


title: 9000189

description:
Gene expression data from bronchial brushing of subject 9000189.
reanalysis of GSM912332


title: 1659

description:
Gene expression data from bronchial brushing of subject 1659.
reanalysis of GSM912326


title: 9000081

description:
Gene expression data from bronchial brushing of subject 9000081.
reanalysis of GSM912338


title: 9000201

description:
Gene expression data from bronchial brushing of subject 9000201.
reanalysis of GSM912333


title: 9000133

description:
Gene expression data from bronchial brushing of subject 9000133.
reanalysis of GSM912321


title: 8000463

description:
Gene expression data from bronchial brushing of subject 8000463.
reanalysis of GSM912329


title: 4000119

description:
Gene expression data from bronchial brushing of subject 4000119.
reanalysis of GSM912328


title: 4000058

description:
Gene expression data from bronchial brushing of subject 4000058.
reanalysis of GSM912327


title: 4000557

description:
Gene expression data from bronchial brushing of subject 4000557.
reanalysis of GSM912319


title: 5000218

description:
Gene expression data from bronchial brushing of subject 5000218.
reanalysis of GSM912322


title: 8000375

description:
Gene expression data from bronchial brushing of subject 8000375.
reanalysis of GSM912320


title: 8000423

description:
Gene expression data from bronchial brushing of subject 8000423.
reanalysis of GSM912342


title: 4000272

description:
Gene expression data from bronchial brushing of subject 4000272.
reanalysis of GSM912318


title: 5000613

description:
Gene expression data from bronchial brushing of subject 5000613.
reanalysis of GSM912323


title: 1128

description:
Gene expression data from bronchial brushing of subject 1128.
reanalysis of GSM912324


title: 1325

description:
Gene expression data from bronchial brushing of subject 1325.
reanalysis of GSM912334


title: 1622

description:
Gene expression data from bronchial brushing of subject 1622.
reanalysis of GSM912325


title: 1949

description:
Gene expression data from bronchial brushing of subject 1949.
reanalysis of GSM912316


title: 2163

description:
Gene expression data from bronchial brushing of subject 2163.
reanalysis of GSM912317


title: 8000608

description:
Gene expression data from bronchial brushing of subject 8000608.
reanalysis of GSM912313


title: 8000407

description:
Gene expression data from bronchial brushing of subject 8000407.
reanalysis of GSM912312


title: 8000556

description:
Gene expression data from bronchial brushing of subject 8000556.
reanalysis of GSM912337


title: 8000427

description:
Gene expression data from bronchial brushing of subject 8000427.
reanalysis of GSM912298


title: 8000584

description:
Gene expression data from bronchial brushing of subject 8000584.
reanalysis of GSM912314


title: 8000536

description:
Gene expression data from bronchial brushing of subject 8000536.
reanalysis of GSM912296


title: 4000307

description:
Gene expression data from bronchial brushing of subject 4000307.
reanalysis of GSM912307


title: 9000029

description:
Gene expression data from bronchial brushing of subject 9000029.
reanalysis of GSM912310


title: 9000169

description:
Gene expression data from bronchial brushing of subject 9000169.
reanalysis of GSM912306


title: 8000552

description:
Gene expression data from bronchial brushing of subject 8000552.
reanalysis of GSM912308


title: 9000181

description:
Gene expression data from bronchial brushing of subject 9000181.
reanalysis of GSM912299


title: 1566

description:
Gene expression data from bronchial brushing of subject 1566.
reanalysis of GSM912315


title: 9000017

description:
Gene expression data from bronchial brushing of subject 9000017.
reanalysis of GSM912303


title: 9000001

description:
Gene expression data from bronchial brushing of subject 9000001.
reanalysis of GSM912304


title: 9000253

description:
Gene expression data from bronchial brushing of subject 9000253.
reanalysis of GSM912295


title: 5000118

description:
Gene expression data from bronchial brushing of subject 5000118.
reanalysis of GSM912301


title: 1274

description:
Gene expression data from bronchial brushing of subject 1274.
reanalysis of GSM912302


title: 9000185

description:
Gene expression data from bronchial brushing of subject 9000185.
reanalysis of GSM912297


title: 8000411

description:
Gene expression data from bronchial brushing of subject 8000411.
reanalysis of GSM912294


title: 8000415

description:
Gene expression data from bronchial brushing of subject 8000415.
reanalysis of GSM912309


title: 9000241

description:
Gene expression data from bronchial brushing of subject 9000241.
reanalysis of GSM912311


title: 5000402

description:
Gene expression data from bronchial brushing of subject 5000402.
reanalysis of GSM912300


title: 8000488

description:
Gene expression data from bronchial brushing of subject 8000488.
reanalysis of GSM912292


title: 9000033

description:
Gene expression data from bronchial brushing of subject 9000033.
reanalysis of GSM912291


title: 8000264

description:
Gene expression data from bronchial brushing of subject 8000264.
reanalysis of GSM912293


title: 1197

description:
Gene expression data from bronchial brushing of subject 1197.
reanalysis of GSM912290


title: 8000572

description:
Gene expression data from bronchial brushing of subject 8000572.
reanalysis of GSM912287


title: 1305

description:
Gene expression data from bronchial brushing of subject 1305.
reanalysis of GSM912288


title: 8000367

description:
Gene expression data from bronchial brushing of subject 8000367.
reanalysis of GSM912289


title: 6000049

description:
Gene expression data from bronchial brushing of subject 6000049.
reanalysis of GSM912286


title: 5000456

description:
Gene expression data from bronchial brushing of subject 5000456.
reanalysis of GSM912279


title: 4000383

description:
Gene expression data from bronchial brushing of subject 4000383.
reanalysis of GSM912283


title: 1852

description:
Gene expression data from bronchial brushing of subject 1852.
reanalysis of GSM912276


title: 8000598

description:
Gene expression data from bronchial brushing of subject 8000598.
reanalysis of GSM912278


title: 8000548

description:
Gene expression data from bronchial brushing of subject 8000548.
reanalysis of GSM912305


title: 5000194

description:
Gene expression data from bronchial brushing of subject 5000194.
reanalysis of GSM912277


title: 4000268

description:
Gene expression data from bronchial brushing of subject 4000268.
reanalysis of GSM912281


title: 8000532

description:
Gene expression data from bronchial brushing of subject 8000532.
reanalysis of GSM912272


title: 6000303

description:
Gene expression data from bronchial brushing of subject 6000303.
reanalysis of GSM912275


title: 1758

description:
Gene expression data from bronchial brushing of subject 1758.
reanalysis of GSM912284


title: 8000516

description:
Gene expression data from bronchial brushing of subject 8000516.
reanalysis of GSM912274


title: 9000097

description:
Gene expression data from bronchial brushing of subject 9000097.
reanalysis of GSM912273


title: 8000443

description:
Gene expression data from bronchial brushing of subject 8000443.
reanalysis of GSM912271


title: 9000129

description:
Gene expression data from bronchial brushing of subject 9000129.
reanalysis of GSM912280


title: 9000013

description:
Gene expression data from bronchial brushing of subject 9000013.
reanalysis of GSM912282


title: 9000077

description:
Gene expression data from bronchial brushing of subject 9000077.
reanalysis of GSM912285


title: 6000061

description:
Gene expression data from bronchial brushing of subject 6000061.
reanalysis of GSM912267


title: 5000441

description:
Gene expression data from bronchial brushing of subject 5000441.
reanalysis of GSM912270


title: 2049

description:
Gene expression data from bronchial brushing of subject 2049.
reanalysis of GSM912268


title: 8000447

description:
Gene expression data from bronchial brushing of subject 8000447.
reanalysis of GSM912262


title: 2005

description:
Gene expression data from bronchial brushing of subject 2005.
reanalysis of GSM912263


title: 6000007

description:
Gene expression data from bronchial brushing of subject 6000007.
reanalysis of GSM912266


title: 6000411

description:
Gene expression data from bronchial brushing of subject 6000411.
reanalysis of GSM912261


title: 2021

description:
Gene expression data from bronchial brushing of subject 2021.
reanalysis of GSM912264


title: 6000094

description:
Gene expression data from bronchial brushing of subject 6000094.
reanalysis of GSM912259


title: 2019

description:
Gene expression data from bronchial brushing of subject 2019.
reanalysis of GSM912265


title: 5000346

description:
Gene expression data from bronchial brushing of subject 5000346.
reanalysis of GSM912260


title: 8000600

description:
Gene expression data from bronchial brushing of subject 8000600.
reanalysis of GSM912258


title: 9000025

description:
Gene expression data from bronchial brushing of subject 9000025.
reanalysis of GSM912255


title: 9000269

description:
Gene expression data from bronchial brushing of subject 9000269.
reanalysis of GSM912256


title: 1543

description:
Gene expression data from bronchial brushing of subject 1543.
reanalysis of GSM912252


title: 1804

description:
Gene expression data from bronchial brushing of subject 1804.
reanalysis of GSM912245


title: 5000444

description:
Gene expression data from bronchial brushing of subject 5000444.
reanalysis of GSM912257


title: 8000512

description:
Gene expression data from bronchial brushing of subject 8000512.
reanalysis of GSM912254


title: 6000001

description:
Gene expression data from bronchial brushing of subject 6000001.
reanalysis of GSM912250


title: 4000670

description:
Gene expression data from bronchial brushing of subject 4000670.
reanalysis of GSM912247


title: 4000164

description:
Gene expression data from bronchial brushing of subject 4000164.
reanalysis of GSM912269


title: 8000279

description:
Gene expression data from bronchial brushing of subject 8000279.
reanalysis of GSM912241


title: 5000314

description:
Gene expression data from bronchial brushing of subject 5000314.
reanalysis of GSM912242


title: 8000399

description:
Gene expression data from bronchial brushing of subject 8000399.
reanalysis of GSM912253


title: 1396

description:
Gene expression data from bronchial brushing of subject 1396.
reanalysis of GSM912244


title: 8000455

description:
Gene expression data from bronchial brushing of subject 8000455.
reanalysis of GSM912239


title: 5000141

description:
Gene expression data from bronchial brushing of subject 5000141.
reanalysis of GSM912249


title: 9000257

description:
Gene expression data from bronchial brushing of subject 9000257.
reanalysis of GSM912240


title: 6000037

description:
Gene expression data from bronchial brushing of subject 6000037.
reanalysis of GSM912237


title: 4000536

description:
Gene expression data from bronchial brushing of subject 4000536.
reanalysis of GSM912233


title: 1312

description:
Gene expression data from bronchial brushing of subject 1312.
reanalysis of GSM912251


title: 1153

description:
Gene expression data from bronchial brushing of subject 1153.
reanalysis of GSM912238


title: 5000270

description:
Gene expression data from bronchial brushing of subject 5000270.
reanalysis of GSM912235


title: 2064

description:
Gene expression data from bronchial brushing of subject 2064.
reanalysis of GSM912248


title: 4000091

description:
Gene expression data from bronchial brushing of subject 4000091.
reanalysis of GSM912234


title: 5000532

description:
Gene expression data from bronchial brushing of subject 5000532.
reanalysis of GSM912229


title: 8000387

description:
Gene expression data from bronchial brushing of subject 8000387.
reanalysis of GSM912236


title: 1777

description:
Gene expression data from bronchial brushing of subject 1777.
reanalysis of GSM912228


title: 9000053

description:
Gene expression data from bronchial brushing of subject 9000053.
reanalysis of GSM912227


title: 1521

description:
Gene expression data from bronchial brushing of subject 1521.
reanalysis of GSM912232


title: 1931

description:
Gene expression data from bronchial brushing of subject 1931.
reanalysis of GSM912231


title: 9000065

description:
Gene expression data from bronchial brushing of subject 9000065.
reanalysis of GSM912230


title: 9000105

description:
Gene expression data from bronchial brushing of subject 9000105.
reanalysis of GSM912243


title: 9000125

description:
Gene expression data from bronchial brushing of subject 9000125.
reanalysis of GSM912223


title: 1458

description:
Gene expression data from bronchial brushing of subject 1458.
reanalysis of GSM912226


title: 4000037

description:
Gene expression data from bronchial brushing of subject 4000037.
reanalysis of GSM912222


title: 1984

description:
Gene expression data from bronchial brushing of subject 1984.
reanalysis of GSM912220


title: 1725

description:
Gene expression data from bronchial brushing of subject 1725.
reanalysis of GSM912224


title: 1116

description:
Gene expression data from bronchial brushing of subject 1116.
reanalysis of GSM912216


title: 1658

description:
Gene expression data from bronchial brushing of subject 1658.
reanalysis of GSM912211


title: 9000057

description:
Gene expression data from bronchial brushing of subject 9000057.
reanalysis of GSM912207


title: 4000007

description:
Gene expression data from bronchial brushing of subject 4000007.
reanalysis of GSM912210


title: 5000075

description:
Gene expression data from bronchial brushing of subject 5000075.
reanalysis of GSM912221


title: 1921

description:
Gene expression data from bronchial brushing of subject 1921.
reanalysis of GSM912215


title: 8000475

description:
Gene expression data from bronchial brushing of subject 8000475.
reanalysis of GSM912206


title: 8000284

description:
Gene expression data from bronchial brushing of subject 8000284.
reanalysis of GSM912212


title: 1584

description:
Gene expression data from bronchial brushing of subject 1584.
reanalysis of GSM912219


title: 2117

description:
Gene expression data from bronchial brushing of subject 2117.
reanalysis of GSM912205


title: 8000431

description:
Gene expression data from bronchial brushing of subject 8000431.
reanalysis of GSM912218


title: 9000037

description:
Gene expression data from bronchial brushing of subject 9000037.
reanalysis of GSM912213


title: 8000363

description:
Gene expression data from bronchial brushing of subject 8000363.
reanalysis of GSM912204


title: 8000395

description:
Gene expression data from bronchial brushing of subject 8000395.
reanalysis of GSM912209


title: 4000270

description:
Gene expression data from bronchial brushing of subject 4000270.
reanalysis of GSM912208


title: 8000604

description:
Gene expression data from bronchial brushing of subject 8000604.
reanalysis of GSM912202


title: 4000188

description:
Gene expression data from bronchial brushing of subject 4000188.
reanalysis of GSM912201


title: 4000129

description:
Gene expression data from bronchial brushing of subject 4000129.
reanalysis of GSM912200


title: 9000021

description:
Gene expression data from bronchial brushing of subject 9000021.
reanalysis of GSM912199


title: 1563

description:
Gene expression data from bronchial brushing of subject 1563.
reanalysis of GSM912197


title: 1593

description:
Gene expression data from bronchial brushing of subject 1593.
reanalysis of GSM912198


title: 150558

description: Gene expression data from nasal brushing of subject 150558.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

value: Benign


title: 250624

description: Gene expression data from nasal brushing of subject 250624.


title: 9000161

description:
Gene expression data from bronchial brushing of subject 9000161.
reanalysis of GSM912203


title: 180509

description: Gene expression data from nasal brushing of subject 180509.


title: 250554

description: Gene expression data from nasal brushing of subject 250554.

value: Cancer


title: 250567

description: Gene expression data from nasal brushing of subject 250567.


title: 230521

description: Gene expression data from nasal brushing of subject 230521.


title: 210569

description: Gene expression data from nasal brushing of subject 210569.


title: 250718

description: Gene expression data from nasal brushing of subject 250718.


title: 160711

description: Gene expression data from nasal brushing of subject 160711.


title: 150575

description: Gene expression data from nasal brushing of subject 150575.


title: 4000515

description:
Gene expression data from bronchial brushing of subject 4000515.
reanalysis of GSM912217


title: 160685

description: Gene expression data from nasal brushing of subject 160685.


title: 170541

description: Gene expression data from nasal brushing of subject 170541.


title: 150549

description: Gene expression data from nasal brushing of subject 150549.


title: 110541

description: Gene expression data from nasal brushing of subject 110541.


title: 210564

description: Gene expression data from nasal brushing of subject 210564.


title: 240507

description: Gene expression data from nasal brushing of subject 240507.


title: 260571

description: Gene expression data from nasal brushing of subject 260571.


title: 6000091

description:
Gene expression data from bronchial brushing of subject 6000091.
reanalysis of GSM912214


title: 170548

description: Gene expression data from nasal brushing of subject 170548.


title: 160628

description: Gene expression data from nasal brushing of subject 160628.


title: 220538

description: Gene expression data from nasal brushing of subject 220538.


title: 260570

description: Gene expression data from nasal brushing of subject 260570.


title: 250716

description: Gene expression data from nasal brushing of subject 250716.


title: 70543

description: Gene expression data from nasal brushing of subject 70543.


title: 190525

description: Gene expression data from nasal brushing of subject 190525.


title: 230515

description: Gene expression data from nasal brushing of subject 230515.


title: 120566

description: Gene expression data from nasal brushing of subject 120566.


title: 160745

description: Gene expression data from nasal brushing of subject 160745.


title: 50595

description: Gene expression data from nasal brushing of subject 50595.


title: 170527

description: Gene expression data from nasal brushing of subject 170527.


title: 160691

description: Gene expression data from nasal brushing of subject 160691.


title: 1853

description:
Gene expression data from bronchial brushing of subject 1853.
reanalysis of GSM912246


title: 160624

description: Gene expression data from nasal brushing of subject 160624.


title: 160652

description: Gene expression data from nasal brushing of subject 160652.


title: 160679

description: Gene expression data from nasal brushing of subject 160679.


title: 50594

description: Gene expression data from nasal brushing of subject 50594.


title: 160630

description: Gene expression data from nasal brushing of subject 160630.


title: 220563

description: Gene expression data from nasal brushing of subject 220563.


title: 280521

description: Gene expression data from nasal brushing of subject 280521.


title: 50621

description: Gene expression data from nasal brushing of subject 50621.


title: 210542

description: Gene expression data from nasal brushing of subject 210542.


title: 220544

description: Gene expression data from nasal brushing of subject 220544.


title: 250747

description: Gene expression data from nasal brushing of subject 250747.


title: 180508

description: Gene expression data from nasal brushing of subject 180508.


title: 160632

description: Gene expression data from nasal brushing of subject 160632.


title: 150530

description: Gene expression data from nasal brushing of subject 150530.


title: 230529

description: Gene expression data from nasal brushing of subject 230529.


title: 160670

description: Gene expression data from nasal brushing of subject 160670.


title: 160659

description: Gene expression data from nasal brushing of subject 160659.


title: 50622

description: Gene expression data from nasal brushing of subject 50622.


title: 250553

description: Gene expression data from nasal brushing of subject 250553.


title: 70546

description: Gene expression data from nasal brushing of subject 70546.


title: 220546

description: Gene expression data from nasal brushing of subject 220546.


title: 260561

description: Gene expression data from nasal brushing of subject 260561.


title: 70547

description: Gene expression data from nasal brushing of subject 70547.


title: 160663

description: Gene expression data from nasal brushing of subject 160663.


title: 50578

description: Gene expression data from nasal brushing of subject 50578.


title: 250635

description: Gene expression data from nasal brushing of subject 250635.


title: 170549

description: Gene expression data from nasal brushing of subject 170549.


title: 150585

description: Gene expression data from nasal brushing of subject 150585.


title: 160733

description: Gene expression data from nasal brushing of subject 160733.


title: 120572

description: Gene expression data from nasal brushing of subject 120572.


title: 260548

description: Gene expression data from nasal brushing of subject 260548.


title: 170555

description: Gene expression data from nasal brushing of subject 170555.


title: 160688

description: Gene expression data from nasal brushing of subject 160688.


title: 160743

description: Gene expression data from nasal brushing of subject 160743.


title: 290504

description: Gene expression data from nasal brushing of subject 290504.


title: 250609

description: Gene expression data from nasal brushing of subject 250609.


title: 260525

description: Gene expression data from nasal brushing of subject 260525.


title: 150554

description: Gene expression data from nasal brushing of subject 150554.


title: 150599

description: Gene expression data from nasal brushing of subject 150599.


title: 160675

description: Gene expression data from nasal brushing of subject 160675.


title: 230530

description: Gene expression data from nasal brushing of subject 230530.


title: 260564

description: Gene expression data from nasal brushing of subject 260564.


title: 160722

description: Gene expression data from nasal brushing of subject 160722.


title: 250650

description: Gene expression data from nasal brushing of subject 250650.


title: NI d21 3

city: Leuven

first: Johan

last: Van Weyenbergh

address: Herestraat 49

department: DMIT

country: Belgium

institute: KU Leuven

description: Mouse Host Respons Panel

hyb_protocol: Hybridization was performed for 24h at 65°C.

scan_protocol: Scanning was performed on an nCounter® MAX Analysis System.

data_processing: Results were sequentially corrected for background (negative control probes), technical variation (positive control probes) and RNA content (housekeeping genes) using nSolver 4.0 (NanoString),

label: no label

source_name: lung tissue

label_protocol: RNA from lung tissue (triplicates for both infected and uninfected conditions at 10 and 21 dpi for nCounter (NanoString) analysis on a nCounter® MAX Analysis System was extracted as described above. RNA extracts were hybridized to 785 unique capture/reporter pairs (50 bp each) targeting 773 immune transcripts and 12 housekeeping genes, as defined in the Murine Host Reponse nCounter® panel, as well as 6 positive and 8 negative control probes (all from NanoString).

extract_protocol: Tissues were stored in RNAlater and processed using the RNeasy plus mini kit (Qiagen) according to the manufacturer’s recommendations.

treatment_protocol: Tsetse flies harbouring metacyclic parasites in the salivary glands were used for natural transmission. Mice were anesthetized with ketamine (100 mg/kg) and xylazine (20 mg/kg) and individual flies (1 fly per mouse) were allowed to bite on the ear dermis. Parasitaemia was monitored by microscopic counting of diluted tail vein blood using a Neubauer improved haemocytometer.

tag: infection status

value: Not infected (NI)

tag: infection time

value: 21 dpi

tag: tissue

value: Lung


title: Inf d10 1

description: Mouse Host Respons Panel

tag: strain

value: Infected (Inf)

value: 10 dpi


title: Inf d21 1

description: Mouse Host Respons Panel


title: Inf d21 2

description: Mouse Host Respons Panel


title: Inf d10 3

description: Mouse Host Respons Panel


title: 50580

description: Gene expression data from nasal brushing of subject 50580.


title: NI d21 2

description: Mouse Host Respons Panel


title: Inf d10 2

description: Mouse Host Respons Panel


title: NI d21 1

description: Mouse Host Respons Panel


title: Inf d21 3

description: Mouse Host Respons Panel


title: 260535

description: Gene expression data from nasal brushing of subject 260535.


title: 170558

description: Gene expression data from nasal brushing of subject 170558.


title: 4000328

description:
Gene expression data from bronchial brushing of subject 4000328.
reanalysis of GSM912225


title: 220570

description: Gene expression data from nasal brushing of subject 220570.


title: 170550

description: Gene expression data from nasal brushing of subject 170550.


title: NI d10 3

description: Mouse Host Respons Panel


title: 160744

description: Gene expression data from nasal brushing of subject 160744.


title: 160703

description: Gene expression data from nasal brushing of subject 160703.


title: 250752

description: Gene expression data from nasal brushing of subject 250752.


title: NI d10 2

description: Mouse Host Respons Panel


title: 220547

description: Gene expression data from nasal brushing of subject 220547.


title: 160653

description: Gene expression data from nasal brushing of subject 160653.


title: 120562

description: Gene expression data from nasal brushing of subject 120562.


title: NI d10 1

description: Mouse Host Respons Panel


title: Pt mycelial cells, 36C, rep2

city: Tianjin

first: Long

last: Chen

address: 17km Jinjing Rd

institute: Tianjin Academy of Agricultural Sciences

data_processing:
fastp/Bowtie2
Fastp was used to filter out low-quality reads and ensure the individual length must be above 75 bp.
To deplete the interference of rRNA, preprocessed raw reads were further trimmed by removing aligned rRNA sequences via Bowtie2.
Exon-exon splice junctions were identified using HISAT2 to map the RNA-seq reads against the reference genome of P. tuoliensis strain JKBL130LB (Reference genome ASM324375v1 accessed from NCBI database).
StringTie was used to assemble aligned RNA-Seq reads into potential transcripts.
Assembly: ASM324375v1
Supplementary files format and content: Gene_ID, ZN25A, ZN25B, ZN25C, ZN32A, ZN32B, ZN32C, ZN36A, ZN36B, ZN36C, prot,description

organism: Pleurotus tuoliensis

source_name: mycelial cells

growth_protocol: Mycelia were cultured on potato dextrose agar and were incubated in the dark at 25°C for 9 days after inoculation prior to treatment.

extract_protocol:
The total RNA was extracted and purified from individual frozen mycelia sample according to the instructions of HiPure Universal RNA Mini kit (Magen, China).
RNA libraries for RNA-seq were prepared using AMPure XP beads following designated protocol prepared for Illumina RNA-Seq.

treatment_protocol: Plates in the group of MHT and SHT were transferred to the incubator with temperature of 32°C and 36°C respectively on the 10th day while the plates of CK group were maintained at 25°C as controls.

tag: cell type

value: mycelial cells

value: Zhongnong No.1

value: Heat stress under 36 celsius degree

tag: time

value: Day 13


title: Pt mycelial cells, 36C, rep3

tag: treatment


title: Pt mycelial cells, 32C, rep3

tag: genotype

value: Heat stress under 32 celsius degree


title: Pt mycelial cells, 32C, rep2


title: 240508

description: Gene expression data from nasal brushing of subject 240508.


title: Pt mycelial cells, 32C, rep1


title: Pt mycelial cells, 25C, rep2

value: Control


title: Pt mycelial cells, 36C, rep1


title: Pt mycelial cells, 25C, rep3


title: Pt mycelial cells, 25C, rep1


title: 230527

description: Gene expression data from nasal brushing of subject 230527.

value: Female


title: 50610

description: Gene expression data from nasal brushing of subject 50610.


title: gut microbiota，B_008

city: Dalian

first: Cong

last: Liu

address: 222 Zhongshan Road

institute: First Affiliated Hospital of Dalian Medical University

data_processing:
Trimmomatic (version 0.35) to to remove low quality base pairs using these parameters (SLIDINGWINDOW: 50:20 MINLEN: 50).
Trimmed reads were then cut adaptors using cutadapt (version:1.16)
PE reads merged using FLASH program (version 1.2.11)
Low quality contigs were removed based on screen.seqs command in mothur (V.1.39.5)
The reads were clustered at 97% sequence identity into OTUs, The chimera sequences and the singleton OTUs were deleted using the UPARSE pipeline (http://drive5.com/usearch/manual/uparse cmds.html).
Supplementary files format and content: Tab-delimited text files include sequences count values for each Sample
Library strategy: DNA-seq

organism: human feces metagenome

source_name: gut microbiota

growth_protocol: In all participants, fresh fecal samples were collected by fecal microbial DNA collection and preservation kits (TinyGene, Shanghai, China). All consumables were aseptic, and fecal samples were frozen and stored at −80°C after collection.

extract_protocol:
The genomic DNA of samples was extracted by the QIAamp DNA Stool Mini Kit.
The V4-V5 region of 16s rRNA were selected, using two step PCR, and pair-end sequencing was performed in accordance with the requirements of Illumina Miseq high-throughput sequencing, to complete the construction of an Miseq library.

value: gut microbiota

tag: disease

value: none, control


title: 160741

description: Gene expression data from nasal brushing of subject 160741.

value: Male

value: Former smoker


title: gut microbiota，B_007


title: gut microbiota，B_006


title: gut microbiota，B_009


title: 210557

description: Gene expression data from nasal brushing of subject 210557.

value: Cancer


title: 220567

description: Gene expression data from nasal brushing of subject 220567.


title: 50588

description: Gene expression data from nasal brushing of subject 50588.

value: Benign


title: 150532

description: Gene expression data from nasal brushing of subject 150532.


title: 210540

description: Gene expression data from nasal brushing of subject 210540.


title: gut microbiota，B_005


title: 50582

description: Gene expression data from nasal brushing of subject 50582.

value: Current smoker


title: 160689

description: Gene expression data from nasal brushing of subject 160689.


title: 250644

description: Gene expression data from nasal brushing of subject 250644.


title: 180512

description: Gene expression data from nasal brushing of subject 180512.


title: gut microbiota，B_010


title: 240502

description: Gene expression data from nasal brushing of subject 240502.


title: 210535

description: Gene expression data from nasal brushing of subject 210535.


title: gut microbiota，B_002


title: 250613

description: Gene expression data from nasal brushing of subject 250613.


title: gut microbiota，M_009

value: melasma


title: 50604

description: Gene expression data from nasal brushing of subject 50604.


title: gut microbiota，B_003


title: 120539

description: Gene expression data from nasal brushing of subject 120539.


title: gut microbiota，B_004


title: gut microbiota，M_006


title: gut microbiota，M_008


title: 210562

description: Gene expression data from nasal brushing of subject 210562.


title: 160629

description: Gene expression data from nasal brushing of subject 160629.


title: 250547

description: Gene expression data from nasal brushing of subject 250547.


title: gut microbiota，M_005


title: 250623

description: Gene expression data from nasal brushing of subject 250623.


title: 190519

description: Gene expression data from nasal brushing of subject 190519.


title: 250556

description: Gene expression data from nasal brushing of subject 250556.


title: gut microbiota，M_004


title: 150564

description: Gene expression data from nasal brushing of subject 150564.


title: gut microbiota，M_007


title: E9.5 single cell mRNA miR-302KO, Sox9KO

city: Houston

first: Rachel

last: Keuls

state: TX

address: One baylor plaza, Alkek N1020

institute: Baylor College of Medicine

description:
filtered feature bc matrix files
674B
h674C_B_rescue

library_source: transcriptomic single cell

data_processing:
Cell Ranger mkfastq version 5.0.1
Cell Ranger count version 5.0.1
Seurat 4.1.0
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Cranial Region

extract_protocol:
The cranial region from each embryo was harvested for single cell mRNA sequencing using a 10X Genomics platform. Embryos were dissected in PBS, the corresponding tissue (whole embryo for E7.5 and cranial region for E8.25-E9.5) was dissociated with papain, neutralized with FBS, and cells were pelleted and resuspended for partitioning on a 10X chromum controller
10x scRNA - Single Cell 3' v3

value: Cranial Region

value: C57BL/6J background

value: miR-302-/-; Sox9Flox/Flox; Wnt1-Cre+

tag: developmental stage


title: E9.5 single cell mRNA WT

description:
filtered feature bc matrix files
674C

value: miR-302+/+; Sox9Flox/Flox; Wnt1-Cre-


title: 46C6

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: Sorted PI- CD45+ CD11B+ LY6G/SIGLECF- cells

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Assembly: mm10
Supplementary files format and content: Matrix table with raw read counts for every gene and every sample

source_name: Tibialis Anterior (skeletal muscle)

extract_protocol:
Mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2) and then perfused with warm PBS.  Following removing the fascia, skeletal muscle was harvested and cut into small pieces with scissors which was then followed by enzymatic digestion with a mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001) for an hour at 37 °C. Samples were vortexed every 20 minutes during incubation. Digested tissues were filtered through a 40-μm cell strainer (FALCON, # 352340), washed with PBS and collected by centrifugation at 545g for 7min.  Cell preparations were blocked with PBS containing 2 mM EDTA and 2% FBS (FACS buffer) + anti-Fcy receptor antibody on ice for 10 minutes and then stained with various antibodies on ice for 15 minutes (Supplementary Table 2). Stained cells were washed for cell sorting. Cell sorting was performed using a BD FACSAria (Becton Dickinson) equipped with three lasers or BD Influx cell sorter both equipped with four lasers.  RNeasy Micro Kit (Qiagen, # 74004) was used to isolate RNA from sorted cells. 10 μ of 2β-mercaptoethanol was added to 1mL of the buffer RLT (lysis buffer) before use.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Paired-end sequencing was performed on the Illumina NextSeq 2000 using the P3 100 cycle Kit (Illumina).

treatment_protocol: TAs of Ifngr1 wt/null or null/null mice were damaged with Notexin. Following injury, mice were treated daily with intraperitoneal injection of either anti-TNFa neutralizing antibody or a proper isotype control. On day 5  after injury, PI- CD45+ CD11B+ LY6G/SIGLECF- cells were sorted for RNA sequencing.

value: anti-TNFA neutralizing antibody

value: Macrophages

value: null/null


title: 220539

description: Gene expression data from nasal brushing of subject 220539.


title: 40C4

value: Isotype antibody


title: 40C2


title: 40B2


title: 250712

description: Gene expression data from nasal brushing of subject 250712.

value: Female


title: 160735

description: Gene expression data from nasal brushing of subject 160735.


title: 46C3


title: 160664

description: Gene expression data from nasal brushing of subject 160664.


title: 220534

description: Gene expression data from nasal brushing of subject 220534.


title: 220561

description: Gene expression data from nasal brushing of subject 220561.


title: 260565

description: Gene expression data from nasal brushing of subject 260565.


title: 250725

description: Gene expression data from nasal brushing of subject 250725.


title: 70551

description: Gene expression data from nasal brushing of subject 70551.


title: 160720

description: Gene expression data from nasal brushing of subject 160720.


title: E9.5 single cell mRNA Sox9KO

description:
filtered feature bc matrix files
674A
h674C_A_sox9ko

value: miR-302+/+; Sox9Flox/Flox; Wnt1-Cre+


title: 160700

description: Gene expression data from nasal brushing of subject 160700.


title: 260572

description: Gene expression data from nasal brushing of subject 260572.


title: gut microbiota，M_003

value: gut microbiota


title: 40A3


title: 40B1

value: wt/null


title: 46C7


title: 40C1


title: 220555

description: Gene expression data from nasal brushing of subject 220555.

value: Former smoker


title: 40A2


title: 250733

description: Gene expression data from nasal brushing of subject 250733.


title: 40C3


title: 250545

description: Gene expression data from nasal brushing of subject 250545.

value: Male

value: Cancer


title: 170531

description: Gene expression data from nasal brushing of subject 170531.

value: Benign