title: LT274443LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT274443LU

tag: ltrc id

tag: disease

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

value: 1-Lung explant,  single

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

value: Multiplex


title: LT090666LI-ILD

status: Public on Apr 30 2023

type: SRA

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

country: USA

institute: Boston University

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT090666LI

library_source: transcriptomic

data_processing:
The 3’ adapter sequence was trimmed using the FASTX toolkit
Reads longer than 15 nt were aligned to hg19 using Bowtie v0.12.730 allowing up to one mismatch and up to 10 locations in the genome.
miRNA expression was quantified by counting the number of reads aligning to mature miRNA loci from miRBase v20 using Bedtools v2.9.0.
The distribution of read lengths for each sample after trimming and alignment was clustering using the Jensen Shannon divergence. 13 samples that clustered separately from the majority samples were excluded from the final analysis set.
7 replicate samples were excluded from the final analysis set.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes raw count for each sample
Supplementary files format and content: Tab-delimited text file includes Log2 Reads per Million (RPM) values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: lung

extract_protocol:
Total RNA was isolated from all lung samples using the QIAcube system (QIAGEN Inc., Valencia, CA) with the miRNeasy kit. RNA quality was determined using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a RNA integrity number greater than 7.0 as the criterion for acceptable quality.
Illumina Small RNA Sample Prep Kit v1.5 or the Illumina TruSeq Small RNA Sample Prep Kit

tag: tissue

value: lung

tag: minor diagnosis

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

tag: bode score

value: 3-Lung lobectomy/wedge resection

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex


title: naïve_1

city: Geneva

first: Liqing

last: Cheng

address: 1 rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

data_processing:
Read were mapped to the UCSC mm10 mouse genome with STAR v.2.7.4.
The biological QC was performed with picard tools
Table of counts was prepared with HTseq v0.9.1.
After normalization, the differential expression analysis was performed with the package edgeR (v1.34.1) in R.
PCA were obtained using Deseq2
Assembly: UCSC mm10 mouse genome
Supplementary files format and content: txt file containing raw counts of each sample (naïve, mLN, LILP)
Supplementary files format and content: excel file containing raw counts of each sample (highOVA, lowOVA)

organism: Mus musculus

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Nextera Smarter following manufacture's protocol

value: Spleen

tag: cell type

value: CD8+ T cells from spleen of OTI mouse

tag: genotype

value: WT

tag: Sex

value: Female

tag: treatment

value: no


title: MRX362

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers University

data_processing:
FastQC for quality control (pre trim)
Cutadapt for adapter and quality trimming
FastQC fo quality control (post trim)
kallisto for pseudoalignment
tximport for import into R (4.0.3)
DEseq2
Assembly: Mouse Ensembl Transcriptome v94
Supplementary files format and content: Post pseudoalignment; each individual sample file (.tsv) contains both est_counts and tpms

source_name: Liver

extract_protocol:
Total RNA was isolated from crushed and frozen livers using Direct-zol RNA Miniprep kit (R2052, Zymo Research) according to the manufacturer's instructions.
NEBNext Ultra II RNA Library Prep kit, performed by Genewiz (Azenta Life Sciences)

value: Liver

value: male

tag: strain

tag: diet

value: HF

tag: dietary fat content

value: SAAR


title: LT152653LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT152653LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: MRX361

tag: tissue

tag: Sex

tag: strain

tag: diet

tag: dietary fat content

value: Ctrl


title: LT282601LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT282601LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 3-African-American (whether Hispanic or not)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: bode score

value: 4-Lung biopsy

tag: qc pass

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: LT253131RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT253131RU

tag: tissue

value: lung

value: Male

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: FOXD3-endo-S-rep2

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

library_source: genomic

data_processing:
Bowtie 2 mapping
Deeptools bamCompare for bigwig file creation
Peak calling with MACS2
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: S phase synchronized cells

growth_protocol: Mouse ESCs were seeded on a 10 cm plate (10^6 cells) in L2i containing growth medium and harvested 2 days after seeding.

extract_protocol:
Lysates were clarified from sonicated nuclei and FOXD3-DNA complexes were isolated with streptavidin magnetic beads.
Libraries were prepared according to manufacturers' instructions (NEBNext Ultra II).

treatment_protocol: For exogenous samples, cells were kept consistently on 0.05µg/ml doxycycline for expression of exogenous FOXD3-Avi.

tag: cell type

value: mESCs

tag: culture conditions

tag: tag insertion

value: endogenous

tag: bait

value: streptavidin magnetic beads


title: LT022251RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT022251RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: bode score

value: 2-Lung explant,  bilateral

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex


title: FOXD3-endo-G1S-rep2

source_name: G1/S phase synchronized cells

tag: cell type

tag: culture conditions

tag: tag insertion


title: FOXD3-endo-G2M-rep2

source_name: G2/M phase synchronized cells

tag: bait


title: LT178967RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT178967RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: Female

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: MRX368

value: Liver

tag: Sex

value: male

tag: strain

tag: diet

value: RF

tag: dietary fat content


title: LT059721LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT059721LU

tag: tissue

tag: ltrc id

tag: disease

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: bode score

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: MRX365

tag: Sex

tag: strain

tag: diet

value: HF

value: Ctrl


title: MRX363

tag: tissue

tag: dietary fat content


title: FOXD3-endo-G2M-rep1

tag: cell type

tag: culture conditions

tag: tag insertion

tag: bait


title: LT249811RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT249811RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

value: Multiplex


title: noBirA-async-rep1

source_name: asynchronous no biotin control

tag: cell type

tag: culture conditions

tag: tag insertion

tag: bait


title: LT222702LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT222702LL

tag: tissue

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: percent emphysema

tag: pack years

tag: bode score

value: 4-Lung biopsy

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-endo-S-rep1

tag: cell type

value: mESCs

tag: culture conditions

tag: tag insertion


title: LT269381RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT269381RU

tag: tissue

tag: ltrc id

tag: age

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT196677RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT196677RU

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: percent emphysema

tag: pack years

tag: bode score

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-exo-ctr-2i-rep3

data_processing:
Bowtie 2 mapping
Deeptools bamCompare for bigwig file creation
Peak calling with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: mESCs

tag: cell type

tag: culture conditions

tag: tag insertion

value: exogenous

tag: bait


title: LT243058RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT243058RU

tag: tissue

tag: ltrc id

tag: disease

value: Male

tag: age

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: FOXD3-exo-ctr-2i-rep2

tag: cell type

tag: culture conditions

tag: tag insertion

value: streptavidin magnetic beads


title: MRX364

tag: tissue

tag: Sex

tag: strain

tag: diet

tag: dietary fat content

value: SAAR


title: FOXD3-exo-ctr-2i-rep1

description: DG13_S61_L006_R1_001.sorted.dedup.CPM.bw

tag: bait


title: LT270821RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT270821RU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex


title: LT216500LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT216500LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: Female

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT230142RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT230142RL

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco


title: LT100654RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT100654RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: tissue type

tag: flow cell

tag: lane

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-exo-2i-rep1

tag: cell type

tag: culture conditions

tag: tag insertion

tag: bait


title: FOXD3-exo-2i-rep2


title: LT043798LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT043798LU

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT131887LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT131887LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: dlco

tag: tissue type

value: 2-Lung explant,  bilateral

tag: flow cell

tag: lane

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: noBirA-async-rep2

tag: cell type

tag: culture conditions

tag: tag insertion

value: endogenous

tag: bait


title: FOXD3-exo-2i-rep3


title: LT139051LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT139051LU

value: lung

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

value: Multiplex


title: OCT4-DOX-24hpD-rep2

description:
counts_oct4_asynchronous.txt
DG63_S31_R1_001

data_processing:
Library strategy: 4SU-seq
STAR mapping
featureCounts read count
Genome_build: mm10
Supplementary_files_format_and_content: count matrices

growth_protocol: Mouse ESCs were seeded on a 10 cm plate (10^6 cells) or for synchronized cells on a well of a 6well plate (170k cells) in L2i containing growth medium.

extract_protocol:
Cells were extracted using Trizol LS.
Libraries were prepared according to manufacturers' instructions (KAPA RNA Hyperprep).

treatment_protocol: Synchronization was achieved using a double thymidine block strategy and cells were release at 24h post tamoxifen treatment. 4SU was added for 30min or 15min for non-synchronized and synchronized cells, respectively.

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype

value: 4SU-labeled RNA


title: OCT4-DOX-24hpD-rep1

description:
counts_oct4_asynchronous.txt
DG62_S30_R1_001


title: LT021748RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT021748RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: lane

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-endo-G1S-rep1

tag: cell type

value: mESCs

tag: culture conditions

tag: tag insertion

tag: bait


title: LT001098RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT001098RU

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: OCT4-H2O-24hpD-rep2

description:
counts_oct4_asynchronous.txt
DG61_S29_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: OCT4-H2O-24hpD-rep1

description:
counts_oct4_asynchronous.txt
DG60_S28_R1_001


title: LT205601LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT205601LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: Male

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT028427LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT028427LU

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT056024RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT056024RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: race

tag: cancer status

tag: dlco

tag: tissue type

tag: flow cell

tag: lane


title: OCT4-H2O-16hpD-rep2

description:
counts_oct4_asynchronous.txt
DG57_S25_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: LT102131RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT102131RL

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: OCT4-H2O-16hpD-rep1

description:
counts_oct4_asynchronous.txt
DG56_S24_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: LT063974LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT063974LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: dlco

tag: tissue type

value: 1-Lung explant,  single

tag: flow cell

tag: lane

tag: replicate


title: LT021461RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT021461RM

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-4HT-32hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG77_S45_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: LT221782LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT221782LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: replicate


title: FOXD3-4HT-32hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG78_S46_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: OCT4-DOX-16hpD-rep2

description:
counts_oct4_asynchronous.txt
DG59_S27_R1_001

tag: molecule subtype


title: FOXD3-EtOH-32hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG76_S44_R1_001


title: LT024967LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT024967LU

tag: tissue

tag: ltrc id

tag: disease

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: FOXD3-4HT-24hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG74_S42_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: FOXD3-EtOH-32hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG75_S43_R1_001

tag: molecule subtype


title: LT213735RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT213735RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: replicate


title: LT121014LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT121014LL

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT271100LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT271100LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: dlco


title: FOXD3-EtOH-24hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG72_S40_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: LT041389RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT041389RL

value: 3-African-American (whether Hispanic or not)

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: FOXD3-4HT-24hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG73_S41_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: FOXD3-EtOH-24hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG71_S39_R1_001

tag: molecule subtype


title: LT067200LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT067200LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

value: 3-Lung lobectomy/wedge resection

tag: multiplex


title: LT253371RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT253371RL

tag: bode score

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol


title: OCT4-DOX-16hpD-rep1

description:
counts_oct4_asynchronous.txt
DG58_S26_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: FOXD3-4HT-14hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG48_S45_L005_R1_001


title: LT095342LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT095342LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

value: yes

tag: multiplex


title: FOXD3-EtOH-14hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG47_S44_L005_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: LT203446LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT203446LL

tag: tissue

tag: ltrc id

value: Female

tag: bode score

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT044225RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT044225RL

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: multiplex


title: FOXD3-EtOH-14hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG45_S42_L005_R1_001

tag: culture conditions

tag: genotype

tag: treatment time

tag: molecule subtype


title: LT230415RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT230415RU

tag: tissue

tag: ltrc id

tag: disease

tag: bode score

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: FOXD3-4HT-8hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG44_S41_L005_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: FOXD3-EtOH-8hpT-rep2

description:
counts_foxd3_asynchronous.txt
DG43_S40_L005_R1_001

tag: molecule subtype


title: LT258372RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT258372RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: multiplex


title: FOXD3-4HT-8hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG42_S39_L005_R1_001

tag: culture conditions

tag: genotype

tag: treatment time


title: FOXD3-EtOH-8hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG41_S38_L005_R1_001

tag: molecule subtype


title: BRSST+sgLuc H3K4me3

city: Hannover

first: Dorit

last: Borchert

address: Carl-Neuberg-Str. 1

department: Pediatric Hematology and Oncology

country: Germany

institute: Hannover Medical School

description:
21_15
ChIP-Seq data for H3K4me3 from BM transplanted mice transduced with BRSST sgRNA +sgLuc

data_processing:
Base calling was performed using standard Illumina software.
Sequencing reads were aligned to the murine mm9 genome using BWA software.
Peak calling was done utilizing MACS2 software.
Peak visualization was performed using the IGV genome browser tool.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigwig files

source_name: Murine whole bone marrow

growth_protocol: 1-4x10^4 LSK cells from Cas9 knockin mice were transduced with the given sgRNA combinations and transplanted after 24 h into irradiated (7 Gy) C57Bl/6J mice. Complete BM was harvested after presenting with signs of leukemia or after 6 month and secondarily transplanted into irradiated Bl6 mice.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody and protein A magnetic beads. DNA was eluted from the beads using 0.75% SDS, protease treatment and the Qia MinElute PCR extraction Kit.
For library construction the TruSeq ChIP Library Preparation Kit from Illumina was used. Size selection was done via agarose gels.

treatment_protocol: Murine bone marrow cells were crosslinked directly after isolation using 1% formaldehyde for 5 min.

tag: tissue

value: Whole bone marrow

tag: strain

tag: treatment

value: BRSST+sgLuc

tag: chip antibody

value: H3K4me3, Millipore #04-745


title: BRSST+sgLuc H3K27me3

description:
23_15
ChIP-Seq data for H3K27me3 from BM transplanted mice transduced with BRSST sgRNA +sgLuc

value: H3K27me3, Millipore #07-449


title: BRSST+sgEzh2 H3K27me3

description:
22_1
ChIP-Seq data for H3K27me3 from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: FOXD3-4HT-14hpT-rep1

description:
counts_foxd3_asynchronous.txt
DG46_S43_L005_R1_001

value: 4SU-labeled RNA


title: BRSST+sgEzh2 1% input

description:
16_1
Input data for BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: LT296771LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT296771LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: bode score

tag: tissue type

value: 2-Lung explant,  bilateral

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

value: Multiplex


title: LT123313RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT123313RM

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: dlco

tag: multiplex


title: LT184901RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT184901RU

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: Male

tag: bode score

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: LT234205RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT234205RL

tag: tissue

tag: ltrc id

tag: disease

value: 9-Hypersensitive Pneumonitis (HP)

tag: gender

tag: age

tag: percent emphysema

value: 4-Lung biopsy

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT066309LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT066309LL

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: multiplex


title: LT111643RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT111643RU

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: LT168204LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT168204LL

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol


title: LT028044RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT028044RU

tag: tissue

tag: ltrc id

tag: disease

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: yes

tag: multiplex


title: LT141870LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT141870LU

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: LT220968RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT220968RU

tag: tissue

tag: ltrc id

tag: disease

value: 1-White (Caucasian)

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT122336LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT122336LU

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: multiplex


title: LT077800RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT077800RU

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: LT069585RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT069585RL

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: FALSE

tag: included

value: no

tag: protocol


title: LT184772RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT184772RL

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: multiplex


title: LT072387LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT072387LU

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: LT91552LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT91552LL

tag: tissue

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT013743LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT013743LL

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: multiplex


title: erf4 imbibed seeds rep2

city: Shenzhen

first: Xi

last: Chen

address: No.97in Buxin road, Dapeng district, Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.20.0, -z 4 -q 20 -u 30 -n 10).
Clean reads were mapped to the Arabidopsis reference genome using the software Hisat2 (version 2.1.0).
Feature Counts (version 2.0.1) was used to count the reads using these common parameters (-p -t exon -g gene_id).
Raw counts were normalized with DEseq2 (version 1.34.0) to compare gene expression in different samples.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Arabidopsis thaliana

source_name: seed

growth_protocol: Arabidopsis seeds were sown in a soil mixture and grown in a growth chamber (Hipoint, FH-1300) under a 16-h-light/8-h-dark cycle (23°C/20°C) with 55-60% humidity. Freshly harvested seeds were immediately used for seed dormancy and germination assay or stored in a cabinet (Huayuxiandai, HYXD-180KWS) with constant conditions (dark, 50% humidity, 22°C) for after-ripening treatment.

extract_protocol:
RNA was extracted from dry and imbibed seeds using FastPure Plant Total RNA Isolation Kit (Polysaccharides and Polyphenolics-rich) (Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions. RNA-Seq library preparation and sequencing were performed at Novogene Biotech.
Library preparation and sequencing were completed at Novogene Biotech (Beijing, China) using an Illumina NovaSeq 6000-PE150

treatment_protocol: Freshly harvested seeds were immediately sampled (dry seeds) or imbibed in saturated filter paper for 6 h prior to sample (imbibed seeds).

tag: tissue

value: seed

tag: ecotype

tag: genotype

value: ERF4 knock out

tag: treatment

value: seeds after imbibition for 6 hours


title: erf4 imbibed seeds rep3


title: LT243794RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT243794RL

value: lung

tag: ltrc id

tag: disease

tag: gender

tag: age

tag: percent emphysema

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included


title: BRSST+sgLuc 1% input

description:
17_15
Input data for BM transplanted mice transduced with BRSST sgRNA +sgLuc

tag: tissue

value: Whole bone marrow

tag: strain

value: BRSST+sgLuc

tag: chip antibody


title: erf4 imbibed seeds rep1

tag: ecotype

tag: genotype

tag: treatment


title: Col-0 imbibed seeds rep3

value: WT


title: BRSST+sgEzh2 H3K4me3

description:
20_1
ChIP-Seq data for H3K4me3 from BM transplanted mice transduced with BRSST sgRNA +sgEzh2

value: H3K4me3, Millipore #04-745


title: LT130603LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT130603LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: protocol

tag: multiplex

value: Multiplex


title: Col-0 imbibed seeds rep2

tag: tissue

tag: ecotype

tag: genotype

tag: treatment


title: LT277036RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT277036RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

value: 1-Lung explant,  single

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes


title: erf4 dry seeds rep2

tag: tissue

tag: ecotype

value: freshly harvested dry seeds


title: LT223106RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT223106RU

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

value: Female

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 2-Lung explant,  bilateral

tag: protocol

tag: multiplex


title: LT251693LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT251693LL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: percent emphysema

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT157177RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT157177RU

tag: tissue

value: lung

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: qc pass

tag: included


title: LT059224RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT059224RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 3-Don't Know

tag: percent emphysema

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: protocol

tag: multiplex


title: erf4 dry seeds rep3

tag: tissue

value: seed

tag: ecotype

tag: genotype

value: ERF4 knock out

tag: treatment


title: Col-0 dry seeds rep2

value: WT


title: Col-0 dry seeds rep3


title: LT028264RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT028264RL

value: 2-Other Control

tag: race

value: 3-African-American (whether Hispanic or not)

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT197821RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT197821RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: Male

tag: percent emphysema

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: Col-0 imbibed seeds rep1

tag: ecotype

tag: genotype

tag: treatment

value: seeds after imbibition for 6 hours


title: Col-0 dry seeds rep1


title: erf4 dry seeds rep1


title: LT191618LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT191618LU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

value: 4-Lung biopsy

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

value: yes


title: LT055396LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT055396LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 1-White (Caucasian)

tag: percent emphysema

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT084808LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT084808LU

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT235441RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT235441RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT205707LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT205707LL

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT126293RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT126293RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

value: 3-Lung lobectomy/wedge resection

tag: index

tag: total reads

tag: total reads aligned


title: LT157856LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT157856LU

value: lung

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT169564RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT169564RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 3-Don't Know

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT190004RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT190004RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT280851LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT280851LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT264283RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT264283RL

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT158795LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT158795LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 4-Asian or Pacific Islander

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT045399RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT045399RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT262371RM-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT262371RM

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT083759RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT083759RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT142933RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT142933RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT222755RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT222755RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT197381LI-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT197381LI

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT017275LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT017275LL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT072789RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT072789RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT177521RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT177521RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT079487LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT079487LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT024857LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT024857LU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT139691RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT139691RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

value: 2-Lung explant,  bilateral

tag: index

tag: total reads

tag: total reads aligned


title: LT166111RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT166111RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT259072LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT259072LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT089958RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT089958RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT096554LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT096554LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT108067RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT108067RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT119682RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT119682RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT030151RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT030151RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT062141RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT062141RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT273284LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT273284LL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT017811RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT017811RM

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT233821RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT233821RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT125521LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT125521LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 5-Native American

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT288719RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT288719RL

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT280646RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT280646RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: LT087826LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT087826LL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT118064RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT118064RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT032411RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT032411RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT176510LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT176510LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned

value: FALSE

value: no


title: LT012933RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT012933RL

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE


title: LT062121LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT062121LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 1-White (Caucasian)

tag: percent emphysema

tag: flow cell

tag: lane

tag: included

value: yes

tag: protocol

tag: multiplex


title: LT165114RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT165114RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT180758RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT180758RM

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: LT076181LI-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT076181LI

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: flow cell

tag: lane

tag: included

tag: protocol

tag: multiplex


title: LT246994RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT246994RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: index

tag: total reads

tag: total reads aligned


title: LT150981RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT150981RU

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass


title: PSC94

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

data_processing:
GENPIPES framework,“stringtie” type “rnaseq” pipeline
Reads were first trimmed using Trimmomatic software
Trimmed reads were aligned to the GRCh38 human reference genome using the STAR aligner following a two-pass mapping protocol
Alignments were then sorted and filtered for duplicates using Picard(sort, markduplicates) (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/http://broadinstitute.github.io/picard/)
Gene-level read counts for downstream processing were calculated from spliced alignments using HTseq count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: Colonic biopsy

extract_protocol:
Biopsies were bead beat 3 times for 1 minute at a setting of nine on a Bullet Blender 24 (Next Advance), with one minute of cooling on ice between each beating. Lysates were processed using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). 500ng of purified RNA was used as input
TruSeq Stranded mRNA Library Prep kit (Illumina) to generate sample libraries according to manufacturer’s specifications. Libraries were multiplexed and sequenced at a depth of 20 million reads per sample (50 base pairs, single read) on a HiSeq4000 sequencer.

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: IBD145

value: Crohn's

value: IBD


title: NC82

value: NC


title: PSC95

value: PSC- no IBD


title: LT0249481LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT0249481LU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 4-Asian or Pacific Islander

value: Male

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: included

tag: protocol

tag: multiplex


title: LT037710RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT037710RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: Multiplex


title: LT106519RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT106519RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

value: 3-Don't Know

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index


title: IBD144

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: NC87


title: LT242161RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT242161RL

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex


title: IBD142

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: tissue


title: LT248906LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT248906LL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: qc pass


title: LT197511LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT197511LU

tag: age

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

tag: protocol

tag: multiplex


title: PSC92

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: NC85

value: NC


title: LT141224LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT141224LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: qc pass


title: LT071706RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT071706RL

value: Male

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

value: 1-Lung explant,  single

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

tag: protocol

tag: multiplex


title: IBD150

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue


title: IBD153

value: UC

value: Yes

value: L


title: IBD141


title: LT213352LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT213352LU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: qc pass

value: TRUE

value: Multiplex


title: IBD154

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location


title: LT277811RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT277811RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

value: yes

tag: protocol

tag: multiplex


title: LT206010LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT206010LU

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: qc pass


title: IBD157

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: NC88

value: NC


title: IBD152


title: LT078347LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT078347LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

value: Female

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

tag: protocol

tag: multiplex


title: LT005419RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT005419RU

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: qc pass


title: IBD139

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT006946RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT006946RM

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

tag: protocol

tag: multiplex


title: IBD147

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: PSC91

value: PSC-UC

value: PSC

tag: tissue


title: LT007392RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT007392RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: bode score

tag: flow cell

tag: lane

tag: index

tag: qc pass


title: LT012861RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT012861RU

tag: pack years

tag: fev1 percent predicted

tag: dlco

tag: tissue type

value: 2-Lung explant,  bilateral

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: included

tag: protocol

tag: multiplex


title: LT196309RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT196309RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: TRUE


title: NC89

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: LT076421LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT076421LL

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

value: Multiplex


title: LT120371LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT120371LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: 3-Lung lobectomy/wedge resection

tag: multiplex


title: LT236519LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT236519LL

value: 9-Hypersensitive Pneumonitis (HP)

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: yes


title: LT076617LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT076617LL

tag: tissue

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: NC84

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: LT297451LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT297451LU

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: NC86

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: LT171097RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT171097RL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: NC80

tag: diagnosis

tag: broad diagnosis

value: Yes

tag: dys broad location

value: L


title: IBD155

value: UC

value: IBD

tag: dysplasia now

tag: tissue


title: LT285671LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT285671LU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD

value: 1-White (Caucasian)

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

value: TRUE

tag: multiplex

value: Multiplex


title: IBD148

tag: diagnosis

value: Crohn's

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: IBD140

tag: tissue


title: IBD149


title: NC90


title: LT173597LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT173597LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

value: yes

tag: protocol


title: NC79

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: NC78

value: No

tag: tissue


title: NC81

value: R

value: Colonic biopsy


title: LT286644RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT286644RL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: Female

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: LT144462RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT144462RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT075462RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT075462RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell


title: IBD143

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location


title: LT016556LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT016556LU

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT285906LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT285906LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: protocol


title: IBD129

tag: diagnosis

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: LT047152LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT047152LL

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

value: 1-Lung explant,  single

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD156

tag: diagnosis

value: UC

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: LT096430LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT096430LU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

value: TRUE

tag: protocol


title: IBD127

tag: diagnosis

value: Crohn's

tag: broad diagnosis

tag: dys broad location


title: LT058691LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT058691LU

tag: tissue

tag: ltrc id

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

value: yes

tag: multiplex

value: Multiplex


title: LT000379LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT000379LU

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: protocol


title: NC74

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: LT180102RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT180102RL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT206871LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT206871LU

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: protocol


title: NC75

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: IBD134


title: LT130546RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT130546RU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)

value: Female

tag: age

tag: percent emphysema

tag: pack years

value: 4-Lung biopsy

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD128

tag: diagnosis

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: LT196199RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT196199RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: protocol


title: PSC89

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now


title: IBD133

value: Crohn's

tag: dys broad location

tag: tissue


title: IBD135


title: LT256221LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT256221LL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

value: 1-White (Caucasian)

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: multiplex


title: LT172093RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT172093RL

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

value: yes

tag: protocol

value: Multiplex


title: IBD137

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: IBD131


title: LT295133LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT295133LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 3-Don't Know

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: NC77

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

value: T


title: LT253677RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT253677RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: protocol


title: NC73

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now


title: IBD136

value: IBD

tag: dys broad location

tag: tissue


title: LT106561LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT106561LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: age

tag: percent emphysema

tag: pack years

value: 1-Lung explant,  single

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT109231RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT109231RU

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: protocol


title: LT036383LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT036383LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned


title: IBD132

tag: diagnosis

value: Crohn's

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: LT184347RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT184347RU

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD130

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: IBD138

tag: dys broad location


title: LT048637LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT048637LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: protocol


title: PSC90

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: tissue


title: PSC87

tag: dys broad location


title: LT167891LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT167891LU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

value: Female

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: multiplex


title: NC72

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: tissue

value: Colonic biopsy


title: LT154455RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT154455RU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: protocol

value: Multiplex


title: IBD106

tag: diagnosis

value: UC

tag: broad diagnosis

tag: dys broad location


title: IBD115

tag: dysplasia now

tag: tissue


title: LT053283RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT053283RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: NC65

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

value: R


title: LT284144LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT284144LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

value: 2-Lung explant,  bilateral

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: protocol


title: LT055841LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT055841LL

tag: smoking status

value: 1-White (Caucasian)

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD118

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT282562RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT282562RM

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

value: TRUE

tag: protocol


title: LT127070RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT127070RL

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

value: yes

tag: multiplex


title: LT026534RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT026534RL

tag: tissue

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years


title: IBD116

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: IBD107


title: LT136415RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT136415RU

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

value: Multiplex


title: PSC84

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: Yes

tag: tissue


title: LT166565RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT166565RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: multiplex


title: LT077264RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT077264RU

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT060406RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT060406RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection


title: IBD105

tag: diagnosis

value: UC

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

value: L


title: LT043343LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT043343LU

value: 1-White (Caucasian)

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD113

tag: diagnosis

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: tissue


title: NC68

value: NC

tag: dys broad location


title: IBD114

value: Crohn's


title: LT142159RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT142159RU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

value: TRUE

value: yes

tag: protocol


title: LT150340LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT150340LU

tag: tissue

value: lung

value: Female

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: IBD102

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: LT190870RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT190870RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: protocol

value: Multiplex


title: PSC86

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: tissue


title: PSC83

value: PSC- no IBD

tag: dys broad location


title: LT286300LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT286300LU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: Male

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT175949LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT175949LL

tag: tissue

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: protocol


title: NC69

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

value: R


title: IBD100

value: Crohn's

value: IBD


title: IBD122


title: IBD101


title: LT038075LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT038075LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 3-Don't Know

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: multiplex


title: IBD121

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: LT002410RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT002410RM

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

value: 4-Lung biopsy

value: yes

tag: protocol


title: LT221510LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT221510LU

tag: smoking status

value: Female

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT178929RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT178929RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: Multiplex


title: LT121928RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT121928RL

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 2-Lung explant,  bilateral

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: protocol


title: IBD120

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: LT231101RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT231101RL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 4-Desquamative interstitial pneumonia (DIP)

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 3-Lung lobectomy/wedge resection

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT166240RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT166240RM

value: 2-Other Control

tag: smoking status

value: 1-White (Caucasian)

value: Male

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: protocol


title: LT181845RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT181845RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted


title: NC70

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

value: R


title: PSC88

value: Crohn's

value: IBD


title: IBD109

value: UC

value: L


title: LT013011LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT013011LU

value: lung

tag: smoking status

value: Female

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: multiplex

value: Multiplex


title: LT099879RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT099879RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 4-Lung biopsy

tag: protocol


title: IBD123

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: IBD104


title: IBD98


title: LT113005RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT113005RU

tag: smoking status

value: 1-White (Caucasian)

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: multiplex


title: LT126767LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT126767LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 8-Acute interstitial pneumonia (AIP)

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: protocol


title: LT080750LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT080750LL

tag: smoking status

value: Male

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: IBD103

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

tag: tissue


title: LT185970RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT185970RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: IBD124

tag: diagnosis

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: NC71

value: NC

value: R

tag: tissue


title: LT058319LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT058319LU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT238531RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT238531RU

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: IBD117

tag: diagnosis

value: Crohn's

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT017495RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT017495RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: TRUE

value: yes


title: PSC26

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: dys broad location

value: T


title: IBD110

value: No

tag: tissue

value: Colonic biopsy


title: LT269763RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT269763RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 2-Lung explant,  bilateral

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: IBD17

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: IBD19

tag: tissue


title: LT198741LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT198741LU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT115251RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT115251RU

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: replicate

tag: qc pass

value: FALSE

tag: included

value: no

tag: protocol

tag: multiplex


title: LT263636RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT263636RU

tag: tissue

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: Male

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell


title: IBD15

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: LT191675RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT191675RL

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 4-Lung biopsy

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol


title: LT143944LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT143944LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: multiplex


title: LT266817LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT266817LL

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT051993RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT051993RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: IBD112

tag: diagnosis

value: UC

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: IBD20


title: IBD21


title: LT244399LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT244399LU

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex

value: Multiplex


title: PSC07

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: tissue


title: IBD119

tag: dys broad location


title: LT155318RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT155318RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: 3-Lung lobectomy/wedge resection

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: IBD125

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: LT162479RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT162479RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: IBD108

tag: diagnosis

tag: broad diagnosis

value: Yes

tag: dys broad location

value: T


title: IBD16

tag: dysplasia now

tag: tissue


title: LT245983LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT245983LU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT279828RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT279828RU

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: NC18

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue