title: LT145086RU-COPD

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
LT145086RU

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: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

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

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

tag: protocol

tag: multiplex

value: Singleplex


title: LT294945LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT294945LU

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

value: 2-Lung explant,  bilateral


title: LT024952RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT024952RU

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


title: LT058156LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT058156LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

value: 3-Lung lobectomy/wedge resection

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT157253RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT157253RL

tag: cancer status

tag: gender

value: Male

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


title: LT211728RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT211728RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT231373LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT231373LU

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 4-Lung biopsy

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT046027RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT046027RL

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


title: LT137431RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT137431RL

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: LT242420LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT242420LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT003990RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT003990RU

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

tag: flow cell


title: LT042988LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT042988LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT113077LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT113077LL

tag: cancer status

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: LT010012LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT010012LU

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


title: LT178307RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT178307RU

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: LT092669LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT092669LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT168219RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT168219RL

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

tag: flow cell


title: LT100984RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT100984RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT056627RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT056627RU

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: LT126571RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT126571RU

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


title: LT262496LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT262496LU

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: LT235584LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT235584LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT023631RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT023631RU

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

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

tag: flow cell


title: LT010491LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT010491LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT152979LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT152979LL

tag: cancer status

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: LT282467LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT282467LL

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


title: LT265199LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT265199LU

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: LT106997RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT106997RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT132625RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT132625RU

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

tag: flow cell


title: LT009615LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT009615LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT219681RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT219681RL

tag: cancer status

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: LT055745RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT055745RU

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


title: LT125775RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT125775RL

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: LT148286LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT148286LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT030041RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT030041RU

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

tag: flow cell


title: LT132314LI-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT132314LI

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT194990RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT194990RU

tag: cancer status

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: LT051568RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT051568RU

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


title: LT291578RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT291578RU

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: LT185066RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT185066RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT075094LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT075094LU

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

tag: flow cell


title: LT104717LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT104717LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT109321RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT109321RL

tag: cancer status

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: LT187987LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT187987LL

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


title: LT166493RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT166493RM

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: FVB_S28

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were trimmed for adaptors and aligned to mouse genome GRCm38/mm10 using STARv 2.5.0c with default settings.
Aligned reads were annotated to gene exons with HTSeq v0.6.11 using GTF release 86 (update 2016-10), using non-stranded union model.
Count matrixes were TMM and voom normalized with limma.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2(CPM) values, normalization done separately for brain regions.

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice were housed in groups in a temperature and humidity controlled facility on a 12h light/dark cycle for the acclimatization period. All mice had ad libitum access to food and water throughout the experiment. Animal procedures were approved by the Regional State Administration Agency for Southern Finland (license numbers ESAVI-3801-041003-2011 and ESAVI/2766/04.10.07/2014) and carried out in accordance to directive 2010/63/EU of the European Parliament and of the Council, and the Finnish Act on the Protection of Animals Used for Science or Educational Purposes (497/2013).

extract_protocol:
Total RNA was extracted with TriReagent (Molecular Research Center, Inc.).
Sequencing libraries were prepared with Nextera kit.

treatment_protocol: Mice were killed by cervical dislocation between 8 am and 11 am to avoid circadian differences in gene expression.

tag: strain

value: FVB/NJ

tag: age on dissection

value: 8  weeks

tag: Sex

value: male


title: FVB_S26


title: D2_S9


title: D2_S12


title: D2_S10


title: C3H_S18


title: C3H_S20


title: C3H_S17


title: B6_S24


title: TNBC sample r2195c

type: RNA

city: Seoul

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

country: South Korea

institute: Sookmyung Women's university

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Probes signal value was transformed by logarithm and normalized by quantile method.

label: biotin

source_name: human breast cancer tissue

label_protocol: Total RNA was amplified and purified using an Ambion Illumina RNA amplification kit (Ambion) to yield biotinylated cRNA according to the manufacturer’s instructions

extract_protocol: Total RNA was isolated using TRIzol reagent (Ambion, Austin, TX, USA), and clean-up was performed using chloroform and isopropanol.

tag: tissue

value: breast


title: adjacent normal sample 9984

source_name: human breast cancer adjacent tissue


title: TNBC sample r9984c


title: B6_S23


title: TNBC sample r2129c


title: adjacent normal sample 2129


title: adjacent normal sample r2195n


title: B6_S21


title: A_S8

value: A/J


title: A_S6


title: 129S1_S16


title: A_S5


title: LT_a_BM

city: Hannover

first: Dorit

last: Borchert

address: Carl-Neuberg-Str. 1

department: Pediatric Hematology and Oncology

country: Germany

institute: Hannover Medical School

description:
Heckl3043C
Gene expression data from BM transplanted mice transduced with +sgLuc

hyb_protocol: Cartridge Array Hybridization was performed according to standard Affymetrix protocols (Affymetrix Pico Kit User Guide (P/N 703262) for Array Plate Hybridization).

scan_protocol: Arrays were scanned using the Affymetrix GCS3000 Scanner (Software GCOS 1.2).

data_processing: The data were analyzed using R 3.5.01 and Bioconductor2. Raw files (.cel) were read in using the function “read.celfiles” from the R package “oligo”. Quality control was performed by inspection of the RLE (Relative Log Expression ) plots and NUSE (normalized unscaled standard error) plots after fitting a Probe Level Model to the raw intensity data by using the function “fitProbeLevelModel” from the package “oligo”. The Raw data was background corrected, quantile-normalized, and log2-transformed using the function “rma” from the ”oligo” package.

source_name: Bone marrow

label_protocol: cRNA was prepared according to the standard Affymetrix protocol from 2 ng total RNA (GeneChIP Pico Reagent Kit, Affymetrix). 10 cycles were used for Pre IVT-PCR.

growth_protocol: Fetal liver cells were isolated from e13.5 embryos. Bone marrow was isolated from mice 3 to 12 months old.

extract_protocol: RNeasy Micro Kit (Qiagen No. 74004).

tag: cell type

value: Bone marrow LT-HSC cells

tag: developmental stage

value: Adult


title: LT_c_BM

description:
Heckl3045C
Gene expression data from BM transplanted mice transduced with +sgLuc


title: LT_b_BM

description:
Heckl3044C
Gene expression data from BM transplanted mice transduced with +sgLuc


title: 129S1_S14


title: MPP_b_BM

description:
Heckl3041
Gene expression data from BM transplanted mice transduced with +sgLuc

value: Bone marrow MPP cells


title: 129S1_S13


title: FVB_S25


title: MPP_c_BM

description:
Heckl3042
Gene expression data from BM transplanted mice transduced with +sgLuc


title: FVB_C8

source_name: frontal cortex


title: ST_c_BM

description:
Heckl3039
Gene expression data from BM transplanted mice transduced with +sgLuc

value: Bone marrow ST-HSC cells


title: FVB_C7


title: ST_b_BM

description:
Heckl3038
Gene expression data from BM transplanted mice transduced with +sgLuc


title: FVB_C6


title: LT-HSC_c_FL

description:
Heckl3036
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc

source_name: Fetal liver

value: Fetal liver LT-HSC cells


title: D2_E8


title: D2_E7


title: ST_a_BM

description:
Heckl3037
Gene expression data from BM transplanted mice transduced with +sgLuc


title: D2_E6


title: C3H_B7


title: C3H_B8


title: C3H_B6


title: ST-HSC_b_FL

description:
Heckl3032B
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc

value: Fetal liver ST-HSC cells


title: B6_F8


title: MPP_c_FL

description:
Heckl3034
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc

value: Fetal liver MPP cells


title: ST-HSC_c_FL

description:
Heckl3035_B
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: LT-HSC_b_FL

description:
Heckl3033
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: ST-HSC_a_FL

description:
Heckl3029
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: LT-HSC_a_FL

description:
Heckl3030
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: MPP_a_BM

description:
Heckl3040
Gene expression data from BM transplanted mice transduced with +sgLuc


title: MPP_a_FL

description:
Heckl3028
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: MPP_b_FL

description:
Heckl3031
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: B6_F5


title: A_C7


title: Luc rpl3

description:
Heckl4033
Gene expression data from BM transplanted mice transduced with +sgLuc

label_protocol: cRNA was prepared according to the standard Affymetrix protocol from 2 ng total RNA (GeneChIP Pico Reagent Kit , Affymetrix). 10 cycles were used for Pre IVT-PCR.

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.

extract_protocol: Zymo RNA Micro Kit (Zymo Research No. R1050).

value: Bone marrow

tag: treatment

value: sgLuc


title: Luc rpl4

description:
Heckl4034
Gene expression data from BM transplanted mice transduced with +sgLuc


title: 129S1_C6


title: BRSST-Luc rpl5

description:
Heckl4009
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc

value: BRSST+sgLuc


title: Luc rpl2

description:
Heckl4032
Gene expression data from BM transplanted mice transduced with +sgLuc


title: 129S1_C7


title: A_C8


title: A_C5


title: BRSST-Ezh2 rpl4

description:
Heckl4004
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: BRSST-Luc rpl3

description:
Heckl4007
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: 129S1_C5


title: BRSST-Luc rpl1

description:
Heckl4005
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: B6_F6


title: GS1011_E-GUS_2

city: Basel

first: Massimo

last: Saini

state: Basel Canton

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

library_source: genomic

data_processing:
For sequencing, each sample was split to two lanes. For analysis, both files were merged.  ATAC-sequencing reads were aligned to the human genome (hg38) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -m1”.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from homer tag directories using makeBigWig.pl.

molecule: genomic DNA

growth_protocol: Cells were cultured in Mammary Epithelial Cell Basal Medium containing 0.004 ml/ml BPE, 10 ng/ml EGF, 5 µg/ml hydrocortisone. Blasticidin S HCl and Puromycin were added at a final concentration of 10 µg/ml and 1 µg/ml, respectively.

extract_protocol:
50000 cells were tagmented in 50 µl with 2.5 µl Tn5 according to Corces et al. 2017.
Illumina Nextera DNA Library Preparation Kit (FC-121-1030) was used for library preparation. Libraries were selected for fragments less than 600 bp using AMPure XP beads for size selection.

treatment_protocol: For ZEB1 or GUS activation, cells were treated with Doxycycline at a final concentration of 1 µg/ml for 7 days.

value: mammary epithelial cells

tag: genotype/variation

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible GUS expression, clone 2

value: 7 days Doxycycline treatment (final conc. 1 µg/ml)


title: GS1012_E-ZEB1_2

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible ZEB1 expression, clone 2


title: GS1009_M-GUS_2

value: HMLE-Twist1-ER EMT-sensitive (M) single-cell clone, inducible GUS expression, clone 2


title: GS1008_E-ZEB1_3

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible ZEB1 expression, clone 3


title: GS1007_E-ZEB1_1

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible ZEB1 expression, clone 1


title: GS1006_E-GUS_1

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible GUS expression, clone 1


title: M3+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 14 days Tamoxifen treatment + 7 days withdrawal

data_processing:
ATAC-seq of HMLE-TWSIT1-ER cells: ATAC-seq reads were aligned to the human genome (hg38) using bowtie (Langmead et al., 2009) with options “-q -n 2 --best --chunkmbs 2000 -p 32 -m1”
RNA-seq HMLE-TWIST1-ER cells: The STAR aligner (v 2.4.2a) with modified parameter settings (--twopassMode=Basic) is used for split-read alignment against the human genome assembly hg19 (GRCh37) and UCSC knownGene annotation (Dobin, A. et al. , 2013).
RNA-seq of primary breast cancer cells: RNA-sequencing reads were aligned to the human reference genome hg19 and quantified using the stranded option of STAR version 2.4.2a30.
Genome_build: ATAC-seq: hg38  RNA-seq: hg19 (GRCh37)
Supplementary_files_format_and_content: ATAC-seq of HMLE-TWIST1-ER cells: bigWig files were generated from homer tag directories using makeBigWig.pl.
RNA-seq of HMLE-TWIST1-ER cells: To quantify the number of reads mapping to annotated genes we use HTseq-count (v0.6.0) (Anders, S., Pyl, P. T. & Huber, W., 2015). FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values are calculated using custom scripts.
RNA-seq of primary breast cancer cells: The DESeq2 package was used to obtain normalized expression values as described (Raffel, S. et al., 2017).

growth_protocol: Human mammary epithelial (HMLE) cells were cultured in Mammary Epithelial Cell Basal Medium containing 0.004 ml/ml BPE, 10 ng/ml EGF, 5 µg/ml hydrocortisone; HMLE-TWIST1-ER cells were propagated in medium containing Blasticidin S HCl at a final concentration of 10 µg/ml.

extract_protocol:
ATAC-seq of HMLE-TWIST1-ER cells: 50000 cells were tagmented in 50 µl with 2.5 µl Tn5 according to Corces et al. 2017
RNA-seq of HMLE-TWIST1-ER cells: Total RNA was isolated using the miRNeasy Mini Kit (Qiagen).
RNA-seq of primary breast cancer cells: Total RNA was isolated using the Arcturus PicoPure RNA isolation kit.
ATAC-seq of HMLE-TWIST1-ER cells: Illumina Nextera DNA Library Preparation Kit (FC-121-1030) was used for library preparation. Libraries were selected for fragments less than 600 bp using AMPure XP beads for size selection.
RNA-seq of HMLE-TWIST1-ER cells: 1 μg of RNA was depleted for cytoplasmatic rRNAs, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix. A-tailing, adaptor ligation, and library enrichment were performed as described in the High Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).
RNA-seq of primary breast cancer cells: Libraries were prepared from 1 μg of total RNA using a TruSeq Stranded Total RNA Kit with Ribo-Zero Human/Mouse/Rat (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For TWIST1 activation, cells were treated with (Z)-4-HydroxyTamoxifen at a final concentration of 20 nM for the indicated number of days.

tag: resistance

value: EMT-sensitive


title: M2+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 14 days Tamoxifen treatment + 7 days withdrawal


title: E3+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 14 days Tamoxifen treatment + 7 days withdrawal

value: EMT-resistant


title: M1+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 14 days Tamoxifen treatment + 7 days withdrawal


title: BRSST-Ezh2 rpl2

description:
Heckl4002
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: E1+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 14 days Tamoxifen treatment + 7 days withdrawal


title: BRSST-Ezh2 rpl1

description:
Heckl4001
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: Luc rpl1

description:
Heckl4031
Gene expression data from BM transplanted mice transduced with +sgLuc


title: BRSST-Ezh2 rpl3

description:
Heckl4003
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2


title: BRSST-Luc rpl2

description:
Heckl4006
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: M1+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 14 days Tamoxifen treatment

value: 14 days Tamoxifen treatment


title: E2+TAMd14-d7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 14 days Tamoxifen treatment + 7 days withdrawal


title: BRSST-Luc rpl4

description:
Heckl4008
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc


title: BGC-R

city: Hangzhou

first: Lifeng

last: Feng

state: Zhejiang

address: No.3 East Qingchun Road

country: China

institute: Zhejiang University, School of Medicine, Sir Run Run Shaw Hospital

description: Gene expression of BGC-R

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: BGC-R

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: BGC823 and SGC7901 cells are maintained in RPMI1640 plus 10%FBS. BGC-R and SGC-R cells are maintained in RPMI1640 plus 10%FBS and 0.5μg/ml cisplatin

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: BGC-R and SGC-R cells were changed to no cisplatin medium for one week, and cells were havested together with BGC823 and SGC7901 under normal culture condition.

value: BGC-R


title: M3+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 14 days Tamoxifen treatment


title: GS1013_E-ZEB1_4

value: HMLE-Twist1-ER EMT-resistant (E) single-cell clone, inducible ZEB1 expression, clone 4


title: GS1010_M-ZEB1_2

value: HMLE-Twist1-ER EMT-sensitive (M) single-cell clone, inducible ZEB1 expression, clone 2


title: M2+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 7 days Tamoxifen treatment

value: 7 days Tamoxifen treatment


title: M1+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 7 days Tamoxifen treatment


title: E2+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 14 days Tamoxifen treatment


title: E1+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 14 days Tamoxifen treatment


title: GS1005_M-ZEB1_1

value: HMLE-Twist1-ER EMT-sensitive (M) single-cell clone, inducible ZEB1 expression, clone 1


title: GS1004_M-GUS_1

value: HMLE-Twist1-ER EMT-sensitive (M) single-cell clone, inducible GUS expression, clone 1


title: SGC-R

description: Gene expression of SGC-R

source_name: SGC-R

value: SGC-R


title: E3+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 7 days Tamoxifen treatment

value: mammary epithelial cells


title: E1+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 7 days Tamoxifen treatment


title: SGC7901

description: Gene expression of SGC7901


title: E2+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 7 days Tamoxifen treatment


title: BGC823

description: Gene expression of BGC823


title: M3-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; untreated

value: untreated


title: M1-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; untreated


title: M2-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; untreated


title: M2+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 14 days Tamoxifen treatment


title: Con_2_NS

city: jinan

first: hai

middle: yan

last: liu

address: huaxianchanglu

institute: bohao

description: Exosomal miRNA expression in RAW 264.7 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8 x 60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Exosomes derived from normal RAW 264.7 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

extract_protocol: Exosomes  were isolated by size-exclusion chromatography using qEV original size exclusion column (IZON science, Oxford, UK). Firstly, the cell supernatant was concentrated by centrifugal filter units (Millipore, Mass, US) through centrifugation at 1500 × g for 20 min. The sample were added into columns, and started to count the fraction, 0.5 ml/fraction, the seven to nine fractions were selected and concentrated.

treatment_protocol: 2 μg/mL LPS were added into complete medium to incubate RAW 264.7 cells, the cell supernatant were selected after 72h to isolated exosomes.

tag: cell line

value: control

tag: source

value: cell supernatant


title: E1-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 1; untreated


title: LPS_T_3_NS

description: Exosomal miRNA expression in LPS-treated RAW 264.7 cells

source_name: Exosomes derived from LPS-treated RAW 264.7 cells

value: 2 μg/mL LPS


title: E2-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 2; untreated


title: crkeap1a/b_liver-2

city: Melbourne

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

country: Australia

institute: PeterMacCallum Cancer Centre

data_processing:
QC, alignment, and counting were performed in Galaxy.
Sample QC was performed using FastQC (v0.72). Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to zebrafish genome (Ensembl danRer11) using RNA STAR (v2.7.5b)
Counting was performed using featurecounts (v1.6.3)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Assembly: Reads were mapped to zebrafish genome (Ensembl danrer11)
Supplementary files format and content: Count file generated by featureCounts

organism: Danio rerio

source_name: Larval liver

growth_protocol: Zebrafish were grown in 10-cm plates in E3 medium at 28C.

extract_protocol:
Pools of 15 larval livers were dissected in TRIzol solution. RNA was extracted using the Direct-zol RNA miniPREP kit. RNA quality was confirmed using the TapeStation system before sequencing.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: Zebrafish embryos were injected with CRISPR/Cas9 targetting genes at the single-cell stage. Livers were dissected into TRIzol solution and RNA was extracted and sequenced at 7dpf.

value: Larval liver

tag: genotype


title: WT_liver-3

value: WT


title: WT_liver-2


title: WT_liver-1


title: M3+TAMd7_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 7 days Tamoxifen treatment

value: EMT-sensitive


title: WT-4

source_name: Whole larvae

extract_protocol:
Pools of 10 larvae were homogenized in TRIzol solution. RNA was extracted using the Direct-zol RNA miniPREP kit. RNA quality was confirmed using the TapeStation system before sequencing.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: Zebrafish embryos were injected with CRISPR/Cas9 targetting genes at the single-cell stage. RNA was extracted and sequenced at 7dpf.

value: Whole larvae

tag: genetic modification

value: wildtype


title: amniotic fluid R7353-750knsp

type: genomic

city: fuzhou

first: su

last: linjuan

address: daoshanlu

institute: Fujian Provincial Maternity and Children's Hospital,

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: amniotic fluid R7353

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: amniotic fluid

tag: indications of invasive prenatal diagnosis

value: hMSS

tag: offspring gender

value: male


title: amniotic fluid R7487-750knsp

source_name: amniotic fluid R7487

value: isolated increased NT

value: female


title: amniotic fluid R7534-750knsp

source_name: amniotic fluid R7534


title: amniotic fluid R6981-750knsp

source_name: amniotic fluid R6981

value: AMA


title: WT-2


title: WT-1


title: amniotic fluid R6828-750knsp

source_name: amniotic fluid R6828


title: crkeap1a/b; Nrf2 KO-4

value: crkeap1a/b; Nrf2 KO

value: keap1a and keap1b crispant; Nrf2a knockout


title: amniotic fluid R6639-750knsp

source_name: amniotic fluid R6639


title: crkeap1a/b; Nrf2 KO-3


title: E3-TAMd1_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 3; untreated

value: mammary epithelial cells

value: EMT-resistant

value: untreated


title: crkeap1a/b_liver-3


title: crkeap1a/b_liver-1


title: LPS_T_2_NS

value: 2 μg/mL LPS

value: cell supernatant


title: LPS_T_1_NS


title: Con_3_NS

value: control


title: amniotic fluid R6399-750knsp

source_name: amniotic fluid R6399


title: crkeap1a/b; Nrf2 KO-2


title: Con_1_NS


title: Nrf2 KO-4

value: Nrf2 KO

value: Nrf2a knockout


title: Nrf2 KO-3

value: Whole larvae


title: amniotic fluid R6127-750knsp

source_name: amniotic fluid R6127

value: amniotic fluid


title: amniotic fluid R5988-750knsp

source_name: amniotic fluid R5988


title: amniotic fluid R5781-750knsp

source_name: amniotic fluid R5781


title: Nrf2 KO-2


title: crkeap1a/b; Nrf2 KO-1


title: amniotic fluid R5768-750knsp

source_name: amniotic fluid R5768


title: amniotic fluid R5696-750knsp

source_name: amniotic fluid R5696

value: AMA and hMSS


title: WT-3

value: WT

value: wildtype


title: amniotic fluid R7305-750knsp

source_name: amniotic fluid R7305

value: hMSS

value: male


title: Nrf2 KO-1


title: amniotic fluid R5691-750knsp

source_name: amniotic fluid R5691

value: isolated increased NT


title: amniotic fluid R5595-750knsp

source_name: amniotic fluid R5595

value: AMA

value: female


title: crkeap1a/b-3

value: keap1a and keap1b crispant


title: E3+TAMd14_ATAC-seq

description: HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 14 days Tamoxifen treatment

value: mammary epithelial cells

value: EMT-resistant

value: 14 days Tamoxifen treatment


title: crkeap1a/b-2


title: amniotic fluid R5119-750knsp

source_name: amniotic fluid R5119


title: crkeap1a/b-1

source_name: Whole larvae


title: amniotic fluid R5204-750knsp

source_name: amniotic fluid R5204


title: crkeap1b-3

value: keap1b crispant


title: crkeap1b-4


title: amniotic fluid R5050-750knsp

source_name: amniotic fluid R5050


title: amniotic fluid R5143-750knsp

source_name: amniotic fluid R5143


title: crkeap1b-2


title: crkeap1b-1


title: amniotic fluid R6254-750knsp

source_name: amniotic fluid R6254


title: amniotic fluid R4930-750knsp

source_name: amniotic fluid R4930


title: crkeap1a-4

value: keap1a crispant


title: amniotic fluid R4859-750knsp

source_name: amniotic fluid R4859


title: crkeap1a-3


title: amniotic fluid R4794-750knsp

source_name: amniotic fluid R4794


title: amniotic fluid R4755-750knsp

source_name: amniotic fluid R4755


title: crkeap1a-1


title: amniotic fluid R4759-750knsp

source_name: amniotic fluid R4759


title: amniotic fluid R4751-750knsp

source_name: amniotic fluid R4751


title: crkeap1a-2


title: crkeap1a/b; Bach1 DKO-4

value: crkeap1a/b; Bach1 DKO

value: keap1a and keap1b crispant; bach1a and bach1b knockout


title: crkeap1a/b; Bach1 DKO-2

value: Whole larvae


title: amniotic fluid R4750-750knsp

source_name: amniotic fluid R4750

value: amniotic fluid


title: amniotic fluid R4659-750knsp

source_name: amniotic fluid R4659


title: crkeap1a/b; Bach1 DKO-1


title: amniotic fluid R4607-750knsp

source_name: amniotic fluid R4607


title: crkeap1a/b; Bach1 DKO-3


title: crkeap1a/b-4


title: Bach1 DKO-4

value: bach1a and bach1b knockout


title: Bach1 DKO-3


title: amniotic fluid R4526-750knsp

source_name: amniotic fluid R4526


title: Bach1 DKO-2


title: amniotic fluid R4971-750knsp

source_name: amniotic fluid R4971


title: amniotic fluid R4505-750knsp

source_name: amniotic fluid R4505


title: amniotic fluid R4290-750knsp

source_name: amniotic fluid R4290


title: Bach1 DKO-1

source_name: Whole larvae


title: amniotic fluid R4315-750knsp

source_name: amniotic fluid R4315


title: amniotic fluid R4213-750knsp

source_name: amniotic fluid R4213


title: amniotic fluid R4108-750knsp

source_name: amniotic fluid R4108


title: amniotic fluid R4091-750knsp

source_name: amniotic fluid R4091


title: amniotic fluid R3753-750knsp

source_name: amniotic fluid R3753


title: amniotic fluid R3844-750knsp

source_name: amniotic fluid R3844


title: amniotic fluid R3676-750knsp

source_name: amniotic fluid R3676


title: amniotic fluid R3608-750knsp

source_name: amniotic fluid R3608


title: amniotic fluid R3410-750knsp

source_name: amniotic fluid R3410


title: amniotic fluid R3153-750knsp

source_name: amniotic fluid R3153


title: amniotic fluid R3211-750knsp

source_name: amniotic fluid R3211


title: amniotic fluid R3136-750knsp

source_name: amniotic fluid R3136


title: amniotic fluid R3152-750knsp

source_name: amniotic fluid R3152


title: amniotic fluid R3052-750knsp

source_name: amniotic fluid R3052


title: amniotic fluid R3140-750knsp

source_name: amniotic fluid R3140


title: amniotic fluid R3041-750knsp

source_name: amniotic fluid R3041


title: amniotic fluid R2823-750knsp

source_name: amniotic fluid R2823


title: amniotic fluid R2860-750knsp

source_name: amniotic fluid R2860


title: amniotic fluid R2253-750knsp

source_name: amniotic fluid R2253


title: amniotic fluid R2477-750knsp

source_name: amniotic fluid R2477


title: amniotic fluid R2000-750knsp

source_name: amniotic fluid R2000


title: amniotic fluid R2007-750knsp

source_name: amniotic fluid R2007


title: amniotic fluid R2158-750knsp

source_name: amniotic fluid R2158


title: amniotic fluid R1999-750knsp

source_name: amniotic fluid R1999


title: amniotic fluid R1654-750knsp

source_name: amniotic fluid R1654


title: amniotic fluid R1744-750knsp

source_name: amniotic fluid R1744


title: amniotic fluid R1460-750knsp

source_name: amniotic fluid R1460


title: amniotic fluid R1678-750knsp

source_name: amniotic fluid R1678


title: amniotic fluid R1592-750knsp

source_name: amniotic fluid R1592


title: amniotic fluid R1122-750knsp

source_name: amniotic fluid R1122


title: amniotic fluid R1208-750knsp

source_name: amniotic fluid R1208


title: amniotic fluid R1038-750knsp

source_name: amniotic fluid R1038


title: amniotic fluid R857-750knsp

source_name: amniotic fluid R857


title: amniotic fluid R624-750knsp

source_name: amniotic fluid R624


title: amniotic fluid R1044-750knsp

source_name: amniotic fluid R1044


title: amniotic fluid R588-750knsp

source_name: amniotic fluid R588


title: amniotic fluid R3441-750knsp

source_name: amniotic fluid R3441


title: amniotic fluid R521-750knsp

source_name: amniotic fluid R521


title: amniotic fluid P9832-750knsp

source_name: amniotic fluid P9832


title: amniotic fluid R524-750knsp

source_name: amniotic fluid R524


title: amniotic fluid R2963-750knsp

source_name: amniotic fluid R2963


title: amniotic fluid P9548-750knsp

source_name: amniotic fluid P9548

value: AMA and hMSS


title: amniotic fluid P9792-750knsp

source_name: amniotic fluid P9792

value: hMSS


title: amniotic fluid P9062-750knsp

source_name: amniotic fluid P9062

value: male


title: amniotic fluid P9178-750knsp

source_name: amniotic fluid P9178


title: amniotic fluid P9519-750knsp

source_name: amniotic fluid P9519


title: amniotic fluid P9846-750knsp

source_name: amniotic fluid P9846


title: amniotic fluid P8876-750knsp

source_name: amniotic fluid P8876

value: isolated increased NT


title: amniotic fluid R1954-750knsp

source_name: amniotic fluid R1954


title: amniotic fluid P8726-750knsp

source_name: amniotic fluid P8726


title: amniotic fluid P8875-750knsp

source_name: amniotic fluid P8875


title: amniotic fluid P8641-750knsp

source_name: amniotic fluid P8641


title: amniotic fluid P8428-750knsp

source_name: amniotic fluid P8428


title: amniotic fluid P8321-750knsp

source_name: amniotic fluid P8321

value: AMA


title: amniotic fluid P7699-750knsp

source_name: amniotic fluid P7699


title: amniotic fluid P8095-750knsp

source_name: amniotic fluid P8095


title: amniotic fluid P8192-750knsp

source_name: amniotic fluid P8192


title: amniotic fluid P7586-750knsp

source_name: amniotic fluid P7586


title: amniotic fluid P7647-750knsp

source_name: amniotic fluid P7647

value: female


title: amniotic fluid P7573-750knsp

source_name: amniotic fluid P7573


title: amniotic fluid P7560-750knsp

source_name: amniotic fluid P7560


title: amniotic fluid P7548 -750knsp

source_name: amniotic fluid P7548


title: amniotic fluid P7330-750knsp

source_name: amniotic fluid P7330


title: amniotic fluid P7413-750knsp

source_name: amniotic fluid P7413


title: amniotic fluid P6875-750knsp

source_name: amniotic fluid P6875


title: amniotic fluid R188-750knsp

source_name: amniotic fluid R188


title: amniotic fluid P7095-750knsp

source_name: amniotic fluid P7095


title: amniotic fluid P7279-750knsp

source_name: amniotic fluid P7279


title: Exp03-T72-41BBminus

city: Prague

first: Veronika

last: Cimermanova

address: Videnska 1083

department: lab of adaptive immunity

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: time point 72h

data_processing:
Quality of raw reads data was checked by FastQC (v0.11.9) on open-source platform Galaxy
Data were trimmed of low-quality ends and shorter reads than 20 nucleotides were discarded by Trimmomatic (v0.38) on open-source platform Galaxy.
Cleared data were mapped to Mouse Reference genome GRCm38 obtained from Ensembl database v102, allowing only primary alignments by Hisat2 (v2.2.1) on open-source platform Galaxy.
Read count tables were created by the featureCounts tool on open-source platform Galaxy and merge together into one csv file.
Assembly: Mouse Reference genome GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes metadata for all samples

source_name: spleen/lymph nodes

growth_protocol: Ex vivo activated T cells were cultured in the incubator at 37C / 5% CO2 in IMDM medium supplemented with 20% FBS, 100 U/mL penicillin, 100 mg/mL streptomycin, and 40 mg/mL gentamicin.

extract_protocol:
Total RNA was extracted by RNeasy Plus Micro Kit (#74034, QIAGEN) following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Takara).

treatment_protocol: Simultaneusly with seeding into 96 well-plate, Dynabeads Mouse T-Activator CD3/CD28 were added for T-cell activation in 1:2 ratio.

value: spleen/lymph nodes

value: CD8+ T cells

value: WT (C57BL/6J)

value: CD3/CD28 TCR ex vivo activation


title: Exp02-T24-41BBminus

description: time point 24h


title: Exp03-T24-41BBminus

description: time point 24h


title: Exp01-T72-41BBminus

description: time point 72h


title: amniotic fluid P6008-750knsp

source_name: amniotic fluid P6008


title: Exp03-T0-41BBminus

description: time point 0h

value: no activation


title: Exp02-T72-41BBminus

description: time point 72h


title: Exp01-T24-41BBminus

description: time point 24h


title: amniotic fluid P6515-750knsp

source_name: amniotic fluid P6515


title: amniotic fluid P5122-750knsp

source_name: amniotic fluid P5122


title: Exp02-T0-41BBminus

description: time point 0h


title: amniotic fluid P6585-750knsp

source_name: amniotic fluid P6585


title: amniotic fluid P6099-750knsp

source_name: amniotic fluid P6099


title: Exp01-T0-41BBminus

description: time point 0h


title: Exp03-T72-41BBplus

description: time point 72h


title: amniotic fluid P4666-750knsp

source_name: amniotic fluid P4666


title: amniotic fluid P4637-750knsp

source_name: amniotic fluid P4637


title: Exp02-T72-41BBplus

description: time point 72h


title: Exp01-T72-41BBplus

description: time point 72h


title: amniotic fluid P4567-750knsp

source_name: amniotic fluid P4567


title: amniotic fluid P5092-750knsp

source_name: amniotic fluid P5092


title: amniotic fluid P2269-750knsp

source_name: amniotic fluid P2269


title: Exp02-T24-41BBplus

description: time point 24h


title: amniotic fluid P2237-750knsp

source_name: amniotic fluid P2237


title: Exp03-T24-41BBplus

description: time point 24h


title: Exp01-T24-41BBplus

description: time point 24h


title: amniotic fluid P1890-750knsp

source_name: amniotic fluid P1890


title: amniotic fluid P1670-751knsp

source_name: amniotic fluid P1670


title: Exp01-T0-41BBplus

description: time point 0h


title: Exp02-T0-41BBplus

description: time point 0h


title: amniotic fluid P996-750knsp

source_name: amniotic fluid P996


title: amniotic fluid P436-750knsp

source_name: amniotic fluid P436


title: amniotic fluid P1383-750knsp

source_name: amniotic fluid P1383


title: amniotic fluid G9692-750knsp

source_name: amniotic fluid G9692


title: amniotic fluid P167-750knsp

source_name: amniotic fluid P167


title: amniotic fluid P245 -750knsp

source_name: amniotic fluid P245


title: amniotic fluid G9944-750knsp

source_name: amniotic fluid G9944


title: amniotic fluid G9494-750knsp

source_name: amniotic fluid G9494


title: amniotic fluid G9315-750knsp

source_name: amniotic fluid G9315


title: amniotic fluid G9406-750knsp

source_name: amniotic fluid G9406


title: amniotic fluid G9375-750knsp

source_name: amniotic fluid G9375


title: Non tumor tissues, Mdr-2 KO

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data (fastq files) was processed with 'cellranger count', version 6.1.2, with 20000 expected cells, aligning against the mouse GRCm38 genome, with gene annotations from Ensembl release 99.
Assembly: GRCm38
Supplementary files format and content: Results of cellranger count are given as is in the HDF5 format (see 10X support for details).

source_name: Liver

extract_protocol:
One liver lobe from Mdr-2 ko mouse was cut into small pieces and washed with cold HBSS. The tissue was dissociated with DNASE (1mg/ml) and Collagense (10 mg/ml), in 37°C and shaking.
Library was prepared accoding to the 10x Genomics single cell 3’ v3 protocol.

value: Liver

value: Mdr-2 KO

tag: age

value: 3 months


title: amniotic fluid G6732-750knsp

source_name: amniotic fluid G6732


title: amniotic fluid G7643-750knsp

source_name: amniotic fluid G7643


title: amniotic fluid G8565-750knsp

source_name: amniotic fluid G8565


title: Apc SI Vehicle Rep1

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: small intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina Stranded mRNA sample prep kit, then run on an Illumina NextSeq 500 using the High Output 75 cycles kit (2x36 cycles, paired end, dual index).

treatment_protocol: Mice were treated with two i.p. injections of 2mg tamoxifen to induce floxing of the Apc allele, then once daily with DZNeP.HCl (5 mg/kg i.p.) starting 24 hours after tamoxifen administration. Tissues were harvested on Day4.

value: Male

value: small intestine

value: VilCreER Apc fl/fl

value: vehicle (PBS)

tag: time

value: Day 4


title: Apc SI DZNeP Rep5

value: Female

value: DZNeP 5 mg/kg


title: Apc SI Vehicle Rep4


title: Apc SI Vehicle Rep3


title: Apc SI DZNeP Rep4


title: chorionic villous sampling C1713-750knsp

source_name: chorionic villous sampling C1713

value: chorionic villous sampling

value: isolated increased NT

value: male


title: Apc SI DZNeP Rep3


title: Apc SI DZNeP Rep2


title: Apc SI Vehicle Rep2


title: Sample 81249

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

data_processing:
Fastqc
Map by STAR
Countby HTSeq
Deseq2
Genome_build: Rnor6.0

organism: Rattus norvegicus

source_name: Tongue epithelia

extract_protocol:
Rats were humanely euthanized with an overdose of sodium pentobarbital (i.p.) prior to tissue collection. Tongue epithelium was isolated as previously described (Venkatesan, Boggs, and Liu 2016; Meisel et al. 2020). Briefly, the tongue was resected, washed in cold Tyrode’s solution, then injected with a mixture of 1mg/ml collagenase and 2mg/ml dispase in Tyrode’s solution and incubated for 30-45 minutes until the epithelium showed signs of bebbling (room temp). The anterior portion of the lingual epithelium, where the highest concentration of fungiform papillae are found, was then resected at the margins, peeled off the tongue, and immediately placed in Trizol reagent containing RNAlater (x volume). RNA extraction was performed per the manufacturer's instructions using the Qiagen RNeasy Micro kit (Cat. No. / ID: 74004) with on column DNAse digestion using the RNAse free DNAse set (Cat. No. / ID: 79254).
libraries were prepared using the Nugen Ovation Model organism (Rat #0349-32) with 1/10th ERCC's. These libraries were run on the NextSeq HO 150 cycle.

treatment_protocol: Rats in the water group consumed 23.78 +/- 0.49 grams (mean+/-SEM) of chow/day, while sucrose rats ate 9.106+/- 0.76 grams of chow/day and 71.21 +/- 2.7 grams of sucrose water/day. There was no significant difference in body weight between groups at the end of the study (419.25+/- 9.4 for water vs 440 +/- 15.8 grams for sucrose).

value: adult

value: sucrose


title: Sample 81251


title: Apc SI DZNeP Rep1


title: Sample 81250


title: Sample 81252

value: water


title: Sample 81253


title: Sample 81248


title: Sample 81255


title: Sample 81254


title: Cerco 100 µM, rep3

city: Singapore

first: Eugene

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratories

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).   R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 --cut 3 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to the Arabidopsis thaliana genome (Araport11) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from Araport release), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package.
Genome_build: Araport11
Supplementary_files_format_and_content: normalized abundance measurements and DESeq2 analysis

organism: Arabidopsis thaliana

source_name: WT (Col-0) whole seedlings

growth_protocol: Plants were grown on standing square Petri dishes on 1/2MS + 1% sucrose, pH5.8. Growth room with a 16h light/8h dark cycle, and temperature of 22oC

extract_protocol:
Standard Trizol RNA extraction
Total RNA was eluted with 50ul of UPW and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Plants were equilibrated for at least 1hour in ddw in petri dishes, then sorted into a set of 12-well plates with ddw in preparation for treatment. Samples were shifted from these holding plates to plates containing various concentrations of Cercosporin, and incubated in the dark for 1 h, followed by 3x wash with DDW. The samples were then incubated in the light (30 µE) for 30 min. Control plates remained in the light for the entire time period.

value: 2 week old

tag: ecotype

tag: agent

value: Cercosporin 100 microM


title: Cerco 10 µM, rep1

value: Cercosporin 10 microM


title: Cerco 10 µM, rep3


title: Cerco 100 µM, rep1


title: Cerco 1 µM, rep3

value: Cercosporin 1 microM


title: Cerco 10 µM, rep2


title: Cerco 1 µM, rep2


title: Cerco 1 µM, rep1


title: Cerco 0.1 µM, rep3

value: Cercosporin 0.1 microM


title: Cerco 0.1 µM, rep1


title: Control, rep3


title: Jurkat FLAG-TAL1-long [AVE_LON62_S16]

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

data_processing:
Reads were aligned using BWA to the hg38 genome
Binding sites were identified from two biological replicates using HOMER v4.11.
Peak calling was performed with JURKAT-empty samples as background, using the findPeaks tool on 'factor' mode and fold change ≥2. Otherwise, default parameters were used.
Assembly: hg38
Supplementary files format and content: bed file of TAL1-short peaks

source_name: T-cell

extract_protocol:
9 × 10^6 cells per sample were cross-linked for 10 min in 1% formaldehyde at RT and quenched with 0.1 M glycine. Cells were washed twice with cold PBS and lysed with lysis buffer (0.5% sodium dodecyl sulfate [SDS], 10 mM ethylenediaminetetraacetic acid [EDTA], 50 mM Tris–HCl, pH 8 and 1×protease inhibitor cocktail). DNA was sonicated in an ultrasonic bath (Diagenode, Bioruptor pico) to an average length of 200–250 bp.
ChIP-seq libraries were prepared using the KAPA DNA HyperPrep kit.

value: T-cell

value: Jurkat

value: T lymphoblast

tag: chip antibody

value: Anti-FLAG™ M2 Magnetic Beads


title: Jurkat FLAG-TAL1-long [AVESH_LONG2_S9]

tag: tissue


title: Control, rep2


title: Jurkat FLAG-TAL1-short [AVESH_SHORT2_S8]

tag: cell type


title: Control, rep1


title: Jurkat Empty [AVESH_EMPTY2_S7]

value: Empty


title: Jurkat FLAG-TAL1-short [AVE_SHO52_S15]


title: Exp03-T0-41BBplus

description: time point 0h

source_name: spleen/lymph nodes

value: spleen/lymph nodes

value: CD8+ T cells

value: WT (C57BL/6J)

value: no activation


title: Jurkat Empty [AVE_EMP52_S14]


title: Cerco 100 µM, rep2


title: LT167906LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT167906LL

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

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

value: Male

tag: percent emphysema

tag: pack years

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: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex

value: Multiplex


title: LT212777RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT212777RU

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


title: LT145196LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT145196LU

value: 2-Other Control

value: 3-Don't Know

value: Female

tag: fev1 percent predicted

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

value: FALSE

value: no


title: LT299181LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT299181LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT056464LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT056464LL

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: 2-Lung explant,  bilateral

tag: flow cell


title: LT195192RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT195192RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-Lung explant,  single

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT271679LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT271679LU

tag: cancer status

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: LT203541RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT203541RU

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


title: LT221983RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT221983RM

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: LT128191LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT128191LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT134719RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT134719RU

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

tag: flow cell


title: LT211455LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT211455LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT174536LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT174536LU

tag: cancer status

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: LT238765RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT238765RL

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


title: LT112491RM-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT112491RM

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: LT228897LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT228897LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT119300LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT119300LU

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

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

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

tag: flow cell


title: LT126327LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT126327LU

tag: tissue

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT125521LL-ILD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT125521LL-2

value: 5-Native American

tag: cancer status

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: LT159988RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT159988RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell


title: LT019699RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT019699RL

tag: cancer status

tag: gender

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


title: t20_foursuRNA_rep2

city: Oxford

first: Ilan

last: Davis

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description:
pd_2
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv

data_processing:
Read trimming/adapter removal: For the SENSE total RNA-seq libraries, Cutadapt was used to remove the first 9 nt from read 1, the first 6 nt from read 2, and Illumina adapters. For the QuantSeq libraries, Illumina adpaters and poly(A) sequences were removed from the reads with BBDuk and additional options "k=13 ktrim=r mink=5 qtrim=r trimq=10 minlength=20"
Quantification: Reads were quantified with Kallisto against a index containing both processed transcripts and introns plus 30 nt of flanking sequence. For the SENSE total RNA-seq libraries, the parameters "--rf-stranded" were used and for the QuantSeq libraries, the parameters "-l 1 -s 1 --single --fr-stranded" were used. Gene-level quantification was obtained by summing quantification of individual transcripts.
Modeling: TPM values for exonic and intronic regions of each gene for total RNA and 4-thiouridine-enriched RNA was input into the INSPEcT R package and used to estimate rates of RNA synthesis, processing, and decay.
Assembly: Drosophila melanogaster, Ensembl release 99, assembly BDGP6.28, plus Lexogen SIRV spike-ins and a subset of the ERCC spike-in set.
Supplementary files format and content: *summary_abundance.csv: abundance measurements by gene
Supplementary files format and content: INSPEcT_rates.csv: RNA synthesis, processing, and decay rates calculated by the INSPEcT R package
Supplementary files format and content: BG3_ph_RNAi_summary_abundance: This file corresponds to data from the literature that was reanalyzed (third-party reanalysis) with our pipeline and is discussed in the linked manuscript.

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Drosophila melanogaster wild type strain Oregon-R flies were raised on standard cornmeal-agar medium at 25˚C.

extract_protocol:
Brains were flash frozen in liquid nitrogen after treatment. Brains were homogenized on ice in SEA buffer (50 mM NaOAc, pH 5.2, 10 mM EDTA, 0.3% Sarkosyl) for 20 seconds using a motorized pestle. RNA was then extracted with the hot acid phenol method.
Libraries were constructed using either a random priming approach (SENSE Total RNA-seq, Lexogen, cat# 009) or a poly(A) priming approach (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen, cat# 015).

treatment_protocol: Larval brains were cultured in the presence or absence of 500 µM 4-thiouridine for 0, 20, or 60 min. Culturing was performed in 80% Schneider's medium, 20% FBS, and 10 µg/ml human insulin

tag: tissue

value: larval brain

tag: developmental stage

value: wandering third instar larvae

tag: library type

value: total RNA-seq / SENSE total RNA-seq

tag: strain

value: Oregon-R

tag: treatment

value: 500 µM 4-thiouridine

tag: incubation time

value: 20 min

tag: rna fraction

value: RNA which has been labelled with 4-thiouridine in vivo and purified using the 4-thiouridine as a handle ('newly-synthesized RNA'; technically, not nascent RNA)


title: t20_foursuRNA_rep3

description:
pd_3
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv


title: LT144769RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT144769RL

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

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex

value: Multiplex


title: t20_foursuRNA_rep1

description:
pd_1
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv

tag: tissue

tag: developmental stage

tag: library type

tag: strain

tag: treatment

tag: incubation time

tag: rna fraction


title: Cerco 0.1 µM, rep2

tag: age

value: 2 week old

tag: ecotype

tag: agent

value: Cercosporin 0.1 microM


title: LT128262RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT128262RU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: FALSE

value: no


title: LT107185RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT107185RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 7-Cryptogenic Organizing Pneumonia (COP)

value: 1-White (Caucasian)

tag: age

tag: flow cell

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: t20_totalRNA_rep3

description:
input_3
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv

value: larval brain

tag: developmental stage

value: wandering third instar larvae

tag: library type

value: total RNA-seq / SENSE total RNA-seq

tag: strain

value: Oregon-R

tag: treatment

tag: incubation time

tag: rna fraction

value: total RNA


title: LT229669RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT229669RU

tag: tissue

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT234774LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT234774LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: age

tag: flow cell

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: t20_totalRNA_rep2

description:
input_2
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv

tag: developmental stage

tag: library type

tag: strain

tag: treatment

value: 500 µM 4-thiouridine

tag: incubation time

value: 20 min

tag: rna fraction


title: hiPSC-EC2, siHAS2-AS1

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

data_processing:
Raw Fastq files were uploaded to the cloud based analysis suite, BioJupies, and analyzed using the default parameters
Assembly: not provided
Supplementary files format and content: Raw read counts in processed data file are listed in a tab delimited .txt file

source_name: Cell line

extract_protocol:
Cells were lysed in Trizol, and total RNA extracts were isolated and submitted for sequencing.
Prepared according to manufactures specificaitons

tag: tissue

value: Cell line

tag: cell line

value: iPSC-EC

tag: cell type

value: Endothelial Cell


title: t20_totalRNA_rep1

description:
input_1
brain_4sU_summary_abundance.csv
INSPEcT_rates.csv


title: hiPSC-EC3, siHAS2-AS1


title: LT102695LL-ILD

first: Joshua

last: Campbell

address: 72 East Concord St.

institute: Boston University

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT102695LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

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: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: yes

value: Multiplex


title: LT083491LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT083491LU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 1-White (Caucasian)

value: Male

tag: age

value: 4-Lung biopsy

tag: flow cell

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: hiPSC-EC1, siHAS2-AS1

tag: cell line

tag: cell type

tag: treatment


title: hiPSC-EC2, siControl

value: siControl


title: LT265662LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT265662LU

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: lane

tag: index

tag: total reads


title: LT195522RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT195522RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 7-Cryptogenic Organizing Pneumonia (COP)

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

tag: age

tag: flow cell

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT059865RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT059865RU

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: TRUE


title: hiPSC-EC1, siControl

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: hiPSC-EC3, SUN, 72Hr [SUN 3]

tag: genotype

value: SUN 3

value: SUN

tag: time

value: 72 hours


title: hiPSC-EC3, siControl

value: Cell line

value: iPSC-EC

value: Endothelial Cell


title: LT070403LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT070403LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: age

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: protocol

tag: multiplex


title: LT089451RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT089451RU

tag: tissue

tag: race

tag: cancer status

tag: gender

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: FALSE

value: no

value: Multiplex


title: hiPSC-EC2, DMSO, 72Hr [Control 2]

tag: cell line

tag: cell type

tag: genotype

value: Control 2

tag: treatment

value: DMSO

tag: time


title: LT148377LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT148377LU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 1-White (Caucasian)

value: Male

tag: age

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

value: yes

tag: protocol

tag: multiplex


title: LT188161LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT188161LL

tag: tissue

tag: race

tag: cancer status

tag: gender

value: Female

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

value: TRUE


title: hiPSC-EC1, DMSO, 72Hr [Control 1]

tag: cell line

tag: cell type

tag: genotype

value: Control 1

tag: treatment

tag: time

value: 72 hours


title: LT184423LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT184423LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: age

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

tag: multiplex


title: hiPSC-EC3, DMSO, 72Hr [Control 3]

tag: tissue

value: Cell line

tag: cell line

value: iPSC-EC

tag: cell type

tag: genotype

value: Control 3

tag: treatment

tag: time


title: LT100821RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT100821RL

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: 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: flow cell


title: LT290677RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT290677RU

tag: tissue

value: 2-Other Control

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

tag: multiplex


title: LT112597RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT112597RU

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: pack years

tag: fev1 percent predicted

value: Multiplex


title: LT111916LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT111916LL

tag: tissue

value: 7-Cryptogenic Organizing Pneumonia (COP)

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: LT022562LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT022562LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

value: 1-Lung explant,  single

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LILP_TMDI_2

city: Geneva

first: Liqing

last: Cheng

address: 1 rue Michel-Servet 1

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)

source_name: large intestine lamina propria

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

tag: tissue

value: large intestine lamina propria

tag: cell type

value: transferred CD45.1+CD8+ OTI T cells

tag: genotype

value: WT

tag: Sex

tag: treatment

value: Lm-OVA infection in recipient mice


title: LILP_control_1

value: Female


title: LILP_TMDI_1


title: CHH2430

city: Farmington

first: Oscar

middle: J.

last: Luo

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

description: Technical replicate

data_processing:
Library strategy: RICh-PET
Basecalls and demultiplexing performed using CASAVA version 1.8.
PET reads from all three sequenced libraries were combined into one dataset.
PET reads were first filtered and trimmed for linker barcodes to identify the DNA sequence tag and RNA sequence tag, then mapped to the reference genome by BatMis. Only uniquely mapped reads on both ends were retained.
Redundant reads were removed. Then PET reads mapping location were extended 500bp upstream on both the DNA and RNA tags for downstream analysis. See the Supplemental information of the paper for detailed data processing procedures.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file documenting the DNA and RNA tag genomic mapping location after 500bp extension.

source_name: HeLa S3

extract_protocol: Approximately 10^8 HeLa S3 cells were subjected to dual-crosslinking with 1% formaldehyde and 1.5 mM EGS. Cells were harvested and lysed. Complexes of lncRNA-chromatin with protein were sheared to fragments of approximately 500 bp, which then were biotinylated with EZlink Iodoacetyl-PEG2-Biotin (IPB). The streptavidin beads-bound lncRNA-chromatin-protein complexes were subjected to RICh-PET library construction. The DNA fragments present in streptavidin beads-bound chromatin were end-repaired using T4 DNA polymerase. The chromatin complexes were split into two aliquots, followed by the addition of RNA linkers with different barcode sets modified with biotin and containing flanking MmeI restriction sites, RNA linker “R1” (tube1) and RNA linker “R2” (tube2). Linkers to the RNA end were annealed, first-strand cDNA was synthesized, and relative DNA linkers “D1” (tube 1) and DNA linker “D2” (tube 2) were ligated. The two tubes were mixed together for proximity ligation. Chromatin-associated RNA fragments with linkers were subjected to second-strand cDNA synthesis. The cDNA-DNA PETs were extracted from the ligation products by MmeI digestion. Released biotinylated PETs were purified by streptavidin-coated magnetic beads, ligated to adaptors, and scaled up by PCR. Gel-purified amplicons of PET templates were sequenced using an Illumina® HiSeq 2500 with paired-end sequencing.

tag: cell line

value: HeLa S3


title: mLN_TMDI_2

source_name: mesenteric lymph node

value: mesenteric lymph node


title: LT158647RU-COPD

city: Boston

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT158647RU

tag: ltrc id

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

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: TRUE

value: yes


title: JCHH2430

description: Technical replicate

tag: cell line


title: hiPSC-EC2, SUN, 72Hr [SUN 2]

tag: tissue

value: Cell line

value: iPSC-EC

tag: cell type

value: Endothelial Cell

tag: genotype

value: SUN 2

tag: treatment

value: SUN

tag: time

value: 72 hours


title: LT244824RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT244824RU

value: lung

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: pack years

tag: fev1 percent predicted

value: 4-Lung biopsy

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: LT168094RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT168094RL

tag: tissue

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

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: mLN_TMDI_1

tag: cell type

value: transferred CD45.1+CD8+ OTI T cells

tag: genotype

value: WT

tag: Sex

tag: treatment

value: Lm-OVA infection in recipient mice


title: hiPSC-EC1, SUN, 72Hr [SUN 1]

tag: cell line

value: SUN 1

tag: time


title: LT199987LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT199987LU

tag: tissue

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: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: mLN_control_2

tag: tissue

value: mesenteric lymph node

tag: cell type

tag: genotype

tag: Sex

tag: treatment


title: LT147658RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT147658RU

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: yes


title: mLN_control_1

tag: tissue

tag: cell type

tag: genotype

tag: Sex


title: LT134776LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT134776LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: cancer status

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: naïve_2

source_name: Spleen

tag: tissue

value: Spleen

tag: cell type

value: CD8+ T cells from spleen of OTI mouse

tag: treatment

value: no


title: JCHH2431

description: Biological replicate

tag: cell line

value: HeLa S3


title: LT123131RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT123131RL

value: lung

tag: ltrc id

tag: disease

tag: smoking status

tag: race

value: 1-White (Caucasian)

value: Male

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: total reads aligned mirna


title: LT264690LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT264690LU

tag: tissue

tag: minor diagnosis

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

value: 4-Lung biopsy

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex

value: Multiplex


title: LT118519RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT118519RL

tag: ltrc id

tag: disease

value: 4-Desquamative interstitial pneumonia (DIP)

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index


title: LILP_control_2

tag: tissue

value: large intestine lamina propria

tag: cell type

value: transferred CD45.1+CD8+ OTI T cells

tag: genotype

value: WT

tag: Sex

tag: treatment

value: Lm-OVA infection in recipient mice


title: LT050246RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT050246RU

tag: minor diagnosis

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: LT046103LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT046103LU

tag: tissue

tag: ltrc id

tag: disease

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

value: yes


title: LT236557RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT236557RL

tag: minor diagnosis

value: 2-Other Control

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT217339RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT217339RL

tag: tissue

tag: ltrc id

tag: disease

tag: smoking status

tag: race

tag: fev1 fvc ratio

tag: bode score

value: 3-Lung lobectomy/wedge resection

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT160089RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT160089RU

tag: minor diagnosis

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index


title: LT228772LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT228772LL

tag: tissue

value: lung

tag: ltrc id

tag: disease

value: 9-Hypersensitive Pneumonitis (HP)

tag: smoking status

tag: race

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate


title: LT084038RM-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT084038RM

tag: minor diagnosis

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

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

tag: bode score

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: MRX367

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)

tag: tissue

value: Liver

tag: Sex

value: male

tag: strain

tag: diet

value: RF

tag: dietary fat content

value: Ctrl


title: MRX366

value: HF

value: SAAR


title: MRX372


title: MRX371


title: MRX369


title: MRX370