title: LT005256RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT005256RL

tag: ltrc id

tag: disease

tag: minor diagnosis

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

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: FALSE

tag: included

value: no

tag: protocol


title: PSC31

status: Public on Apr 30 2023

type: SRA

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

country: USA

institute: University of Chicago

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Colonic biopsy

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

tag: diagnosis

value: PSC- no IBD

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: LT115840LL-Control

city: Boston

first: Joshua

middle: David

last: Campbell

state: MA

address: 72 East Concord St.

institute: Boston University

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT115840LL

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

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

value: 2-Other Control

tag: smoking status

value: 1-White (Caucasian)

tag: pack years

tag: fev1 percent predicted

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

value: TRUE

value: yes

tag: multiplex

value: Multiplex


title: IBD23

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: IBD13

tag: tissue


title: LT082461RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT082461RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: 4-Lung biopsy

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT151920RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT151920RL

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

value: Male

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: PSC30

tag: diagnosis

value: PSC-Indeterminate Colitis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: PSC27

value: PSC-UC


title: LT203431RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT203431RL

tag: ltrc id

tag: disease

tag: minor diagnosis

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

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: FALSE

tag: included

value: no

tag: protocol


title: LT089723LL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT089723LL

value: lung

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: PSC32

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: LT147610LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT147610LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

value: Multiplex


title: LT075917RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT075917RU

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: PSC01

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT009099RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT009099RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: 3-Lung lobectomy/wedge resection

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: IBD22

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: PSC23

value: Yes

tag: tissue


title: IBD27


title: LT195484RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT195484RU

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

value: Female

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: IBD14

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: LT030662LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT030662LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

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

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

value: 4-Lung biopsy

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: NC12

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now


title: NC10

tag: dys broad location

tag: tissue


title: LT207073RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT207073RU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: Male

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: LT191020LI-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT191020LI

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: IBD11

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: IBD12


title: LT236045LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT236045LL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 1-White (Caucasian)

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

value: TRUE

tag: multiplex


title: LT280560LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT280560LU

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

value: yes

tag: protocol

value: Multiplex


title: LT140046RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT140046RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: 3-Don't Know

tag: pack years

tag: fev1 percent predicted

tag: bode score

tag: dlco

tag: tissue type

value: 3-Lung lobectomy/wedge resection

tag: flow cell


title: LT233620RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT233620RU

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: fev1 fvc ratio

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: multiplex


title: LT056301LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT056301LL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: pack years

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: NC05

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: IBD10

value: Crohn's

value: IBD


title: IBD09

value: Indefinite

value: L


title: LT241811LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT241811LL

value: 2-Other Control

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

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


title: NC04

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

tag: tissue


title: NC11

tag: dys broad location


title: LT084406RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT084406RU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT192758RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT192758RU

tag: tissue

value: Male

tag: percent emphysema

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


title: LT287158LU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT287158LU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: pack years

value: 4-Lung biopsy

tag: total reads aligned mirna

tag: replicate


title: IBD03

tag: diagnosis

value: UC

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: PSC08

value: PSC-Crohn's

value: PSC


title: PSC14


title: LT081282RM-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT081282RM

value: 1-White (Caucasian)

value: 3-Don't Know

tag: percent emphysema

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: qc pass

value: TRUE

tag: included

value: yes

tag: protocol

tag: multiplex

value: Multiplex


title: NC03

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: LT081077RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT081077RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

value: 3-Lung lobectomy/wedge resection

tag: total reads aligned mirna

tag: replicate


title: LT000216LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT000216LL

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT004173LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT004173LL

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: 1-Lung explant,  single


title: PSC09

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: PSC06

value: PSC-UC


title: NC02

value: NC


title: LT020426LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT020426LU

value: lung

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT002501RL-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT002501RL

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

tag: multiplex


title: PSC11

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: PSC70


title: PSC03


title: LT195011RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT195011RL

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

tag: fev1 percent predicted

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

tag: replicate

tag: qc pass

tag: included

tag: protocol


title: LT286056RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT286056RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

tag: multiplex


title: LT046539RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT046539RL

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


title: PSC78

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: IBD48

value: UC

value: IBD


title: NC28


title: LT105618RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT105618RL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 4-Desquamative interstitial pneumonia (DIP)

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: LT025997RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT025997RU

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

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: yes

value: Multiplex


title: PSC42

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT130350RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT130350RU

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: IBD31

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location


title: IBD66

tag: tissue


title: NC43

value: NC


title: LT038591LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT038591LU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

value: Female

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT093297LU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT093297LU

value: 2-Other Control

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT139649RU-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT139649RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell


title: LT156481LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT156481LL

tag: race

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: NC25

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: NC49

value: Yes


title: LT173946RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT173946RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: IBD02

tag: diagnosis

value: UC

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location


title: LT175399RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT175399RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: race

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

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

value: TRUE


title: Donor 5 Vehicle

type: RNA

city: Rochester

first: Adebowale

last: Bamidele

state: Minnesota

address: Medicine, 200 First Street SW, Guggenheim 10

department: Medicine

institute: Mayo Clinic

description:
Control
SAMPLE 5

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their MS Excel-based analysis tool: https://www.arraystar.com/nurna-central-metabolism-pcr-array/
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GUSB, HSP90AB1, 18S
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: naïve CD4 T cells

label_protocol: PCR assays were performed using  NuRNA Human Central Metabolism PCR Array (RNA ARRAYSTAR INC: Roche Light Cycler 480) according to manufacturers’ instructions. Reverse transcription was performed rtSTARTM First-Strand cDNA Synthesis Kit and subjected to Arraystar SYBR Green Real-time qPCR Master Mix.

growth_protocol: Human naive cells were differentiated into iTregs in cRPMI 1640 media (RPMI 1640 + L-Glutamine [Gibco] supplemented with 10% FCS, 10 mmol/L HEPES pH 7.4, 1 mmol/L sodium pyruvate, 2 mmol/L L-glutamine, 1% non-essential amino acids, penicillin, streptomycin, and 50 µmol/L β-mercaptoethanol)

extract_protocol: Total RNA was extracted with Rneasy Plus Mini Kit (Qiagen).

tag: individual

value: Donor 5

tag: cell type

value: Induced Tregs

tag: treatment

value: Vehicle

tag: time


title: NC46

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

value: L

tag: tissue


title: LT275526RU-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT275526RU

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: age

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

tag: flow cell

tag: replicate

tag: qc pass

tag: included

value: yes

tag: protocol

tag: multiplex

value: Multiplex


title: Donor 5 IL-21

description:
Test
SAMPLE 6

tag: individual

tag: cell type

tag: treatment

tag: time


title: LT245084RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT245084RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

value: 3-Don't Know

tag: gender

tag: percent emphysema

tag: pack years

value: 3-Lung lobectomy/wedge resection

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: IBD56

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

value: No

tag: dys broad location

value: Colonic biopsy


title: PSC82

value: PSC-UC

value: PSC

tag: tissue


title: Donor 4 IL-21

description:
Test
SAMPLE 4

tag: individual

value: Donor 4

tag: cell type

tag: treatment

tag: time


title: Donor 2 IL-21

description:
Test
SAMPLE 2

value: Donor 2


title: Donor 4 Vehicle

description:
Control
SAMPLE 3


title: Donor 2 Vehicle

description:
Control
SAMPLE 1


title: LT001600RL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT001600RL

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

tag: age

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 2-Lung explant,  bilateral

tag: flow cell

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: syn_gRNA_NTC-rep3

city: AARHUS C

first: Karim

last: Rahimi

address: C.F. Møllers Allé 3

country: Denmark

institute: Aarhus University

description: Cas13.design1_gtsgRNA_KDsgRNA_NTC.DESeq2.mRNA.txt

data_processing:
Filtering and trimming of mRNA-sequencing reads was performed using trim_galore (version 0.6.5dev). The processed reads were mapped to the human reference genome (hg19) using STAR (version 2.7.3a)(Dobin et al., 2013) with default settings. The mapped reads were then quantified per gene annotation using featureCounts (Liao, Smyth and Shi, 2014) with gene annotation from Gencode (version 28). Differential expression analysis (DEA) was based on the featureCounts count data using DESeq2 (Love, Huber and Anders, 2014) in R (http://www.r-project.org).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited DESeq2 output text files include raw and normalized counts, gene annotation info, and statistics

molecule: polyA RNA

source_name: Neuroblastoma SH-SY5Y cells

growth_protocol: SH-SY5Y cells were maintained in Dulbecco’s modified Eagle’s media (DMEM/F12) (Invitrogen, GIBCO, MA, USA) supplemented with 10% fetal bovine serum (FBS; Invitrogen, GIBCO, MA, USA) and 1% Penicillin-Streptomycin (P/S) (Thermo Fisher Scientific, MA, USA). The cells were passaged before reaching 90% confluency using 0.05% trypsin (Thermo Fisher Scientific). Cells were cultured at 37°C and 5% CO2.

extract_protocol:
RNA extraction was started by lysing the cells in TRIzol reagent (Invitrogen) and followed by the usage of Direct-zol RNA Miniprep Kit (ZYMO RESEARCH, CA, USA) according to the manufacturer’s instructions including DNase on-column treatment for 15 min at room temperature. RNA concentrations and purity were determined using Nanodrop Lite (Thermo Fisher Scientific).
RNA concentrations were measured using the Qubit RNA HS Assay Kit (Thermo Fisher  Scientific) on a Qubit 4 Fluorometer (Thermo Fisher Scientific), as well as using Nanodrop Lite (Thermo Fisher Scientific). RNA quality was checked using Agilent Bioanalyzer 2100 (Agilent Technologies) and all RNA integrity (RIN) values exceeded 8.0. Library preparation, and poly(A) RNA sequencing was performed by Beijing Genomics Institute (BGI) in Copenhagen. Briefly, 1 mg total RNA input was used. Non-stranded and polyA-selected RNA library preparation was applied and PE100 sequencing was performed following the specific protocol for sequencing on a DNBSEQ sequencing platform (MGI, Shenzhen, China). Library size and purity control was performed on a Agilent 2100 Bioanalyzer (Agilent Technologies) using a High-Sensitivity DNA-Chip.

treatment_protocol: SH-SY5Y cells were transfected at a confluency of 70-80%. For CasRx experiments, the pcDNA3_CasRx-GFP vector (2 mg per 6-well) was co-transfected with either pre-gRNA or gRNA expression plasmids (1 mg per 6-well) using Lipofectamine 3000 kit (5 ml Lipo 3000 and 5 ml P3000 reagents per 6-well; Thermo Fisher Scientific) according to the manufacturer’s guidelines. AgoshRNA expression vectors (2.5 mg per 6-well) were transfected using Lipofectamine 3000 kit (7.5 ml Lipo 3000 and 5 ml P3000 reagents per 6-well; Thermo Fisher Scientific) according to the manufacturer’s instruction. After overnight incubation with the transfection reagents, a media change with fresh DMEM/F12 media (10%FBS, 1%P/S) was performed. RNA samples were harvested 48 hours post-transfection.

tag: cell line

tag: cell type

value: Neuroblastoma cell

tag: treatment


title: IBD95

tag: diagnosis

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue


title: PSC81

value: PSC-Crohn's


title: syn_gRNA_NTC-rep2


title: LT059975LU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT059975LU

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: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna


title: LT156171LL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT156171LL

tag: tissue

tag: ltrc id

tag: disease

value: 2-Other Control

value: 3-Don't Know

value: Male

tag: dlco

tag: tissue type

tag: flow cell

tag: replicate

tag: qc pass

tag: included

value: yes

tag: protocol

tag: multiplex

value: Multiplex


title: LT131432RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT131432RU

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

value: 3-Lung lobectomy/wedge resection


title: IBD94

tag: diagnosis

value: Indeterminate Colitis

tag: broad diagnosis

tag: dysplasia now

value: Yes

tag: dys broad location

value: R

tag: tissue

value: Colonic biopsy


title: syn_gRNA_NTC-rep1

tag: cell line

tag: cell type

value: Neuroblastoma cell

tag: treatment


title: syn_gRNA_CDR1as_KD-rep3


title: LT155982RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT155982RU

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

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

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: PSC79

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: No

tag: dys broad location

tag: tissue


title: syn_gRNA_CDR1as_KD-rep2

tag: cell line

tag: cell type

tag: treatment


title: LT109097LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT109097LL

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

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

tag: smoking status

tag: race

value: 1-White (Caucasian)

tag: cancer status

tag: gender

tag: age

tag: percent emphysema

tag: pack years

tag: fev1 percent predicted

tag: fev1 fvc ratio

tag: bode score

tag: dlco

tag: tissue type

value: 4-Lung biopsy

tag: flow cell

tag: lane

tag: index


title: NC14

tag: diagnosis

value: NC

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: syn_gRNA_CDR1as_KD-rep1

tag: cell line

tag: cell type

tag: treatment


title: LT163513RL-Control

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT163513RL

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Female

tag: age

tag: percent emphysema

tag: pack years

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

value: Multiplex


title: pre-gRNA_NTC-rep3

description: Cas13.design1_gtpregRNA_KDpregRNA_NTC.DESeq2.mRNA.txt

tag: cell line

tag: cell type

tag: treatment


title: IBD60

tag: diagnosis

value: UC

tag: broad diagnosis

value: IBD

tag: dysplasia now

value: Yes

tag: dys broad location

value: L

tag: tissue


title: LT135390LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT135390LL

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: 1-Lung explant,  single

tag: flow cell

tag: lane

tag: index

value: TRUE


title: NC13

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: IBD52

value: No


title: pre-gRNA_NTC-rep2

tag: cell line

tag: cell type

value: Neuroblastoma cell

tag: treatment


title: pre-gRNA_NTC-rep1


title: IBD50


title: LT291578RU-COPD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT291578RU_HiSeq

value: lung

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: Male

tag: age

tag: percent emphysema

tag: pack years

value: 2-Lung explant,  bilateral

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

value: no

tag: protocol

tag: multiplex

value: Singleplex


title: IBD43

tag: diagnosis

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: pre-gRNA_CDR1as_KD-rep3

tag: cell line

tag: cell type

tag: treatment


title: LT201348LL-ILD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT201348LL

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: 4-Lung biopsy

tag: flow cell

tag: lane

tag: index

value: FALSE


title: LT185066RL-ILD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT185066RL_HiSeq

tag: tissue

tag: ltrc id

tag: disease

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

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: LT157253RL-ILD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT157253RL_HiSeq

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

value: 3-Lung lobectomy/wedge resection


title: PSC25

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: dys broad location

tag: tissue


title: pre-gRNA_CDR1as_KD-rep2

tag: cell line

tag: cell type

tag: treatment


title: PSC47

value: Yes

value: R


title: LT024952RU-COPD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT024952RU_HiSeq

tag: ltrc id

tag: disease

tag: minor diagnosis

tag: smoking status

tag: race

tag: dlco

tag: tissue type

tag: flow cell

tag: lane

tag: index

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

value: TRUE

tag: included

tag: protocol

tag: multiplex


title: pre-gRNA_CDR1as_KD-rep1

tag: cell line

tag: cell type

value: Neuroblastoma cell

tag: treatment


title: gRNA_NTC-rep3

description: Cas13.design1_gtgRNA_KDgRNA_NTC.DESeq2.mRNA.txt


title: IBD92

tag: diagnosis

value: UC

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: gRNA_NTC-rep2


title: NC52

value: NC

value: No


title: LT211728RU-COPD-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT211728RU_HiSeq

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: 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

value: no

value: Singleplex


title: IBD58

tag: diagnosis

value: Crohn's

tag: broad diagnosis

tag: dysplasia now

tag: dys broad location

tag: tissue


title: LT046027RL-Control-Replicate

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT046027RL_HiSeq

tag: ltrc id

tag: disease

tag: minor diagnosis

value: 2-Other Control

tag: smoking status

tag: race

tag: cancer status

tag: gender

value: 3-Lung lobectomy/wedge resection

tag: total reads

tag: total reads aligned

tag: total reads aligned mirna

tag: replicate

tag: qc pass

tag: included

tag: protocol

tag: multiplex


title: PSC65

tag: diagnosis

value: PSC-UC

tag: broad diagnosis

value: PSC

tag: dysplasia now

tag: dys broad location


title: LT045346RU-COPD

description:
microRNA_raw_counts.txt.gz
microRNA_normalized.txt.gz
LT045346RU

tag: tissue

tag: ltrc id

tag: disease

tag: minor diagnosis

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

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

value: TRUE

value: yes

value: Multiplex


title: gRNA_NTC-rep1

tag: cell line

tag: cell type

value: Neuroblastoma cell

tag: treatment


title: IBD79

tag: diagnosis

value: UC

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: gRNA_CDR1as_KD-rep2


title: NC24

value: NC

value: No


title: gRNA_CDR1as_KD-rep1


title: AgoshRNA_NTC-rep3

description: Cas13.design1_gtagosh_KDagosh_NTC.DESeq2.mRNA.txt


title: AgoshRNA_NTC-rep2


title: IBD35


title: BPE7 RNA-seq EpCAM low

city: Basel

first: Massimo

last: Saini

state: Basel Canton

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description:
Effusion Patient 1 (BPE7) sorted EpCAM-low fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx

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.

value: breast cancer cells

tag: individual

value: Patient 1 (ER-)

value: no treatments


title: BPE7 RNA-seq EpCAM neg

description:
Effusion Patient 1 (BPE7) sorted EpCAM-neg fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx


title: BPE22 RNA-seq EpCAM neg

description:
Effusion Patient 6 (BPE22) sorted EpCAM-neg fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx

value: Patient 6 (ER+)


title: BPE7 RNA-seq  EpCAM high

description:
Effusion Patient 1 (BPE7) sorted EpCAM-high fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx


title: PSC76

value: PSC-Crohn's


title: IBD77


title: BPE22 RNA-seq EpCAM low-neg

description:
Effusion Patient 6 (BPE22) sorted EpCAM-low/neg fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx


title: BPE22 RNA-seq EpCAM high

description:
Effusion Patient 6 (BPE22) sorted EpCAM-high fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx


title: PSC66

value: PSC-UC


title: AgoshRNA_CDR1as_KD-rep3


title: IBD29

value: Crohn's


title: BPE22 RNA-seq EpCAM low

description:
Effusion Patient 6 (BPE22) sorted EpCAM-low fraction
RNA-seq_primary breast cancer cells_raw_counts.xlsx


title: AgoshRNA_NTC-rep1


title: AgoshRNA_CDR1as_KD-rep2


title: PSC62

value: PSC


title: AgoshRNA_CDR1as_KD-rep1


title: 16IC_7391

city: Montreal

first: Sherif

middle: Samer

last: Attalla

state: Quebec

address: 1160 Ave. Pine W

department: Goodman Cancer Institute

country: Canada

institute: McGill

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were trimmed using Trimmomatic (Bolger et al., 2014)
Reads were aligned to the GRCm38 mouse reference genome assembly using STAR (Dobin et al., 2012)
Read counts were obtained using HTSeq (Anders et al., 2015) with parameters -m intersection-nonempty -stranded=no
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015)
To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’slmfit function(method="robust" parameter was applied for end-stage tumor dataset)
Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method
Distinct patterns of gene expression changes were identified using unsupervised hierarchical clustering method (R function hclust with Euclidean distance and complete linkage metrics)
Assembly: GrCM38/mm10
Supplementary files format and content: A tab-delimited text files includes RPKM values for all samples.

organism: Mus musculus

source_name: Mammary

growth_protocol: Cells grown in 10% FBS DMEM supplemented with EGF, Insulin and pitutary extract as described in Attalla et al, 2023. Cells either maintained with Doxycycline (Dox) 10ug/mL

extract_protocol:
Qiagen RNEasy Mini kit was used according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II Library Prep Kit following manufacturer's protocols.

tag: strain

value: FVB/N

tag: Sex

value: Female

value: Mammary

value: 16IC Cell line

tag: genotype

value: Doxycyline (10ug/mL)


title: IBD78

value: IBD


title: gRNA_CDR1as_KD-rep3

value: Neuroblastoma cell


title: 16IC_1984


title: NC20

value: NC

value: Colonic biopsy


title: EIC_7559

value: EIC Cell line

value: EIC/WT


title: PSC57

value: No


title: liver-SIRT2-KOhep-2

city: Shanghai

first: qinghua

last: zhao

address: No. 100, Hai Ning Road

department: Department of Orthopedics

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The data obtained by sequencing is called raw reads or raw data, and then quality control (QC) is performed on raw reads.
After passing the quality control, compare the filtered clean reads to the reference genome.
After the comparison is completed, it is judged whether the comparison result has passed the second quality control (QC of alignment) by statistical comparison rate and the distribution of reads on the reference sequence.
If it passes, quantitative gene analysis and various analyses based on gene expression level will be conducted.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was processed using mRNA enrichment or rRNA removal methods.
1.Fragmentation of the obtained RNA using an interrupt buffer, reverse transcription with random N6 primers, and synthesis of cDNA double stranded DNA. 2.The ends of the synthesized double stranded DNA were flattened and phosphorylated at the 5 'end, forming a sticky end protruding from an "A" at the 3' end, and then connected to a bubbly junction with a protruding "T" at the 3 'end. 3.The connecting products were amplified by PCR using specific primers. 4.The PCR product was thermally denatured into a single strand, and then cyclized with a bridge primer to obtain a single stranded circular DNA library. The ends of the synthesized double stranded DNA were flattened and phosphorylated at the 5 'end, forming a sticky end protruding from an "A" at the 3' end, and then connected to a bubbly junction with a protruding "T" at the 3 'end. The connecting products were amplified by PCR using specific primers. The PCR product was thermally denatured into a single strand, and then cyclized with a bridge primer to obtain a single stranded circular DNA library.

tag: strain background

value: KO

value: liver


title: liver-SIRT2-KOhep-3


title: IBD73

value: UC


title: liver-Loxp-3

value: WT


title: EIC_4026


title: PSC49

value: PSC-Crohn's

value: PSC


title: liver-Loxp-2


title: liver-SIRT2-KOhep-1


title: EIC_NT

value: FVB/N

value: Female


title: IBD38


title: PSC75

value: Yes

value: R


title: Tumor 3 Doxorubicin/GTN

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

data_processing:
paired-end reads from  FASTQ file were aligned using STAR aligner version 2.6.0a
RSEM version 168 1.3.0 (19) to estimate TPM (Transcripts per million) and raw read counts
differential analysis using DESeq2 R library
Assembly: GRCm38
Supplementary files format and content: count data file: Count_mabrouk.csv

source_name: 4T1 murine colorectal carcinoma cell line

extract_protocol:
4T1 solid tumors were removed at day 16, flash frozen on liquid nitrogen and RNA was harvested using Trizol reagent. BGIseq500 sequencing system was used.
Sequencing, data quality, and reds repartition were performed by BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: 4T1-bearing mice (500 000 4T1 cells in s.c) were treated or not (Nacl, i.p.) with GTN (5 mg/kg, s.c.) 3 times a week (start day 1) and/or doxorubicin (8 mg/kg, i.p.) once a week (start day 8)

value: tumor

value: Balb/c

tag: tumor stage

value: 16 days after 4T1 injection


title: NC44

value: NC

value: L

value: Colonic biopsy


title: Tumor 2 Doxorubicin/GTN


title: liver-Loxp-1


title: IBD47

value: Crohn's

value: IBD

value: No


title: Tumors from 16IC mouse [IC167476]

source_name: Tumors from 16IC mouse

value: Mammary Tumor

value: Doxycyline (2mg/ml)


title: Tumors from 16IC mouse [IC165484]


title: Tumor 1 Doxorubicin/GTN


title: Tumors from 16IC mouse [IC165273]


title: 16IC_4982

value: Mammary

value: 16IC Cell line

value: Doxycyline (10ug/mL)


title: Tumors from 16IC mouse [IC164476]

value: FVB/N

value: Female


title: KIRA_RSV4 [RNASeq]

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description: KIRA+RSV infected bioreplicate4

data_processing:
Trimmomatic was used to process raw fastq files and QC statistics.
The trimmed paired-end reads were aligned against human genome hg38 using Salmon 1.3
Mapped paired-end reads for both genes and transcripts (isoforms) were counted in each sample using RNA-Seq by Expectation Maximization (RSEM).
Contrasts were compared for genotypes and treatment conditions using DESeq2
Assembly: hg38
Supplementary files format and content: master_annotated_abundance.xls
Supplementary files format and content: tab deliminted file of transcript abundance by treatment type

source_name: Lung

growth_protocol: Immortalized primary hSAECs were obtained from commercial repository and grown in SAGM small airway epithelial cell growth medium (Lonza, Walkersville, MD, USA) in 5% CO2.

extract_protocol: 4 x 10^6 trypsinized cells were aliquoted and incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 minutes at 4 oC. A basic wash buffer (WB) consisting of 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-1000, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine was used throughout. Between incubation steps, the nuclei were pelleted at 600x g, 3 minutes at 4 oC. Prior to antibody binding, the isolated nuclei were incubated with nutation at 4 oC for 5 minutes in WB containing 2 mM EDTA, followed by nutation at 4 oC for 25 minutes in WB. The nuclei were resuspended in antibody buffer produced by diluting 5 mg of FLAG-M2 in 500 ml of Triton X-100-free WB, and incubated with nutation overnight at 4 oC.  After washing three times in 500 ml of WB on ice (10 minutes each time), the nuclei were incubated at 4 oC for 1 h in 50 ml of WB containing 2.5 ml of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Washing as above, targeted chromatin cleavage was then conducted by incubating the nuclei on ice for 1 h in 150 ml of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 ml of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 ml).  The samples were further incubated with nutation at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. Phenol-chloroform DNA precipitation with 80 mg of glycogen was performed and the Cut&Run-enriched DNA was dissolved in 20 ml of 0.1x TE buffer. Following DNA quantitation by a Qubit fluorometer, Cut&Run DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments (down to ~170 bp in post-library amplification size). The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilend, CA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

treatment_protocol: Sucrose cushion purified RSV Long was prepared and tittered using methylcellulose plaque assay.  hSAECs were treated in triplicate replicates with or without RSV infection (MOI = 1.0, 24 h).

value: Lung

value: hSAEC

value: lung epithelial

value: KIRA+RSV infected


title: Tumors from 16IC mouse [IC163207]


title: KIRA_RSV3 [RNASeq]

description: KIRA+RSV infected bioreplicate3


title: PSC60

value: PSC-UC

value: PSC


title: KIRA_RSV2 [RNASeq]

description: KIRA+RSV infected bioreplicate2


title: Tumor 3 GTN

value: tumor

value: Balb/c

value: 16 days after 4T1 injection


title: Tumors from EIC mouse [EIC7799]

source_name: Tumors from EIC mouse

value: EIC/WT


title: IBD53

value: UC

value: IBD

value: No

value: Colonic biopsy


title: Tumor 2 GTN


title: Tumors from EIC mouse [EIC7670]

value: Mammary Tumor

value: Doxycyline (2mg/ml)


title: PSC64


title: Tumors from EIC mouse [EIC6017]

value: FVB/N

value: Female


title: RSV4 [RNASeq]

description: RSV infected bioreplicate 4

value: Lung

value: hSAEC

value: RSV infected


title: Tumor 1 GTN


title: KIRA_RSV1 [RNASeq]

description: KIRA+RSV infected bioreplicate1

value: lung epithelial

value: KIRA+RSV infected


title: PSC28

value: PSC-Crohn's

value: PSC


title: Tumor 3 Doxorubicin

value: tumor

value: Balb/c

value: 16 days after 4T1 injection


title: RSV3 [RNASeq]

description: RSV infected bioreplicate 3


title: IBD34

value: UC

value: IBD


title: RSV2 [RNASeq]

description: RSV infected bioreplicate 2


title: Tumors from EIC mouse [EIC5527]

value: EIC/WT


title: Tumors from EIC mouse [EIC6011]

value: Mammary Tumor


title: IBD61

value: No

value: Colonic biopsy


title: PSC59

value: PSC-UC


title: CON4 [RNASeq]

description: control bio replicate 4

value: Lung

value: control


title: SJMHE1_RNA

city: Zhenjiang

first: Xuerong

last: Gao

address: No.438, Jiefang Road, Jingkou District, Zhenjiang City, Jiangsu Province

institute: Jiangsu Univercity

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: Genome_build: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

source_name: spleen B cells

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each mice sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: Six week female BALB/c mice were randomly divided into three groups: Control, PBS, and SJMHE1. Mice in the PBS, and SJMHE1 groups sensitized with OVA (10 μg) and 2 mg of Al(OH)3 in 200 μl PBS intraperitoneally on days 0, 7 and 14. Subsequently, the mice were challenged intranasally with OVA (100 µg) on days 21–27 and 29-35. On days 0, 14 and 28, mice in PBS,and SJMHE1 groups were separately treated with PBS, and SJMHE1 (10µg).All mice are sacrificed on day 36 and spleen B cells are collected.

value: spleen B cells

value: female

tag: age

value: 13 weeks old


title: PBS_RNA


title: Tumor 2 Doxorubicin


title: RSV1 [RNASeq]

description: RSV infected bioreplicate 1

value: hSAEC

value: lung epithelial

value: RSV infected


title: Tumor 2 NaCl

value: tumor

value: Balb/c


title: PSC34

value: PSC- no IBD

value: PSC


title: control_RNA


title: NC22

value: NC


title: Tumor 3 NaCl

value: 16 days after 4T1 injection


title: CON3 [RNASeq]

description: control bio replicate 3


title: CON2 [RNASeq]

description: control bio replicate 2


title: Tumor 1 NaCl


title: IBD54

value: UC

value: IBD

value: No


title: CON1 [RNASeq]

description: control bio replicate 1

value: Lung


title: Fendrr Null_Embryonic lung Day 14.5 replica 1

city: Frankfurt am Main

first: Phillip

last: Grote

state: Hessen

address: Paul-Ehrlich-Str. 42-44

department: Genome Regulation

country: Germany

institute: Georg-Speyer-Haus

data_processing:
alignment with STAR aligner
Count reads over genes with  GenomicAlignments bioconductor package
normalize read count using DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: txt format

source_name: E14.5_Fendrr Null_lung

growth_protocol: Embryos were harvested at either E12.t for lung ex vivo culturing or at E14.5 to harvest the lung for RNA-seq.

extract_protocol:
To isolate RNA from lung tissue, the tisuue were homogenized in 900 µl Qiazol (Qiagen, #79306). To remove the DNA 100 µl gDNA Eliminator solution was added and 180 µl Chloroform (AppliChem, #A3633) to separate the phases. The extraction mixture was centrifuge at full speed, 4°C for 15min. The aqueous phase was mixed with the same amount of 70 % Ethanol and transferred to a micro or mini columns depending of the amount of tissue and cells. The following steps were done according to the manufactural protocol.
Libraries for RNA-seq were constructed according to the ScriptSeq v2 Complete (Mouse/Human/Rat) Low Input Kit (Illumina/Epicenter)

tag: source

value: in vivo

value: mutant


title: T1_iMSC_3

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

data_processing:
Total reads were aligned to hg19 AmpliSeq Transcriptome ERCCv1
Aligned reads raw count data were analyzed
The count data analyses were performed using R studio with the ‘DESeq2’ package and by filtering the lowly expressed genes
Normalized count data were used for the detection of differentially expressed genes and gene set enrichment
Assembly: hg19
Supplementary files format and content: tab-delimited csv files include normalized data count

growth_protocol: iPS cells were cultured in plastic dishes coated with iMatrix-511 silk (Nippi, 892021) fed with StemFit AK03N (Ajinomoto) under xeno-free culture conditions. Cells were dissociated into a cell suspension using Accutase® (Sigma Aldrich, A6964) and passaged when they reached more than 70% confluence.

extract_protocol:
Generated iMSCs on passage Number 3 were used for RNA extraction
RNA samples were extracted using the RNeasy® Mini kit (Qiagen)
Libraries were prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (A31446),and Ion Torrent Ion Chef Instrument (4484177) (Thermo Fisher Scientific, Tokyo, Japan)

treatment_protocol: iMSCs were generated by inducing hiPSCs into neural crest cells (NCCs), and then into iMSCs, which were then maintained in a plastic dish coated with Fibronectin (Chemicon, FC010-10MG).

value: induced mesenchymal stem cells

value: WT

value: Day 21


title: T1_iMSC_2


title: T1_iMSC_1


title: NC55

value: Yes

value: L

value: Colonic biopsy


title: Tumor 1 Doxorubicin

value: tumor

value: Balb/c


title: human right ventricle rep 3

city: Akita

first: Yosuke

last: Okamoto

address: 1-1-1 Hondo

department: Cell Physiology

institute: Akita University Graduate School of Medicine

data_processing:
NovaSeq Control software v1.4.0 was used for basecalling.
fastp software (version 0.12.4) was used for read quality control and adapter removal.
Reads were aligned using STAR software (version 2.7.0a).
The fasta and gtf files of GRCh38/release105 obtained from the Ensemble database were used as reference genome and gene annotation information. The count values of each gene were quantified from the alignment results by featureCounts software. We calculated the Transcripts Per Kilobase Million (TPM) values based on the calculated gene lengths and gene counts
Assembly: GRCh38
Supplementary files format and content: Comma separted values (CSV) file indludes Transcripts Per Kilobase Million (TPM) values.

source_name: human right ventricle

extract_protocol:
RNAs were extracted in our laboratory using QIAGRNAs were extracted in our laboratory using QIAGEN RNeasy mini columns (Cat. No. 74004).
First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation.

tag: tissue type

value: donated heart

value: human right ventricle

tag: disease state

value: persitsten atrial fibrillation

tag: ethnicity

value: caucasian

value: female


title: WT Embryonic lung Day 14.5 replica 3

value: wild type


title: WT Embryonic lung Day 14.5 replica 2

value: Lung


title: human sinoatrial node rep 3

source_name: human sinoatrial node

value: human sinoatrial node


title: IBD51

value: Crohn's

value: IBD

value: No


title: human pulmonary vein rep 3

source_name: human pulmonary vein

value: human pulmonary vein


title: XSF-iMSC_3

tag: cell line

value: induced mesenchymal stem cells

tag: cell type

value: WT

tag: treatment

value: Day 21


title: PSC41

tag: diagnosis

value: PSC-Crohn's

tag: broad diagnosis

value: PSC

tag: dysplasia now

value: Colonic biopsy


title: NC27

value: NC

value: Yes

tag: dys broad location

value: R

tag: tissue


title: XSF-iMSC_2


title: Fendrr Null_Embryonic lung Day 14.5 replica 3

tag: strain

value: in vivo

value: mutant


title: WT Embryonic lung Day 14.5 replica 1

value: Lung

tag: genotype

value: wild type


title: Ex vivo lung fendrr null replica 2

source_name: Fendrr Null

value: ex vivo


title: NC37


title: human left ventricle rep 3

source_name: human left ventricle

value: donated heart

value: human left ventricle

value: persitsten atrial fibrillation

value: caucasian

tag: Sex

value: female


title: human left appendage rep 3

source_name: human left appendage

value: human left appendage


title: Fendrr Null_Embryonic lung Day 14.5 replica 2


title: NC29

source_name: Colonic biopsy

value: No


title: PSC58

value: PSC-UC

value: PSC


title: Ex vivo lung fendrr null replica 1


title: human left atrium rep 3

source_name: human left atrium

value: human left atrium


title: Fendrr box deletion_Embryonic lung Day 14.5 replica 2

source_name: E14.5_Fendrr Box deletion_lung


title: NC51

value: NC

value: Colonic biopsy


title: Fendrr box deletion_Embryonic lung Day 14.5 replica 1

value: in vivo


title: IBD75

value: UC

value: IBD


title: Ex vivo lung fendrr box deletion replica 1

source_name: Fendrr Box Deletion

value: Lung

value: mutant


title: Ex vivo lung fendrr box deletion replica 2

value: ex vivo


title: Ex vivo lung WT replica 2

source_name: WT

value: wild type


title: PSC51


title: XSF-iMSC_4

value: induced mesenchymal stem cells

value: WT

value: Day 21


title: human right atrium rep 3

source_name: human right atrium

value: donated heart

value: human right atrium

value: persitsten atrial fibrillation

value: caucasian

value: female


title: IBD67

value: No


title: human left appendage rep 2

value: human left appendage

value: male


title: human left ventricle rep 2

value: human left ventricle


title: lymph_Foxp3_GFP_Cre_FTHlox5

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Read alignment done by HISAT2 version 2.1.0.
Reads were trimmed using Trimmomatic version 0.36.
Count data were generated by means of the HTSeq method.
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: Treg cells

growth_protocol: Lymph nodes were smashed using a 70 µm mesh in PBS containing 3% FBS and 1mM EDTA. Cells were washed and enrichment for CD4 T cells was performed using MagniSort™ Mouse CD4 T cell Enrichment Kit. Negative fraction was recovered, centrifuged and stained with the following antibody panel: anti-CD11b A647, anti-B220 A647, anti-CD8 A647, anti-CD4 PerCPCy5.5, anti-CD62L PeCy7 and anti-CD44 eF450. Foxp3 positive cells were selected based on the endogenous Foxp3-EGFP/icre expression or Foxp3-YFP/cre. Sorting was performed using FACS Aria (BD Biosciences) and naïve T cells (CD11b/B220/CD8 - CD4 + Foxp3 - CD44 - CD62L+), memory/activated T cells (CD11b/B220/CD8 - CD4 + Foxp3 - CD44 + CD62L-) and Tregs (CD11b/B220/CD8 - CD4 + Foxp3+) were recovered.

extract_protocol:
Total RNA was extracted from (CD4+GFP+) TReg cells isolated from lymph nodes of Foxp3GFP-Fth∆/∆ (n=5) and control Foxp3GFP-Fth∆/∆ mice (n=5) using the Nucelospin RNA XS kit (Macherey-Nagel) as per manufacturer's instructions.
Library preparation was done using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s description.

value: Treg

tag: group

value: FTH deficient

tag: mouse strain

value: lymph node


title: human right ventricle rep 2

value: human right ventricle


title: Synchronized L4/young adult wt animals grown on 2% glucose - 4

city: Tucson

first: Marcas

last: Agostinelli

state: Arizona

address: 2690 W Avenida Azahar

department: Bioinformatics

institute: Novogene

data_processing:
Raw data of fastq format were  processed through in-house perl scripts. The clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
gene_count.xls generated using featureCounts 1.5.0-p3
Assembly: WBcel235
Supplementary files format and content: gene_count.xls of raw gene counts

organism: Caenorhabditis elegans

source_name: Whole extract

extract_protocol:
Trizol-chloroform followed by purification with Quiagen RNA purification kit.
Libraries were prepared using NEBNext Ultra II RNA Library Prep by Illumina. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.

value: Whole extract

tag: developmental stage

value: L4/young adult

value: N2 Bristol

value: 2% glucose


title: Synchronized L4/young adult wt animals grown on 2% glucose - 3


title: Mock_infected cells, biological rep2

city: Nanjing

first: Maoda

last: Pang

address: NO.1 Zhongling Street

institute: Nanjing Agricultural University

description: Expression data from canine alveolar macrophages

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 7G Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Canis lupus familiaris

source_name: Canine alveolar macrophage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary canine alveolar macrophages (CAMCs) were obtained from broncho-alveolar lavage (BAL) of beagle dog and cultured at 37 °C under 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from 1×10e6 cells of primary CAMCs infected and mock-infected with JS/10 for 24 h using TRIzol reagent (Invitrogen, New York, USA). RNA samples were spectroscopically verified for purity, quality of the intact RNA without genomic DNA contamination was assessed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Primary CAMCs were seeded onto sterile 24-well plates at a density of 2×105 cells/well, infected with JS/10 or phosphate buffered saline (PBS).

tag: breed

value: beagle

value: canine alveolar macrophages (CAMCs)

tag: infection

value: control


title: Ex vivo lung WT replica 1

value: Lung

tag: source

value: ex vivo

value: wild type


title: Synchronized L4/young adult wt animals grown on 2% glucose - 2


title: IBD57

value: Crohn's

value: IBD

value: Yes

value: L

value: Colonic biopsy


title: XSF-iMSC_1

tag: cell line

value: induced mesenchymal stem cells

value: WT

value: Day 21


title: lymph_Foxp3_GFP_Cre_FTHlox4

tag: cell type

value: Treg

value: FTH deficient

value: lymph node


title: Virus_infected cells, biological rep1

value: beagle

value: H3N2 canine influenza virus (CIV) JS/10


title: IBD69

value: UC

value: No


title: Virus_infected cells, biological rep2

value: canine alveolar macrophages (CAMCs)


title: Synchronized L4/young adult wt animals grown on 2% glucose - 1

value: Whole extract

value: L4/young adult

value: N2 Bristol

tag: treatment

value: 2% glucose


title: PSC35

tag: diagnosis

value: PSC-UC

value: PSC


title: lymph_Foxp3_GFP_Cre_FTHlox2


title: lymph_Foxp3_GFP_Cre_FTHlox3


title: human pulmonary vein rep 2

tag: tissue type

value: donated heart

value: human pulmonary vein

tag: disease state

value: persitsten atrial fibrillation

tag: ethnicity

value: caucasian

value: male


title: IBD37

value: Crohn's

tag: broad diagnosis

value: IBD

tag: dysplasia now

tag: dys broad location

tag: tissue

value: Colonic biopsy


title: NC21

value: NC


title: Synchronized L4/young adult wt animals grown on NGM - 3

tag: genotype

value: NGM


title: NC42

value: No


title: Synchronized L4/young adult wt animals grown on NGM - 2

value: Whole extract


title: IBD55

value: UC


title: Synchronized L4/young adult wt animals grown on NGM - 4

value: L4/young adult

value: N2 Bristol


title: lymph_Foxp3_GFP_Cre_FTHlox1

value: Treg

tag: group

value: FTH deficient

tag: mouse strain

value: lymph node


title: Synchronized L4/young adult wt animals grown on NGM - 1

tag: developmental stage


title: human pulmonary vein rep 1

value: donated heart

value: human pulmonary vein

tag: Sex


title: human sinoatrial node rep 2

value: human sinoatrial node

value: persitsten atrial fibrillation

value: caucasian


title: human right atrium rep 2

value: human right atrium

value: male


title: Mock_infected cells, biological rep1

tag: breed

value: beagle

value: canine alveolar macrophages (CAMCs)

tag: infection

value: control


title: human right ventricle rep 1

value: human right ventricle


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on 2% glucose - 4

value: Whole extract

value: 2% glucose


title: human left ventricle rep 1

value: human left ventricle


title: NC41

value: NC

value: No

value: Colonic biopsy


title: lymph_Foxp3_GFP_Cre_4

tag: cell type

value: Treg

value: lymph node


title: lymph_Foxp3_GFP_Cre_2


title: human right atrium rep 1

value: donated heart


title: IBD81

value: Crohn's

value: IBD


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on 2% glucose - 2

value: L4/young adult

tag: treatment


title: human left atrium rep 2

value: human left atrium

value: persitsten atrial fibrillation

value: caucasian

value: male


title: lymph_Foxp3_GFP_Cre_1

value: control


title: human left atrium rep 1


title: IBD30

tag: diagnosis


title: NC34


title: human left appendage rep 1

tag: tissue type

value: human left appendage


title: human sinoatrial node rep 1

value: human sinoatrial node

tag: disease state


title: PSC50

value: PSC-Crohn's

value: PSC


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on NGM - 4

value: Whole extract

value: NGM


title: lymph_Foxp3_GFP_Cre_5

value: Treg


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on NGM - 3


title: NC32

value: NC

value: No

value: Colonic biopsy


title: PSC52

value: PSC-UC


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on NGM - 2

value: L4/young adult


title: right atrial appendage from sinus rhythm patient rep 2

source_name: right atrial appendage

extract_protocol:
RNAs were extracted in our laboratory using ISOGEN II (NIPPON GENE CO., LTD. Kandashiki-machi, Tokyo, Japan)
First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation.

value: Cut-outs during mitral valve replacement.

value: right atrial appendage

value: cronic atrial fibrillation

tag: race

value: Japanese


title: right atrial appendage from atrial fibrillation patient rep 2

value: female


title: right atrial appendage from atrial fibrillation patient rep 1

value: male


title: lymph_Foxp3_GFP_Cre_3

value: control

value: lymph node


title: IBD74

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

value: UC

tag: broad diagnosis

value: IBD

value: Yes

value: R


title: IBD44

value: Crohn's

tag: dysplasia now


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on NGM - 1

value: Whole extract

value: NGM


title: IBD63

value: No

tag: dys broad location

value: Colonic biopsy


title: Synchronized L4/young adult pgph-2 oe animals grown on 2% glucose - 4

tag: tissue

value: L4/young adult

value: pgph-2 oe

value: 2% glucose


title: IBD36


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on 2% glucose - 3

tag: genotype


title: Synchronized L4/young adult pgph-2 oe animals grown on 2% glucose - 3


title: IBD72


title: Synchronized L4/young adult pgph-2 oe animals grown on 2% glucose - 2


title: IBD71


title: Synchronized L4/young adult pgph-2 oe animals grown on NGM - 4


title: Synchronized L4/young adult pgph-2 oe animals grown on 2% glucose - 1


title: IBD65


title: IBD62


title: Synchronized L4/young adult pgph-2 oe animals grown on NGM - 3


title: Synchronized L4/young adult pgph-2 oe ; hlh-30 animals grown on 2% glucose - 1


title: PSC74

value: PSC-UC

value: PSC


title: Synchronized L4/young adult pgph-2 oe animals grown on NGM - 2


title: NC54

value: NC


title: IBD45


title: Synchronized L4/young adult hlh-30 animals grown on 2% glucose - 2


title: Synchronized L4/young adult pgph-2 oe animals grown on NGM - 1


title: NC35

value: L


title: Synchronized L4/young adult hlh-30 animals grown on 2% glucose - 4


title: Synchronized L4/young adult hlh-30 animals grown on 2% glucose - 3


title: IBD28


title: NC31


title: Synchronized L4/young adult hlh-30 animals grown on 2% glucose - 1


title: PSC39

value: PSC-Crohn's


title: Synchronized L4/young adult hlh-30 animals grown on NGM - 4


title: Synchronized L4/young adult hlh-30 animals grown on NGM - 3


title: right atrial appendage from sinus rhythm patient rep 1

value: Cut-outs during mitral valve replacement.

value: right atrial appendage

value: cronic atrial fibrillation

value: Japanese

value: male


title: NC53


title: PSC77

value: Indefinite

value: R


title: Synchronized L4/young adult hlh-30 animals grown on NGM - 2

value: Whole extract

value: NGM


title: IBD59

value: Crohn's

value: IBD

value: No

value: Colonic biopsy


title: Synchronized L4/young adult hlh-30 animals grown on NGM - 1

value: L4/young adult


title: Xenograft form fresh SIX2+CITED1+ from Wilms Tumor

city: Los Angeles

first: Stefano

last: Da Sacco

state: CA

address: 4650 Sunset Blvd MS#35

institute: Children's Hospital Los Angeles

data_processing:
Import raw data in fastq file format from sequencing center into Partek Flow software system.
Trim Adaptor sequence from 3' end (Partek Flow)
Alignment performed using STAR (Partek Flow)
Generate Gene Counts (Partek Flow)
Normalize Counts using "Recommended" Settings (Partek Flow)
Generate Gene Analysis (Partek Flow)
Filter by FDR step-up 0.05, fold change <-2 or >2,
Genome_build: Homo sapiens GRCh38/hg38

source_name: Wilms Tumor

extract_protocol:
Enzymatic dissociation was performed with 125 U/ml collagenase I in RPMI-1640 at 37 °C for 35 min. The digested cells were then passed through a 100-μm cell strainer and a 40-μm cell strainer with washes of 1x PBS. The cell suspension was than centrifuged at 1500 rpm for 5 min and erythrocytes were eliminated using a red blood cell lysis kit.  WT SIX2+CITED1+ cells were isolated using SIX2-Cy5 and CITED1-Cy3 Smartflare RNA probes following manufacturer’s instructions
Approximately 3,000 cells were captured on a 10x Chromium device using a 10X V2 Single Cell 3′ Solution kit.  All protocols were performed following manufacturer's instructions. Final library concentrations were determined using a Qubit high Sensitivity DNA assay Kit. Final sequencing libraries were analyzed on a Sequencing: HiSeq 4000, 2x150bp PE, and ~625M total reads/lane (QuickBiology) to determine the library size;  Approximately, 300 million reads per sample were sequenced
scRNAseq

value: Wilms Tumor

tag: age

value: 7 years old

tag: tumor type

value: Favorable COG Stage II

value: Freshly isolated SIX2+CITED1+ generated xenografts


title: SIX2+CITED1+ from Wilms Tumor

value: Freshly isolated SIX2+CITED1+


title: SIX2+CITED1+ from human fetal kidney

source_name: Human Fetal kidney

value: Human Fetal kidney

value: 16 GWA


title: Xenograft form cultured SIX2+CITED1+ from Wilms Tumor

value: Cultured SIX2+CITED1+ (passage 6) generated xenografts


title: M1+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0975

value: mammary epithelial cells

tag: resistance

value: EMT-sensitive


title: foursu_t60_totalRNA_rep3

city: Oxford

first: Ilan

last: Davis

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
foursu_input_60min_3
brain_incubation_summary_abundance.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

value: larval brain

tag: developmental stage

value: wandering third instar larvae

tag: library type

value: 3′ RNA-seq / QuantSeq

tag: strain

value: Oregon-R

value: 500 µM 4-thiouridine

tag: incubation time

value: 60 min

tag: rna fraction

value: total RNA


title: E3+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0972

tag: cell type

value: EMT-resistant

tag: treatment


title: M2+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0974


title: E1+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0971


title: M3+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0973


title: E2+TAMd14-d7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 14 days Tamoxifen treatment + 7 days withdrawal
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0970


title: mock_t60_totalRNA_rep1

description:
mock_input_60min_1
brain_incubation_summary_abundance.csv


title: M2+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0968

value: 14 days Tamoxifen treatment


title: M3+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0967


title: M1+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0969


title: mock_t60_totalRNA_rep3

description:
mock_input_60min_3
brain_incubation_summary_abundance.csv


title: mock_t0_totalRNA_rep2

description:
mock_input_0min_2
brain_incubation_summary_abundance.csv

value: 0 min


title: E3+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0966


title: mock_t0_totalRNA_rep3

description:
mock_input_0min_3
brain_incubation_summary_abundance.csv


title: M1+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0963

value: 7 days Tamoxifen treatment


title: mock_t0_totalRNA_rep1

description:
mock_input_0min_1
brain_incubation_summary_abundance.csv


title: E2+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0964


title: E1+TAMd14_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 14 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0965


title: M2+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0962


title: M3+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0961


title: E3+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 3; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0960


title: E1+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 1; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0959


title: M1-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 1; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0957

value: untreated


title: M2-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 2; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0956


title: E2+TAMd7_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 2; 7 days Tamoxifen treatment
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0958


title: Wilms Tumor total

value: Wilms Tumor

value: 7 years old

value: Favorable COG Stage II

value: Total tumor


title: M3-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-sensitive, clone 3; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0955

value: mammary epithelial cells

value: EMT-sensitive


title: E3-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 3; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0954


title: mock_t60_totalRNA_rep2

description:
mock_input_60min_2
brain_incubation_summary_abundance.csv

value: larval brain

value: wandering third instar larvae


title: E1-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 1; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0953


title: X6

city: Hangzhou

first: Yinfang

last: Wu

address: Yuhangtang RD 866

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke（v1.5.2） by Removing reads containing sequencing adapter；
Removing reads whose low-quality base ratio （base quality less than or equal to 5）is more than 20%
removing reads whose unknown base （’N’ base）ratio is more than 5%，afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to reference genome using HISAT2（v2.0.4）.
Genome_build: Bowtie2（v2.2.5）was applied to align the clean reads to the reference coding gene set ，then expression level of gene was calculated by RSEM (v1.2.12).
Supplementary_files_format_and_content: The heatmap was drawn by Pheatmap（v1.0.8）according to the gene expression in different samples.Essentially，differential expression analysis was performed using the DESeq2（v1.4.5） with Q value ≤0.05.

source_name: macrophage

growth_protocol: Bone marrow cells were isolated and cultured with DMEM containing 10% (v/v) FBS and 10 ng/ml mouse M-CSF for 5 days to obtain BMDMs.

extract_protocol:
BMDM were harvested for RNA extraction using TRIzol.  RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -80℃ under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDM treated with IL4, or IL4 + fatostatin, or IL4 + betulin,  or IL4  + 25-HC,  or IL4 + PF429424, or IL4 + 1,10-Phen for 24 hours.

value: Bone marrow derived macrophage

value: co-treated IL4 and 1,10-Phen for 24 hours


title: E2-TAM_RNA-seq

description:
HMLE-TWIST1-ER cells, EMT-resistant, clone 2; untreated
RNA-seq_HMLE_TWIST1_ER_all_counts.xlsx
ISF0952

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.


title: foursu_t60_totalRNA_rep2

description:
foursu_input_60min_2
brain_incubation_summary_abundance.csv

value: 3′ RNA-seq / QuantSeq

value: Oregon-R

value: 500 µM 4-thiouridine

value: 60 min


title: foursu_t60_totalRNA_rep1

description:
foursu_input_60min_1
brain_incubation_summary_abundance.csv

value: total RNA


title: X4

value: co-treated IL4 and 25-HC for 24 hours


title: X2

value: co-treated IL4 and Fatostatin for 24 hours


title: X5

value: co-treated IL4 and PF429424 for 24 hours


title: X3

value: co-treated IL4 and Betulin for 24 hours


title: X1

value: treated with IL4 for 24 hours


title: Abomasum3, Adult

city: Chengdu

first: Li

middle: yi

last: Liu

state: None Selected

address: #16, South Section, 1st Ring Road, Chengdu, Sichuan, China, Post Code 610041

institute: Southwest Minzu University

data_processing:
Raw data (raw reads) were processed using Trimmomatic.
The raw reads containing ploy-N and the low-quality reads were removed to obtain the clean reads.
FPKM value of each gene was calculated using cufflinks, and the number of reads mapped to each gene was counted by htseq-count.  For transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress.
The reads were reassembled using StringTie. Then the gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile.
Assembly: BosGru_v2.0
Supplementary files format and content: report_Filtered_data_stat-Rum, Ret, Oma, Abo
Supplementary files format and content: counts_anno-Rum, Ret, Oma,Abo
Supplementary files format and content: FPKM_anno-Rum, Ret, Oma, Abo

organism: Bos grunniens

source_name: Abomasum

extract_protocol:
The total RNA of each sample was extracted using the mirVana miRNA Isolation Kit (Ambion-1561) following the manufacturer’s instructions.
The libraries were constructed following the manufacturer’s protocol at Shanghai OE Biotech (Shanghai, China), using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) .

value: Abomasum

value: Adult


title: Abomasum2, Adult


title: Abomasum1, Adult


title: long bone Emb-GFP- biol rep 4 [s191]

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: fpkm.genes.ensembl_id.protein_coding.txt

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 100 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: femur+tibia

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA quality and quantity were verified by using an Agilent 2100 Bioanalyzer system.
cDNA libraries were generated using the Illumina SMART-Seq v4 plus Nextera XT DNA Library Preparation Kit

value: femur+tibia

tag: cell line

value: primary long bone cells

value: WT

tag: Sex

value: male

value: postnatal day 10


title: long bone Emb+GFP- biol rep 1 [s190]


title: long bone Emb-GFP- biol rep 3 [s189]


title: long bone Emb-GFP- biol rep 2 [s187]


title: long bone Emb+GFP- biol rep 1 [s186]


title: long bone Emb+GFP- biol rep 1 [s192]


title: long bone Emb+GFP- biol rep 1 [s188]


title: verteral Emb-GFP+ biol rep 4 [s176]

source_name: spine

value: spine

value: primary vertebral cells


title: Abomasum1, Day15m

value: Day 15m


title: verteral Emb-GFP+ biol rep 3 [s172]


title: Abomasum3, Day15m


title: Abomasum2, Day15m


title: long bone Emb-GFP- biol rep 1 [s185]


title: verteral Emb-GFP+ biol rep 1 [s164]


title: verteral Emb-GFP+ biol rep 2 [s168]


title: verteral Emb-GFP- biol rep 4 [s175]


title: Abomasum3, Day60

value: Day 60


title: verteral Emb-GFP- biol rep 2 [s167]


title: verteral Emb-GFP- biol rep 3 [s171]


title: Abomasum2, Day60


title: verteral Emb-GFP- biol rep 1 [s163]


title: Abomasum3, Day20

value: Day 20


title: Abomasum1, Day60


title: verteral Emb+GFP+ biol rep 3 [s170]


title: verteral Emb+GFP+ biol rep 4 [s174]


title: verteral Emb+GFP+ biol rep 2 [s166]


title: verteral Emb+GFP+ biol rep 1 [s162]


title: Abomasum3, Day0

value: Day 0


title: Abomasum1, Day0


title: Jurkat shTAL1 TAL1-long 3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
The processed reads were aligned with TopHat , allowing for 5 mismatches to the reference human genome  GRCh38, with annotations from Ensembl release 106.
Quantification was done with htseq-count
Normalization, quality control plots (PCA, MA-plots) and differential expression analysis were performed using the DESeq2 package
Pair-wise comparisons were tested with default parameters using the Wald test, without using the independent filtering algorithm. Significance threshold was taken as p-adj<0.1. In addition, significant genes were further filtered by the log2(fold change) value. This filtering was baseMean-dependent and required a baseMean above 5 and an absolute log2FoldChange higher than 5/sqrt(baseMean) + 0.3.for highly expressed genes this means a requirement for a fold-change of at least 1.2, while genes with a very low expression would need a 5.8 -fold change to pass the filtering
Assembly: GRCh38, with annotations from Ensembl release 106
Supplementary files format and content: DESeq2 normalized base mean conts per gene ( ensembl gene id, Symbol) per samples

source_name: T-cell

growth_protocol: The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.

extract_protocol:
Total RNA Purification kit (Norgen Biotek Corp.)
KAPA Stranded mRNA-seq Kit (Roche)

value: T-cell

value: Jurkat

value: silenced endogenous TAL1 by stable transfection of inducible TAL1 shRNA targeting its 3' UTR

value: over expression of Long TAL gene isoform


title: Omasum2, Adult

source_name: Omasum

value: Omasum


title: verteral Emb-GFP+ biol rep 2 [s165]


title: Omasum3, Adult

value: Adult


title: verteral Emb-GFP+ biol rep 3 [s169]


title: Abomasum2, Day0

value: Abomasum


title: verteral Emb-GFP+ biol rep 4 [s173]


title: Jurkat shTAL1 TAL1-long 2

treatment_protocol: The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.


title: Omasum3, Day15m


title: LowOVA_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

value: large intestine lamina propria

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

value: Female

value: Lm-OVA infection in recipient mice


title: verteral Emb-GFP+ biol rep 1 [s161]

value: spine

value: WT

value: male

value: postnatal day 10


title: Jurkat shTAL1 TAL1-long 1


title: Omasum1, Adult


title: Jurkat shTAL1 TAL1-short 3

value: over expression of Short TAL gene isoform


title: LowOVA_1


title: Omasum2, Day15m

value: Day 15m


title: HighOVA_2


title: Omasum1, Day15m


title: Omasum3, Day60

value: Day 60


title: Jurkat shTAL1 TAL1-short 2

value: T-cell

value: Jurkat