title: DGM-11379_M3_sm (demographics_pollution)

description:
DGM-11379
307SAE-S_PM2.5_resid.csv


title: DGM-11465_M0_sm (demographics_pollution)

status: Public on Jun 19 2018

type: RNA

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

country: USA

institute: Weill Cornell Medical College

description:
DGM-11465
307SAE-S_PM2.5_resid.csv

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Gene expression was normalized using the Single-channel array normalization (SCAN)/Universal exPression Codes (UPC) method and University of Michigan HG-U133 Plus 2.0 microarray probeset definitions (version 21) . Genes with a UPC value of <0.2 in all samples were excluded.  SAE gene expression was modeled as a linear function of 30-day mean PM2.5 level. P values were calculated by two-sided Wald test, reflecting the probability that the regression coefficient for the pollution variable is non-zero.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: COPD smoker

tag: 30-day mean pm2.5 exposure level

tag: time of serial bronchoscopy (month)

tag: cell type

value: small airway epithelium brushing


title: DGM-11379_M6_sm (demographics_pollution)

description:
DGM-11379
307SAE-S_PM2.5_resid.csv


title: DGM-11379_M0_sm (demographics_pollution)

description:
DGM-11379
307SAE-S_PM2.5_resid.csv


title: DGM-11298_M3_sm (demographics_pollution)

description:
DGM-11298
307SAE-S_PM2.5_resid.csv


title: DGM-11298_M6_sm (demographics_pollution)

description:
DGM-11298
307SAE-S_PM2.5_resid.csv


title: DGM-11298_M12_sm (demographics_pollution)

description:
DGM-11298
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025373-batch1-rep1

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

description:
Nanostring miRNA measurement for blood sample
NB00000080

hyb_protocol: 250 ng of total RNA was obtained from 233 samples, and hybridized to the nCounter Human miRNA sample probes (Seattle, WA).

scan_protocol: Each sample was scanned for 600 FOV on the nCounter Digital Analyzer

data_processing: We first loaded raw RCC files for 233 samples into nSolver (v2.5) and extracted the raw counts, then substracted background noise based on mean of negative controls, normalized to positive controls, finally performed global normalization using all miRNAs.

label: miRNA-specific probes

label_protocol: Not applicable

extract_protocol: Using PAXgene Blood RNA Kit(PreAnalytiX Cat#:762164) for RNA extraction following the manufaturer's protocol.

tag: diagnosis

value: control

tag: gender

value: famale

tag: age

tag: cap score

value: cont

tag: tissue

value: blood


title: blood-HD-NS00025367-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000079

value: HD

value: male

value: high


title: blood-control-NS00025412-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000081


title: blood-control-NS00025353-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000077


title: blood-HD-NS00025352-batch2-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000076

value: med


title: blood-HD-NS00025351-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000075


title: DGM-11298_M0_sm (demographics_pollution)

description:
DGM-11298
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025354-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000078


title: blood-HD-NS00025335-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000074


title: DGM-11276_M0_sm (demographics_pollution)

description:
DGM-11276
307SAE-S_PM2.5_resid.csv


title: DGM-11270_M0_sm (demographics_pollution)

description:
DGM-11270
307SAE-S_PM2.5_resid.csv


title: DGM-11269_M6_sm (demographics_pollution)

description:
DGM-11269
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025332-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000073


title: blood-HD-NS00025306-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000072


title: DGM-11269_M3_sm (demographics_pollution)

description:
DGM-11269
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025304-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000071


title: DGM-11269_M12_sm (demographics_pollution)

description:
DGM-11269
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025301-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000070


title: DGM-11269_M0_sm (demographics_pollution)

description:
DGM-11269
307SAE-S_PM2.5_resid.csv


title: DGM-11268_M0_sm (demographics_pollution)

description:
DGM-11268
307SAE-S_PM2.5_resid.csv


title: DGM-11261_M0_sm (demographics_pollution)

description:
DGM-11261
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025250-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000068


title: blood-HD-NS00025227-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000066


title: DGM-11276_M3_sm (demographics_pollution)

description:
DGM-11276
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025231-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000067


title: DGM-11192_M3_sm (demographics_pollution)

description:
DGM-11192
307SAE-S_PM2.5_resid.csv


title: DGM-11192_M0_sm (demographics_pollution)

description:
DGM-11192
307SAE-S_PM2.5_resid.csv


title: DGM-11192_M6_sm (demographics_pollution)

description:
DGM-11192
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025224-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000065


title: DGM-11192_M12_sm (demographics_pollution)

description:
DGM-11192
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025204-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000062


title: blood-HD-NS00025211-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000063


title: blood-HD-NS00025221-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000064


title: DGM-11184_M0_sm (demographics_pollution)

description:
DGM-11184
307SAE-S_PM2.5_resid.csv


title: DGM-11163_M6_sm (demographics_pollution)

description:
DGM-11163
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025204-batch0-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000061


title: DGM-11163_M3_sm (demographics_pollution)

description:
DGM-11163
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025172-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000060


title: blood-HD-NS00025167-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000059


title: DGM-11163_M12_sm (demographics_pollution)

description:
DGM-11163
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025160-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000057


title: DGM-11163_M0_sm (demographics_pollution)

description:
DGM-11163
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025274-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000069


title: blood-control-NS00025160-batch0-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000058


title: DGM-11268_M3_sm (demographics_pollution)

description:
DGM-11268
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025126-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000055


title: DGM-11122_M6_sm (demographics_pollution)

description:
DGM-11122
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025136-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000056


title: DGM-11122_M3_sm (demographics_pollution)

description:
DGM-11122
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025115-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000054


title: blood-HD-NS00025110-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000053


title: DGM-11122_M12_sm (demographics_pollution)

description:
DGM-11122
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025060-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000052


title: DGM-11077_M3_sm (demographics_pollution)

description:
DGM-11077
307SAE-S_PM2.5_resid.csv


title: DGM-11122_M0_sm (demographics_pollution)

description:
DGM-11122
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025055-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000051


title: DGM-11077_M12_sm (demographics_pollution)

description:
DGM-11077
307SAE-S_PM2.5_resid.csv


title: DGM-11077_M6_sm (demographics_pollution)

description:
DGM-11077
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025050-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000050


title: blood-control-NS00025036-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000049


title: DGM-11061_M0_sm (demographics_pollution)

description:
DGM-11061
307SAE-S_PM2.5_resid.csv


title: DGM-11030_M0_sm (demographics_pollution)

description:
DGM-11030
307SAE-S_PM2.5_resid.csv


title: DGM-11060_M0_sm (demographics_pollution)

description:
DGM-11060
307SAE-S_PM2.5_resid.csv


title: DGM-11010_M0_sm (demographics_pollution)

description:
DGM-11010
307SAE-S_PM2.5_resid.csv


title: DGM-11001_M6_sm (demographics_pollution)

description:
DGM-11001
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025011-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000047


title: blood-HD-NS00024776-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000045


title: DGM-11007_M0_sm (demographics_pollution)

description:
DGM-11007
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00025003-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000046


title: blood-HD-NS00024771-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000043


title: DGM-11001_M3_sm (demographics_pollution)

description:
DGM-11001
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024771-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000042


title: blood-HD-NS00024760-batch2-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000039


title: blood-HD-NS00024766-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000040


title: DGM-10988_M0_sm (demographics_pollution)

description:
DGM-10988
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00024757-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000038


title: DGM-11077_M0_sm (demographics_pollution)

description:
DGM-11077
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00025032-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000048


title: DGM-10984_M3_sm (demographics_pollution)

description:
DGM-10984
307SAE-S_PM2.5_resid.csv


title: DGM-10984_M12_sm (demographics_pollution)

description:
DGM-10984
307SAE-S_PM2.5_resid.csv


title: DGM-10984_M6_sm (demographics_pollution)

description:
DGM-10984
307SAE-S_PM2.5_resid.csv


title: DGM-10946_M0_sm (demographics_pollution)

description:
DGM-10946
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024754-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000037


title: blood-HD-NS00024772-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000044


title: DGM-10824_M0_sm (demographics_pollution)

description:
DGM-10824
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024713-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000035


title: blood-HD-NS00024712-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000034


title: DGM-10984_M0_sm (demographics_pollution)

description:
DGM-10984
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024704-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000032


title: DGM-10800_M6_sm (demographics_pollution)

description:
DGM-10800
307SAE-S_PM2.5_resid.csv


title: DGM-11001_M0_sm (demographics_pollution)

description:
DGM-11001
307SAE-S_PM2.5_resid.csv


title: DGM-10800_M12_sm (demographics_pollution)

description:
DGM-10800
307SAE-S_PM2.5_resid.csv


title: DGM-10800_M0_sm (demographics_pollution)

description:
DGM-10800
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00024726-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000036


title: blood-HD-NS00024672-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000030


title: blood-HD-NS00024671-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000029


title: blood-HD-NS00024667-batch2-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000028


title: blood-control-NS00024767-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000041


title: blood-HD-NS00024667-batch2-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000027


title: DGM-10799_M0_sm (demographics_pollution)

description:
DGM-10799
307SAE-S_PM2.5_resid.csv


title: DGM-10794_M6_sm (demographics_pollution)

description:
DGM-10794
307SAE-S_PM2.5_resid.csv


title: DGM-10794_M3_sm (demographics_pollution)

description:
DGM-10794
307SAE-S_PM2.5_resid.csv


title: DGM-10794_M12_sm (demographics_pollution)

description:
DGM-10794
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00024637-batch2-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000025


title: DGM-10794_M0_sm (demographics_pollution)

description:
DGM-10794
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00024711-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000033


title: blood-HD-NS00024645-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000026


title: DGM-10800_M3_sm (demographics_pollution)

description:
DGM-10800
307SAE-S_PM2.5_resid.csv


title: DGM-10786_M0_sm (demographics_pollution)

description:
DGM-10786
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024631-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000024


title: DGM-10744_M0_sm (demographics_pollution)

description:
DGM-10744
307SAE-S_PM2.5_resid.csv


title: DGM-10727_M0_sm (demographics_pollution)

description:
DGM-10727
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024675-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000031


title: blood-HD-NS00024570-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000022


title: blood-HD-NS00024566-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000021


title: DGM-10549_M3_sm (demographics_pollution)

description:
DGM-10549
307SAE-S_PM2.5_resid.csv


title: DGM-10635_M0_sm (demographics_pollution)

description:
DGM-10635
307SAE-S_PM2.5_resid.csv


title: DGM-10549_M6_sm (demographics_pollution)

description:
DGM-10549
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024522-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000019


title: DGM-10549_M0_sm (demographics_pollution)

description:
DGM-10549
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024530-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000020


title: DGM-10539_M0_sm (demographics_pollution)

description:
DGM-10539
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024473-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000016


title: DGM-10539_M3_sm (demographics_pollution)

description:
DGM-10539
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024463-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000013


title: DGM-10504_M6_sm (demographics_pollution)

description:
DGM-10504
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024466-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000014


title: DGM-10504_M12_sm (demographics_pollution)

description:
DGM-10504
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024516-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000018


title: DGM-10504_M0_sm (demographics_pollution)

description:
DGM-10504
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024631-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000023


title: blood-HD-NS00024466-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000015


title: blood-HD-NS00024463-batch0-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000012


title: blood-HD-NS00024460-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000011


title: DGM-10421_M0_sm (demographics_pollution)

description:
DGM-10421
307SAE-S_PM2.5_resid.csv


title: DGM-10406_M0_sm (demographics_pollution)

description:
DGM-10406
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024443-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000010


title: DGM-10401_M0_sm (demographics_pollution)

description:
DGM-10401
307SAE-S_PM2.5_resid.csv


title: DGM-10359_M0_sm (demographics_pollution)

description:
DGM-10359
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024441-batch2-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000009


title: DGM-10340_M6_sm (demographics_pollution)

description:
DGM-10340
307SAE-S_PM2.5_resid.csv


title: DGM-10340_M3_sm (demographics_pollution)

description:
DGM-10340
307SAE-S_PM2.5_resid.csv


title: blood-control-NS00024440-batch1-rep2

description:
Nanostring miRNA measurement for blood sample
NB00000008


title: blood-control-NS00024440-batch0-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000007


title: blood-HD-NS00024503-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000017


title: DGM-10340_M12_sm (demographics_pollution)

description:
DGM-10340
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024372-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000004


title: blood-HD-NS00024416-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000005


title: DGM-10335_M6_sm (demographics_pollution)

description:
DGM-10335
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024361-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000003


title: DGM-10335_M12_sm (demographics_pollution)

description:
DGM-10335
307SAE-S_PM2.5_resid.csv


title: DGM-10421_M3_sm (demographics_pollution)

description:
DGM-10421
307SAE-S_PM2.5_resid.csv


title: DGM-10329_M0_sm (demographics_pollution)

description:
DGM-10329
307SAE-S_PM2.5_resid.csv


title: DGM-10286_M6_sm (demographics_pollution)

description:
DGM-10286
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024355-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000002


title: DGM-10335_M0_sm (demographics_pollution)

description:
DGM-10335
307SAE-S_PM2.5_resid.csv


title: DGM-10286_M12_sm (demographics_pollution)

description:
DGM-10286
307SAE-S_PM2.5_resid.csv


title: DGM-10286_M0_sm (demographics_pollution)

description:
DGM-10286
307SAE-S_PM2.5_resid.csv


title: DGM-10283_M6_sm (demographics_pollution)

description:
DGM-10283
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024432-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000006


title: DGM-10283_M12_sm (demographics_pollution)

description:
DGM-10283
307SAE-S_PM2.5_resid.csv


title: DGM-10283_M3_sm (demographics_pollution)

description:
DGM-10283
307SAE-S_PM2.5_resid.csv


title: DGM-10283_M0_sm (demographics_pollution)

description:
DGM-10283
307SAE-S_PM2.5_resid.csv


title: LEB

type: SRA

city: Paris

first: Thierry

last: Bienvenu

address: 24 rue du faubourg St jacques

country: France

institute: INSERM

description: LEB

library_source: transcriptomic

data_processing:
Libraries were sequenced on IlluminaNextSeq 500 (Illumina) using 75 base-lengths read with V5 chemistry in paired-end mode
After sequencing, a primary analysis based on AOZAN software (ENS, Paris, France) was applied to demultiplex sequences and control the quality of raw data (based on FastQC modules/version 0.11.5).
Obtained FastQ files were then aligned using Star algorithm (version 2.5.2b) and quality of the alignment was controlled using Picard tools (version 2.8.1).
Reads were count using Feature count (version Rsubread 1.24.1) and statistical analysis wasperformed using DESeq2 package version 1.14.1 to determine the proportion of differentially expressed genes between samples.
Genome_build: Ensembl : GRCh38.p10-release89
Supplementary_files_format_and_content: Raw count files obtained with featureCount, in text format, and a normalized matrix with DESeq2 method (rle)

source_name: KMT2A c.3460C>T;p.Arg1154Trp

growth_protocol: Fibroblasts were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (1g/L glucose, pyruvate +; ThermoFisher Scientific, Waltham, MA, USA) supplemented with 10% (v/v) Fetal Bovine Serum (FBS) (ThermoFisher Scientific), 100 U/mL Penicillin, 100 µg/mL Streptomycin (ThermoFisher Scientific) and 10µg/mL Ciprofloxacine (Sigma, Saint Louis, MO, USA). At confluence, cells were treated with DMEM supplemented with 50% FBS for two hours followed by 22 hours with serum-free medium (supplemented with antibiotics)

extract_protocol:
Total RNA was isolated using RNeasyMini Kit (Qiagen, Hilden, Germany) with a DNase step, according to the manufacturer's instructions
libraries were prepared with 1 µg of high quality RNA using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions

value: fibroblasts

tag: kmt2a genotype

value: KMT2A c.3460C>T;p.Arg1154Trp

tag: patient diagnosis

value: Wiedemann Steiner syndrome


title: DGM-10262_M6_sm (demographics_pollution)

description:
DGM-10262
307SAE-S_PM2.5_resid.csv


title: F70274


title: DGM-10262_M3_sm (demographics_pollution)

description:
DGM-10262
307SAE-S_PM2.5_resid.csv


title: F66867


title: DGM-10335_M3_sm (demographics_pollution)

description:
DGM-10335
307SAE-S_PM2.5_resid.csv


title: DGM-10262_M0_sm (demographics_pollution)

description:
DGM-10262
307SAE-S_PM2.5_resid.csv


title: blood-HD-NS00024350-batch1-rep1

description:
Nanostring miRNA measurement for blood sample
NB00000001


title: F298

source_name: WT

value: WT


title: DGM-10157_M6_sm (demographics_pollution)

description:
DGM-10157
307SAE-S_PM2.5_resid.csv


title: DGM-10157_M3_sm (demographics_pollution)

description:
DGM-10157
307SAE-S_PM2.5_resid.csv


title: Te05


title: F157


title: Te04


title: DGM-10157_M0_sm (demographics_pollution)

description:
DGM-10157
307SAE-S_PM2.5_resid.csv


title: Te03


title: DGM-10145_M0_sm (demographics_pollution)

description:
DGM-10145
307SAE-S_PM2.5_resid.csv


title: H3K4me2_Etoposide

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

library_source: genomic

data_processing:
Raw FastQ files were aligned to the hg19/ncbi37 genome assembly using bowtie2.
Regions of significant enrichment were called using MACSv2 with sonicated DNA input controls
Genome_build: ncbi37/hg19

molecule: genomic DNA

source_name: IMR90 fetal lung fibroblasts

growth_protocol: IMR90 fibroblasts were grown in DMEM with 10% FBS at 3% oxygen.

extract_protocol:
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor. For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module. For ATAC-seq, cells were harvested, nuclei were prepped,and transposase was added for 30 minutes at 30C.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.
Sequencing libraries for ATAC-seq were constructed using custom Nextera-compatible primers, from Nextera-adapted DNA fragments

treatment_protocol: Proliferating IMR90 fibroblasts were treated with etoposide

tag: cell line

tag: treatment

value: etoposide (100uM, 6hrs)

tag: passages

value: Passage # 30-35

tag: antibody


title: F66262

source_name: KMT2A c.8558T>G; p.Met2853Arg

value: KMT2A c.8558T>G; p.Met2853Arg


title: DGM-10132_M3_sm (demographics_pollution)

description:
DGM-10132
307SAE-S_PM2.5_resid.csv

value: COPD smoker


title: CS-1_untreated_rep3

city: Providence

first: Richard

middle: M

last: Terek

state: RI

address: 1 Hoppin St

institute: Rhode Island Hospital

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip® Human Transcriptome Array 2.0 (Affymetrix) for 16 hours at 45° C and the washing, stainng was done according to Affymetrix  instructions on a GeneChip® Fluidics Station 450 (Affymetrix) at the Brown University Genomics Core Facility.

scan_protocol: Array scanning was performed using GeneChip® Scanner 3000 7G (Affymetrix) at the Brown University Genomics Core Facility.

data_processing: The raw data was processed with Affymetrix® Expression Console™ Software to perform background correction and normalization, and to generate  .CHP files from .CEL files. Data analysis was performed using Partek® Genomics Suite®  software using  an ANOVA analysis with linear contrast to do the comparisons. P value < 0.05 with FDR correction was used.

label: Biotin

source_name: Grade III human chondrosarcoma

label_protocol: WT PLUS Reagent Kit (Affymetrix ) was used to prepare hybridization-ready targets from total RNAsamples for analysis with GeneChip® Human Transcriptome Array 2.0. The kit generates amplified and biotinylated sense-strand DNA targets from total RNA using a reverse transcription priming method that primes the entire length of RNA, including both poly(A) and non-poly(A) mRNA to provide complete and unbiased coverage of the transcriptome.

growth_protocol: CS-1 cells were cultured in Gibco RPMI 1640 Medium (Life Technologies, Grand Island, NY) with 10% FBS in a humidified incubator (NuAire Inc, Plymouth, MN) under 5% CO2 and ambient oxygen.

extract_protocol: Total RNA was extracted cells using RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The concentration and quality of total RNA were determined with a NanoDrop 2000C spectrophotometer (Thermo Fisher Scientific, Waltham, MA). Samples with purity of 1.8-2 and integrity over 1.8 were used for array analysis.

treatment_protocol: Transduction-ready FIV-based pseudoviral particles were generated using pPACK-H1 Lentivector Packaging System together with 293TN cell line (SBI), at a titer of 1.06 × 109 IFU/ml.  Control was Lenti-scramble Hairpin control pseudoviral particles at a titer of 1 × 109 IFU/ml.  pmiRZIP lentivector expressing anti-miR-181a (SBI, Mountain View, CA) was used for permanent miR-181a knockdown.  Cells were cultured in 12-well plates at a density of 1× 105/well for 1 day, infected by pseudoviral particles (using a multiplicity of infection of 100 viruses per cell) and cultured for 72 hrs, then selected for puromycin (5µg/ml) resistance for stable cell lines. Stably transduced cells were used for the experiment. Transfections were performed with GenMute transfection reagent (SignaGen Laboratories, Gaithersburg, MD).

value: untreated


title: DGM-10157_M12_sm (demographics_pollution)

description:
DGM-10157
307SAE-S_PM2.5_resid.csv

value: small airway epithelium brushing


title: CS-1_anti-miR-181a lentivector_rep1

value: anti-miR-181a lentivector


title: CS-1_anti-miR-181a lentivector_rep2


title: CS-1_anti-miR-181a lentivector_rep3


title: DGM-10132_M12_sm (demographics_pollution)

description:
DGM-10132
307SAE-S_PM2.5_resid.csv


title: CS-1_untreated_rep2


title: TBT rep 4

city: Irvine

first: Bassem

middle: Merit

last: Shoucri

state: CA

address: 4351 Natural Sciences 2

institute: University of California Irvine

data_processing:
The csfasta/QV.qual sequences were aligned to the NCBI37/mm9 mouse genome reference sequence to obtain the bam format aligned read data using the NovoAlignCS color- space aligner (Novocraft Technologies) with the following command line: “novoalignCS -d Mouse.mm9.Exons.index -f csfastafile.csfasta -H -k -oSAM -t 110 -v 0 0 70 [>]([^:]*) -F CSFASTAnQV -r All 10 -oSAM.” The bam-format data of mapped reads were examined using the fastQC deep-sequencing reads quality control tool (Simon Andrews, Babraham Institute) to exclude poor-quality reads from the study. Quality control-passed mapped reads were subjected to extraction of uniquely mapped reads using samtools
Uniquely mapped reads were assigned to the mm9 gene model and on-exon reads were counted using the Bioconductor package “Rsubread”. The assigned read counts were normalized using Bioconductor package “DESeq2” using the regularized logarithm (rlog) transformation.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: RNA_counts.txt was generated in Rsubread as indicated above. reg.log.norm.counts.txt was generated in DESeq2 as described above.

organism: Mus musculus

growth_protocol: Mouse bone marrow-derived mesenchymal stem cells (MSCs; OriCell, Cyagen Biosciences, Santa Clara, CA) from female C57BL/6 mice were stored at passage 9 in liquid N2. Cells were maintained and expanded at subconfluence in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% calf bovine serum, 10 mM HEPES, 1 mM sodium pyruvate, 100 IU/mL penicillin, and 100 ug/mL streptomycin.

extract_protocol:
RNA for sequencing was isolated using a miRNeasy Micro Kit (Qiagen). Intact RNA integrity (RIN > 9.0) of total RNA samples was confirmed using the Agilent RNA 6000 Nano Kit for Bioanalyzer (Agilent Technologies).
After ribosomal RNA removal using the RiboMinus Eukaryote System v2 kit (Life Technologies), non-directional RNA-seq deep sequencing libraries for the ABI/SOLiD platform were constructed using the SOLiD Total RNA-seq Kit and EZ Bead (Life Technologies). Deep sequencing was performed using the SOLiD 5500XL deep sequencer (50 nt, single non-directional reads; Life Technologies), and the XSQ-format raw data were converted to the csfasta/QV.qual format using the XSQ tool Linux script provided by Life Technologies.

treatment_protocol: To differentiate MSCs into adipocytes cells were plated at 15,000 cells/cm2 and allowed to proliferate for 72 hours, at which point they were confluent and ready for adipose induction. Media was then switched to Minimal essential medium alpha medium (αMEM) supplemented with 15% fetal bovine serum, 10 mM HEPES, 2 mM L-Glutamine, 100 IU/mL penicillin, 100 ug/mL streptomycin, and an adipose induction cocktail (MDI) containing 1 uM dexamethasone, 5 ug/mL insulin, and 0.5 mM isobutylmethylxanthine. Ligands (0.1% DMSO, 500 nM rosiglitazone, 50 nM tributyltin) were added in conjunction with differentiation media.

tag: strain

tag: passage


title: CS-1_untreated_rep1


title: DGM-10132_M0_sm (demographics_pollution)

description:
DGM-10132
307SAE-S_PM2.5_resid.csv

tag: smoking status


title: SKNMC_PHF19KO_2

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts and FPKM values for each sample

source_name: SK-N-MC

growth_protocol: RD-ES (CLS), CADO-ES1 (DSMZ) SK-N-MC and SK-NEP1 cell lines (ATCC) were maintained in RPMI-1640 media (Life Technologies) supplemented with 10% FBS. CHLA-10 cells (Children’s Oncology Group) were maintained in DMEM (Life Tech) supplemented with 10% FBS. All cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with DMSO or 500nM JQ1 for 48 hrs followed by total RNA extraction. For shFLI or shBRD4, cells were infected with lentivirus and selected using Puromycin . For PHF19KO, SKNMC cells were infected with the guide RNA containing lentivirus  and selected using Puromycin.

value: Ewing Sarcoma

value: SK-N-MC

value: knockout of PHF19 gene


title: SKNMC_PHF19KO_1


title: DGM-10132_M6_sm (demographics_pollution)

description:
DGM-10132
307SAE-S_PM2.5_resid.csv

tag: 30-day mean pm2.5 exposure level


title: SKNMC_JQ1_2

value: JQ1 treatment for 48hrs


title: TBT rep 2

source_name: bone marrow-derived mesenchymal stem cells


title: TBT rep 1


title: CS-1_control lentivector_rep2

value: control lentivector


title: CS-1_control lentivector_rep1


title: ROSI rep 4


title: DGM-10130_M6_sm (demographics_pollution)

description:
DGM-10130
307SAE-S_PM2.5_resid.csv

tag: time of serial bronchoscopy (month)


title: CS-1_control lentivector_rep3


title: TBT rep 3


title: ROSI rep 3


title: DGM-10130_M3_sm (demographics_pollution)

description:
DGM-10130
307SAE-S_PM2.5_resid.csv

tag: cell type


title: ROSI rep 2


title: SKNMC_DMSO_1

value: control cells dmso treated


title: SKNMC_DMSO_2


title: ROSI rep 1


title: DGM-10130_M12_sm (demographics_pollution)

description:
DGM-10130
307SAE-S_PM2.5_resid.csv


title: DMSO rep 3


title: SKNMC_JQ1_1


title: DGM-02164_M3_sm (demographics_pollution)

description:
DGM-02164
307SAE-S_PM2.5_resid.csv


title: DMSO rep 2


title: RDES_JQ1_2

source_name: RD-ES

value: RD-ES


title: DMSO rep 1


title: RDES_JQ1_1


title: DGM-02164_M12_sm (demographics_pollution)

description:
DGM-02164
307SAE-S_PM2.5_resid.csv


title: RDES_DMSO_2


title: mouse 1wk phalanx PZ4

city: Bethesda

first: Julian

middle: CK

last: Lui

state: MD

address: 10 Center Drive

institute: NICHD, NIH

description: mouse 29

data_processing:
Library was sequenced on HiSeq 3000 System (Illumina)
Approximately 40 million 50bp paired-end total reads were generated from each sample.
Alignment of RNA-Seq data was performed with RNA-STAR (v2.4.2) against the mouse mm10 build and rat rn6 build
Gene-based read quantitation was performed using SubRead featureCounts (v1.4.6)
Read counts were normalized by Ralative Log Expression (RLE) method and evaluated for differential expression using the Bioconductor package DESeq2
Genome_build: mm10 and rn6
Supplementary_files_format_and_content: excel file containing normalized raw counts of mapped genes in each sample

source_name: 1wk phalanx PZ4

growth_protocol: animals were fed ad lib

extract_protocol:
freshly frozen bone/cartilage were sectioned and microdissected with laser capture microdissection and RNA were extracted with Rneasy Micro Kit
RNA-Seq libraries were then constructed using Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA)

value: 1 week

value: phalanx

tag: zone

value: proliferative zone of growth plate

value: chondrocytes


title: mouse 1wk phalanx PZ5

description: mouse 30

source_name: 1wk phalanx PZ5


title: mouse 1wk phalanx PZ3

description: mouse 28

source_name: 1wk phalanx PZ3


title: RDES_DMSO_1


title: DGM-02164_M0_sm (demographics_pollution)

description:
DGM-02164
307SAE-S_PM2.5_resid.csv


title: DGM-01961_M0_sm (demographics_pollution)

description:
DGM-01961
307SAE-S_PM2.5_resid.csv


title: DGM-02164_M6_sm (demographics_pollution)

description:
DGM-02164
307SAE-S_PM2.5_resid.csv


title: CHLA10_shBRD4_2

value: shBRD4 knockdown


title: mouse 4wk tibia PZ 5

description: mouse 25

source_name: 4wk tibia PZ 5

value: 4 weeks

value: tibia


title: CHLA10_shFLI1_2

value: shFLI1 knockdown


title: CHLA10_shBRD4_1


title: DGM-01753_M6_sm (demographics_pollution)

description:
DGM-01753
307SAE-S_PM2.5_resid.csv

value: COPD smoker

value: small airway epithelium brushing


title: mouse 1wk phalanx PZ1

description: mouse 26

source_name: 1wk phalanx PZ1


title: DGM-01753_M3_sm (demographics_pollution)

description:
DGM-01753
307SAE-S_PM2.5_resid.csv


title: DMSO rep 4


title: mouse 4wk tibia PZ 4

description: mouse 24

source_name: 4wk tibia PZ 4


title: mouse 1wk phalanx PZ2

description: mouse 27

source_name: 1wk phalanx PZ2


title: Control, biological rep3

city: Hangzhou

first: Ping

last: Wang

address: 38 West Lake Avenue

country: China

institute: Affiliated 3rd Hospital of Hangzhou

hyb_protocol: After fragmentation, cRNA was hybridized for 16 hr at 45C on Human GeneChip primeview. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray raw data was normalized and analyzed using Affy and Limma program package in R language. RMA algorithm was employed for data normalized in Affy package.

label_protocol: Biotinylated cRNA were performed according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: melanoma cell line

tag: genotype/variation

value: Control


title: Control, biological rep1


title: CHLA10_shFLI1_1

value: Ewing Sarcoma


title: Control, biological rep2


title: DGM-01753_M12_sm (demographics_pollution)

description:
DGM-01753
307SAE-S_PM2.5_resid.csv


title: CHLA10_JQ1_2

value: JQ1 treatment for 48hrs


title: rat 1wk phalanx HZ 5

description: rat 30

organism: Rattus norvegicus

source_name: 1wk phalanx HZ 5

tag: age

value: hypertrophic zone of growth plate

value: Sprague Dawley


title: UEB2S knock down, biological rep3

description: UBE2S knock down-3

source_name: A375_UEB2S knockdown

value: UEB2S knockdown


title: mouse 4wk tibia PZ 3

description: mouse 23

source_name: 4wk tibia PZ 3


title: DGM-01753_M0_sm (demographics_pollution)

description:
DGM-01753
307SAE-S_PM2.5_resid.csv

source_name: small airway epithelium brushing


title: DGM-01275_M0_sm (demographics_pollution)

description:
DGM-01275
307SAE-S_PM2.5_resid.csv


title: CHLA10_JQ1_1


title: rat 1wk phalanx HZ 3

description: rat 28

source_name: 1wk phalanx HZ 3

value: 1 week


title: CHLA10_DMSO_2

value: control cells dmso treated


title: genomic DNA from semen sample 6

type: genomic

city: Chengdu

first: Luyao

last: Li

address: Fa Yi Building, No.16, Section 3, Renmin Nan Road, Chengdu, China

institute: Institute of Forensic Medicine, West China School of Basic Sciences and Forensic Medicine, Sichuan University

description: normal semen sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Cy5 and Cy3

source_name: semen sample 6

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: ethnicity

value: Chinese

tag: gender

value: male

value: semen

tag: age(years)


title: mouse 4wk tibia PZ 1

description: mouse 21

source_name: 4wk tibia PZ 1

value: 4 weeks

tag: tissue

value: proliferative zone of growth plate

value: chondrocytes


title: DGM-01749_M0_sm (demographics_pollution)

description:
DGM-01749
307SAE-S_PM2.5_resid.csv

value: COPD smoker


title: rat 1wk phalanx HZ 4

description: rat 29

source_name: 1wk phalanx HZ 4

value: phalanx


title: rat 1wk phalanx HZ 2

description: rat 27

source_name: 1wk phalanx HZ 2


title: mouse 4wk tibia PZ 2

description: mouse 22

source_name: 4wk tibia PZ 2

value: tibia


title: CHLA10_DMSO_1

tag: cell line


title: mouse 1wk tibia PZ 5

description: mouse 20

source_name: 1wk tibia PZ 5


title: mouse 1wk tibia PZ 4

description: mouse 19

source_name: 1wk tibia PZ 4


title: DGM-00061_M6_sm (demographics_pollution)

description:
DGM-00061
307SAE-S_PM2.5_resid.csv

value: small airway epithelium brushing


title: DGM-00167_M0_sm (demographics_pollution)

description:
DGM-00167
307SAE-S_PM2.5_resid.csv


title: rat 1wk phalanx HZ 1

description: rat 26

source_name: 1wk phalanx HZ 1


title: mouse 1wk tibia PZ 3

description: mouse 18

source_name: 1wk tibia PZ 3


title: rat 1wk phalanx PZ5

description: rat 25

source_name: 1wk phalanx PZ5


title: UEB2S knock down, biological rep2

description: UBE2S knock down-2

value: melanoma cell line


title: UEB2S knock down, biological rep1

description: UBE2S knock down-1


title: genomic DNA from semen sample 4

description: normal semen sample

source_name: semen sample 4


title: CadoES_JQ1_1

source_name: Cado-ES

value: Ewing Sarcoma

value: Cado-ES

tag: treatment

value: JQ1 treatment for 48hrs


title: CadoES_JQ1_2


title: DGM-00061_M3_sm (demographics_pollution)

description:
DGM-00061
307SAE-S_PM2.5_resid.csv


title: genomic DNA from semen sample 3

description: normal semen sample

source_name: semen sample 3


title: genomic DNA from semen sample 5

description: normal semen sample

source_name: semen sample 5


title: rat 1wk phalanx PZ3

description: rat 23

source_name: 1wk phalanx PZ3

value: Sprague Dawley


title: CadoES_DMSO_1


title: DGM-00061_M12_sm (demographics_pollution)

description:
DGM-00061
307SAE-S_PM2.5_resid.csv

source_name: small airway epithelium brushing


title: mouse 1wk phalanx HZ 4

description: mouse 14

value: 1 week

value: hypertrophic zone of growth plate


title: genomic DNA from semen sample 1

description: normal semen sample

source_name: semen sample 1

value: Chinese


title: genomic DNA from semen sample 2

description: normal semen sample

source_name: semen sample 2

value: male


title: rat 1wk phalanx PZ4

description: rat 24

source_name: 1wk phalanx PZ4


title: mouse 1wk tibia PZ 2

description: mouse 17

source_name: 1wk tibia PZ 2


title: CadoES_DMSO_2

value: control cells dmso treated


title: Biopsy tube4 part3

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description:
single cell RNA-seq
Renal biopsy was minced into small pieces and incubated in freshly prepared dissociation buffer containing 0.25% trypsin and 40U/ml DNase I. Dissociated cells were harvested every 10 min by filtering the cell suspension through a 70 µm cell strainer (pluriSelect) into 10% FBS buffer on ice. The residual biopsy tissue trapped on the cell strainer was dissociated once again with 1 mL dissociation buffer for 10 min, passed through cell strainer into the same FBS buffer from the first collection. We repeated this dissociation procedure three times until most of the tissue had been dissociated into single cells (total dissociation time was 30 min). Finally, cells were collected by centrifugation at 400 g for 5 min, resuspended in inDrop cell suspension buffer (9% Optiprep) and strained by a 40 µm cell mesh (pluriSelect) to further remove cell clumps and large fragments.
InDrop was performed as previous described. In brief, cells were diluted into 60,000 cells/mL in 9% Optiprep buffer. Single cell encapsulation was carried out using an inDrop instrument and microfluidic chip manufactured by 1CellBio. In total, four tubes of cells with an estimate of 1,000 cells/tube were collected. Library preparation was performed according to the protocol provided by the manufacturer. We used low PCR cycles (8-9 cycles) to amplify the libraries from this sample. Libraries were sequenced by HiSeq 2500 and NextSeq with a sequencing depth of 50K reads/cell.

data_processing:
Pair-end reads were processed by a newly developed inDrop computational pipeline (https://github.com/hms-dbmi/dropEst). In brief, cell barcodes and UMIs from the library were extracted from read1 by the dropTag program and added to the names of the transcript reads, resulting in a new fastq file for read alignment. We used STAR (version 2.5.3a) to map the high quality reads to the human genome (GRCh38). Only reads that were uniquely mapped to the genome (~70% of the total reads) were used for UMIs counts. We next ran the dropEst program to estimate the accurate molecular counts, which generated a UMI count matrix for each gene in each cell.
Supplementary_files_format_and_content: counts

source_name: Transplant kidney

extract_protocol:
RNA libraries were prepared for sequencing using standard inDrops procedure
Single cell RNA-seq

tag: protocol

value: inDrop

value: 21 yrs


title: DGM-00061_M0_sm (demographics_pollution)

description:
DGM-00061
307SAE-S_PM2.5_resid.csv


title: mouse 1wk phalanx HZ 5

description: mouse 15

source_name: 1wk phalanx HZ 5

value: chondrocytes


title: mouse 1wk tibia PZ 1

description: mouse 16

source_name: 1wk tibia PZ 1

value: proliferative zone of growth plate


title: Biopsy tube4 part4


title: rat 1wk phalanx PZ2

description: rat 22

source_name: 1wk phalanx PZ2

value: phalanx


title: rat 4wk tibia HZ 5

description: rat 20

source_name: 4wk tibia HZ 5

value: 4 weeks

value: tibia


title: rat 4wk tibia HZ 4

description: rat 19

source_name: 4wk tibia HZ 4


title: mouse 1wk phalanx HZ 3

description: mouse 13

source_name: 1wk phalanx HZ 3


title: rat 1wk phalanx PZ1

description: rat 21

source_name: 1wk phalanx PZ1


title: mouse 1wk phalanx HZ 2

description: mouse 12

source_name: 1wk phalanx HZ 2


title: Biopsy tube4 part2


title: Y2-Tvm-Unstim

city: Clayton

first: Kylie

last: Quinn

state: VIC

address: 19 Innovation Walk

country: Australia

institute: Monash University

description: old_prefix: Y2_Tvm_Unstim

data_processing:
Adapters were trimmed with Trim Galore and trimmed reads were aligned to mm10 genome with TopHat2 keeping the strand information. Only concordantly aligned read pairs were retained, duplicate fragments were removed using picard MarkDuplicates and read pairs with mapping quality less than 5 were discarded. Retained read pairs were assigned to genes using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts file was generated by featureCounts

source_name: Young T-cells memory unstimulated

growth_protocol: We sorted TN cells (CD44lo), TVM cells (CD49dlo CD44hi) and CD8 conventional memory T (TMEM) (CD49dhi CD44hi) cells from naive young mice (3 months old) or aged mice (18 months old). To sort enough cells of each type, we pooled 4 mice, so each replicate represents a pooled sample of 4 mice.

extract_protocol:
We had 24 samples stored frozen in TRIzol until RNA extraction (young (Y) and aged (A); replicate 1 and replicate 2, with cells pooled from 4 mice in each replicate; TN, TVM and TMEM cells; unstim and stim match across each replicate). Due to lane capacity limits for sequencing, we processed these samples for RNA and sequencing in two batches (Batch 1- Y1_Tn_Unstim, Y1_Tvm_Unstim, Y1_Tmem_Unstim, Y1_Tn_Stim, Y1_Tvm_Stim, Y1_Tmem_Stim, A1_Tn_Stim, A1_Tvm_Stim, A1_Tmem_Stim, A2_Tn_Stim, A2_Tvm_Stim, A2_Tmem_Stim. Batch 2- Y2_Tn_Unstim, Y2_Tvm_Unstim, Y2_Tmem_Unstim, Y2_Tn_Stim, Y2_Tvm_Stim, Y2_Tmem_Stim, A1_Tn_Unstim, A1_Tvm_Unstim, A1_Tmem_Unstim, A2_Tn_Unstim, A2_Tvm_Unstim, A2_Tmem_Unstim). Of note, in Batch 2 we ran a duplicate of Y1_Tn_Unstim (Y1_Tn_Unstim_norm) to test for any batch effect, but none was observed. RNA was extracted using chloroform extraction followed by isopropanol precipitation, extracted RNA was treated with recombinant DNAse I (Roche) according to the manufacturer’s instructions then purified using the RNeasy MinElute Cleanup columns (Qiagen) and analysed for RNA quality using the RNA 6000 Nano kit (Agilent) on an Agilent 2100 Bioanalyzer. Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq.
Samples were prepared with the Illumina TruSeq RNA v2 sample preparation protocol (cDNA synthesis, adapter ligation, PCR amplification) (Illumina) and run using 100 bp paired end sequencing on an Illumina Hi-Seq.

treatment_protocol: Each replicate of biological material was split in half, with half the sample frozen in TRIzol immediately for our directly ex vivo or "unstim" sample and the other half of the sample stimulated with plate-bound anti-CD3 (10ug/mL), anti-CD8a (10ug/mL) and antiCD11a (5 ug/mL) and soluble recombinant human IL-2 (10U/mL) for 5 hours, before being frozen in TRIzol as our stimulated or "stim" samples. We therefore collected 2 replicates for each cell subsets (designated "1" and "2") and the "unstim" and "stim" samples are matched.

tag: mouse age

value: Young (3 months old)

tag: replicate

value: Virtual memory (Tvm)

tag: stimulation

value: Unstimulated (ex vivo processed)


title: mouse 1wk phalanx HZ 1

description: mouse 11

source_name: 1wk phalanx HZ 1

tag: strain


title: Y2-Tvm-Stim

description: old_prefix: Y2_Tvm_Stim

source_name: Young T-cells virtual memory stimulated


title: DmSTING RNAi, c-di-GMP, rep1

city: Pullman

first: Alan

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

description: Gene expression data following inoculation'

hyb_protocol: Affynetrix GeneChip Hybridization, Wash, and Stain Kit, Fluidics Station 450 (fluidics Midi_euk3 v3) and Hybridization Oven 640

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: GeneSpring GX 14.5 using the default summarization/scaling/normalization algorithms.

organism: Drosophila melanogaster

source_name: S2cells DmSTING RNAi, c-di-GMP treated

label_protocol: Affymetrix GeneChip 3' IVT Express Kit

growth_protocol: Schneider's medium containing 10% FBS and antibiotics was used to grow S2 cells

extract_protocol: Total RNA was extracted using Thermo GeneJet RNA purification kit. RNA QC was performed using Advanced Analytical Technology Fragment Analyzer

treatment_protocol: S2 cells were first transfected with dsRNAs for DmSTING RNA or scrambled RNAi, using Invitrogen CellfectinII following manufacturer's instructions.  72h post-transfection, cells were transfected with a c-di-GMP (Biolog C057) or mock transfected with Cellfectin alone. Total RNA was extracted 24h later.

tag: genotype

value: DmSTING RNAi

value: S2 cells

value: c-di-GMP

tag: hours post-infection


title: DmSTING RNAi, c-di-GMP, rep2


title: mouse 4wk tibia HZ 5

description: mouse 10

value: hypertrophic zone of growth plate

tag: cell type


title: Y2-Tn-Unstim

description: old_prefix: Y2_Tn_Unstim

source_name: Young T-cells natural unstimulated

value: True naive (Tn)


title: rat 4wk tibia HZ 1

description: rat 16

source_name: 4wk tibia HZ 1

tag: zone

value: Sprague Dawley


title: DmSTING RNAi, mock, rep2

source_name: S2cells DmSTING RNAi, mock treated

value: scrambled RNAi

value: mock (Cellfectin only)


title: rat 4wk tibia PZ 5

description: rat 15

source_name: 4wk tibia PZ 5


title: rat 4wk tibia HZ 3

description: rat 18

source_name: 4wk tibia HZ 3


title: rat 4wk tibia HZ 2

description: rat 17

source_name: 4wk tibia HZ 2


title: Y2-Tn-Stim

description: old_prefix: Y2_Tn_Stim

source_name: Young T-cells natural stimulated


title: Y2-Tmem-Unstim

description: old_prefix: Y2_Tmem_Unstim

value: Conventional memory (Tmem)


title: mouse 4wk tibia HZ 3

description: mouse 8

value: chondrocytes


title: mouse 4wk tibia HZ 4

description: mouse 9


title: mouse 4wk tibia HZ 2

description: mouse 7


title: mouse 4wk tibia HZ 1

description: mouse 6


title: DmSTING RNAi, mock, rep1


title: rat 4wk tibia PZ 3

description: rat 13

source_name: 4wk tibia PZ 3

value: proliferative zone of growth plate


title: rat 4wk tibia PZ 4

description: rat 14

source_name: 4wk tibia PZ 4


title: Y2-Tmem-Stim

description: old_prefix: Y2_Tmem_Stim

source_name: Young T-cells memory stimulated


title: mouse 1wk tibia HZ 5

description: mouse 5

source_name: 1wk tibia HZ 5

value: 1 week


title: Y1-Tn-Unstim-norm

description: old_prefix: Y1_Tn_Unstim_norm

source_name: Same as Y1-Tn-Unstim


title: A2-Tvm-Unstim

description: old_prefix: A2_Tvm_Unstim

source_name: Aged T-cells virtual memory unstimulated

value: Aged (18 months old)


title: scrambled RNAi, c-di-GMP, rep1

source_name: S2cells scrambled RNAi, c-di-GMP treated


title: rat 4wk tibia PZ 2

description: rat 12

source_name: 4wk tibia PZ 2

value: 4 weeks

value: tibia


title: scrambled RNAi, c-di-GMP, rep2


title: scrambled RNAi, mock, rep1

source_name: S2cells scrambled RNAi, mock treated


title: listeria infected DmSTING RNAi flies, rep2

source_name: whole flies, DmSTING RNAi, listeria inoculated

growth_protocol: Flies were raised on standard cornmeal at 25C and 65% relative humidity.

extract_protocol: Flies were homogenized and total RNA was extracted using Thermo GeneJet RNA purification kit. RNA QC was performed using Advanced Analytical Technology Fragment Analyzer

treatment_protocol: Intrathoracic injection with 23 nl of 10e7 CFU/ml listeria using Drummond scientific nanoject II

value: DmSTING RNAi flies

value: whole adult flies

tag: pathogen

value: listeria monocytogenes


title: mouse 1wk tibia HZ 4

description: mouse 4

source_name: 1wk tibia HZ 4

tag: age


title: scrambled RNAi, mock, rep2

value: S2 cells


title: A2-Tn-Unstim

description: old_prefix: A2_Tn_Unstim

source_name: Aged T-cells natural unstimulated

value: Unstimulated (ex vivo processed)


title: rat 4wk tibia PZ 1

description: rat 11

source_name: 4wk tibia PZ 1


title: listeria infected DmSTING RNAi flies, rep1


title: mouse 1wk tibia HZ 3

description: mouse 3

source_name: 1wk tibia HZ 3

value: hypertrophic zone of growth plate


title: mouse 1wk tibia HZ 2

description: mouse 2

source_name: 1wk tibia HZ 2


title: A2-Tmem-Unstim

description: old_prefix: A2_Tmem_Unstim

source_name: Aged T-cells memory unstimulated


title: A1-Tvm-Unstim

description: old_prefix: A1_Tvm_Unstim

value: Virtual memory (Tvm)


title: mouse 1wk tibia HZ 1

description: mouse 1

source_name: 1wk tibia HZ 1


title: mock infected DmSTING RNAi flies, rep2

source_name: whole flies, DmSTING RNAi, PBS inoculated

value: PBS


title: rat 1wk tibia HZ 3

description: rat 8

value: Sprague Dawley


title: A1-Tn-Unstim

description: old_prefix: A1_Tn_Unstim

value: True naive (Tn)


title: rat 1wk tibia HZ 2

description: rat 7


title: A1-Tmem-Unstim

description: old_prefix: A1_Tmem_Unstim

value: Conventional memory (Tmem)


title: Y1-Tmem-Unstim

description: old_prefix: 12_

source_name: Young T-cells memory unstimulated

value: Young (3 months old)

value: Conventional memory (Tmem


title: rat 1wk tibia HZ 1

description: rat 6

value: 1 week

value: chondrocytes


title: mock infected DmSTING RNAi flies, rep1


title: rat 1wk tibia PZ 5

description: rat 5

source_name: 1wk tibia PZ 5

value: proliferative zone of growth plate


title: listeria infected control flies, rep1

source_name: whole flies, control, listeria inoculated

value: control flies


title: Y1-Tvm-Unstim

description: old_prefix: 11_

source_name: Young T-cells virtual memory unstimulated


title: rat 1wk tibia HZ 5

description: rat 10

source_name: 1wk tibia HZ 5

value: tibia


title: Y1-Tn-Unstim

description: old_prefix: 10_

source_name: Young T-cells natural unstimulated


title: S_18h_N3: 18 Hour Stressed Control

city: Notre Dame

first: David

middle: Sungin

last: Kang

state: IN

address: 44 Galvin Life Science Center, Department of Biological Sciences, Severson Lab

institute: University of Notre Dame

data_processing:
FASTQC run statistics
EdgeR and DESeq2 alignment and differential expression
DEseq2 normalization
WGCNA analysis of gene correlation networks
Cluster tree visualziation
Multiple dimensional scaling plot and global-cross talk mapping
Genome_build: AaegL3.31
Supplementary_files_format_and_content: FastQ files and csv files with processed values

organism: Aedes aegypti

source_name: Naïve bloodmeal

growth_protocol: Rearing chambers were kept at 26°C, 85% relative humidity with a 16 hour light:8 hour dark (L:D) cycle with a 30 minute crepuscular period.  Larvae were then raised under density induced nutritionally stressed or optimal conditions. 75 first instar larvae were placed in 1 liter of distilled water for the optimal treatment, and 750 larvae in the same volume of water, for the stressed treatment. One day after hatching, larvae were provided 75 mg of bovine liver powder (MP Biomedicals, LLC), then on day two 0 mg, 75 mg on day three, 113 mg on day four and finally 150 mg on day five. Upon pupation, individuals were transferred to 500 mL of fresh water in 20x20x30 cm mesh cages until adult eclosion. Mosquitoes were then maintained on 10% sucrose saturated cotton balls until 7 days post eclosion. As previously described

extract_protocol:
Qiagen RNeasy
TruSeq RNA Library Prep

treatment_protocol: For the infectious blood meals, frozen DENV2 supernatant (TCID50 of 106.5) was thawed and mixed with defibrinated sheep blood (Colorado Serum Company) in an equal ratio before being offered to female mosquitoes using an artificial glass membrane feeder with a rat skin membrane at 37°C. Stressed and optimal exposure to dengue were performed simultaneously from the same aliquots of DENV2.

value: Whole body

tag: hours infected

tag: optimal/stressed

value: Stressed


title: mock infected control flies, rep1

source_name: whole flies, control, PBS inoculated

value: whole adult flies


title: rat 1wk tibia HZ 4

description: rat 9


title: mock infected control flies, rep2


title: listeria infected control flies, rep2

value: listeria monocytogenes


title: rat 1wk tibia PZ 4

description: rat 4

source_name: 1wk tibia PZ 4


title: S_18h_N1: 18 Hour Stressed Control


title: Y1-Tmem-Stim

description: old_prefix: 9_

source_name: Young T-cells memory stimulated


title: rat 1wk tibia PZ 3

description: rat 3

source_name: 1wk tibia PZ 3


title: S_18h_3: 18 Hour Stressed Dengue

source_name: DENV2 JAM1409


title: Y1-Tvm-Stim

description: old_prefix: 8_

source_name: Young T-cells virtual memory stimulated


title: rat 1wk tibia PZ 2

description: rat 2

source_name: 1wk tibia PZ 2


title: Y1-Tn-Stim

description: old_prefix: 7_

source_name: Young T-cells natural stimulated


title: YMW, biological rep3

city: Wageningen

first: Soumya

middle: Kanti

last: Kar

state: I am not in the U.S. or Canada

address: De Elst1

department: Animal Science Group

country: Netherlands

institute: WUR

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c35

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: Yellow meal worm (YMW), exposed for six hours, duodenum

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Female C57BL/6J mice, aged 9 weeks, were purchased from Harlan (Horst, the Netherlands), and housed in a light and temperature-controlled animal facility of Wageningen University (12:12 h light/dark cycle, 20±2 °C). Mice had free access to to standard diet (AIN93M) and water.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer's protocol. RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice were euthanized and dissected to remove the duodenum which was used to generate the enteroids. Three wells of 96-wells plate with confluent 2D monolayer of enteroids culture was exposed to 4% (w/v) of each protein source (viz. soybean meal, SBM; casein, CAS; spray dried plasma protein, SDPP; and yellow meal worm, YMW) or DMEM as a control and incubated for 6 hours. Total RNA was isolated to perform microarray. Three wells of 96-wells plate with confluent 2D monolayer of enteroids culture which was exposed to of one of the protein source or DMEM is considered as 1 sample (n); n= 3 per treatment or control group.

value: Duodenum

tag: Sex

value: Female

value: 9 weeks

value: Confluent 2D monolayer of enteroids

tag: agent

value: YMW


title: rat 1wk tibia PZ 1

description: rat 1

source_name: 1wk tibia PZ 1

tag: tissue

value: Sprague Dawley


title: SDPP, biological rep3

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c33

source_name: Spray dried plasma protein (SDPP), exposed for six hours, duodenum

value: SDPP


title: S_18h_2: 18 Hour Stressed Dengue


title: S_18h_N2: 18 Hour Stressed Control


title: CAS, biological rep3

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c32

source_name: Casein (CAS) , exposed for six hours, duodenum

value: CAS


title: Media blank, biological rep3

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c36

source_name: Media blank (B), exposed for six hours, duodenum

value: Media blank


title: S_18h_1: 18 Hour Stressed Dengue


title: Media blank, biological rep2

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c30


title: SBM, biological rep3

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c31

source_name: Soybean (SBM), exposed for six hours, duodenum

value: SBM


title: A2-Tmem-Stim

description: old_prefix: 6_

source_name: Aged T-cells memory stimulated

value: Aged (18 months old)

value: Conventional memory (Tmem


title: S_3h_N2: 3 Hour Stressed Control


title: A2-Tvm-Stim

description: old_prefix: 5_

source_name: Aged T-cells virtual memory stimulated

value: Virtual memory (Tvm)


title: A2-Tn-Stim

description: old_prefix: 4_

source_name: Aged T-cells natural stimulated

value: True naive (Tn)


title: YMW, biological rep2

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c29


title: S_3h_N1: 3 Hour Stressed Control

source_name: Naïve bloodmeal

value: Whole body

value: Stressed


title: A1-Tvm-Stim

description: old_prefix: 2_


title: S_3h_1: 3 Hour Stressed Dengue


title: A1-Tn-Stim

description: old_prefix: 1_


title: S_3h_3: 3 Hour Stressed Dengue


title: O_18h_N2: 18 Hour Optimal Control

value: Optimal


title: O_18h_N3: 18 Hour Optimal Control


title: SDPP, biological rep2

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c27

value: Duodenum


title: S_3h_N3: 3 Hour Stressed Control


title: O_18h_N1: 18 Hour Optimal Control


title: O_18h_3: 18 Hour Optimal Dengue


title: A1-Tmem-Stim

description: old_prefix: 3_


title: O_18h_2: 18 Hour Optimal Dengue


title: Media blank, biological rep1

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c24

value: Female


title: YMW, biological rep1

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c23

value: 9 weeks


title: MS2-082A

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

description:
CisR-MS2 overexpression
01.RPKM_normalized.txt

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Lactococcus lactis subsp. cremoris NZ9000, NC_017949.1,  GI:389853198, Assembly: GCF_000143205.1, 12-AUG-2015
Supplementary_files_format_and_content: Tab delimited text file

organism: Lactococcus cremoris

source_name: Cell culture

growth_protocol: Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: cells were induced with nisin to overexpress (MS2-)LLMGnc_082 (CisR)

tag: accession

value: CisR-MS2 overexpression

tag: growth stage

value: Exponential


title: OIR1

city: Changsha

first: Yedi

last: Zhou

state: Hunan

address: No. 139, Middle Renmin Road

department: Department of Ophthalmology

institute: The Second Xiangya Hospital, Central South University

description: Experimental animals were postnatal day 17 pups of C57BL/6 mice (Hunan SJA Laboratory Animal Co. Ltd. Changsha, China)

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

source_name: Retina

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: The pups were sacrificed and the retinas were isolated and collected from the posterior segment of the eyes.

value: Postnatal day 17

tag: treatment

value: exposed to 75% oxygen at postnatal day (P)7 for 5 days


title: O_3h_N3: 3 Hour Optimal Control


title: LLMGnc_082B

description:
CisR overexpression
01.RPKM_normalized.txt

value: CisR overexpression


title: O_18h_1: 18 Hour Optimal Dengue


title: S_3h_2: 3 Hour Stressed Dengue


title: MS2-082B


title: OIR2


title: SBM, biological rep2

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c25

value: Confluent 2D monolayer of enteroids


title: OIR3


title: N3

value: room control


title: LLMGnc_082A


title: SDPP, biological rep1

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c21

value: SDPP


title: NZ9000_pNZ_LLMGnc_082_B

description:
CisR overexpression
02.RPKM_normalized.txt


title: CAS, biological rep2

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c26

value: CAS


title: O_3h_N1: 3 Hour Optimal Control


title: SBM, biological rep1

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c19

value: SBM


title: CAS, biological rep1

description:
Confluent 2D monolayer of enteroids are derived from a female C57BL/6J mice aged 9 weeks.
c20


title: A1552ΔqstR-TntfoX (1631+ara), replicate 2

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

data_processing:
Sequencing and data processing was done by Microsynth (Balgach, Switzerland) according to ChIP-Seq analysis pipeline (customized prokaryotic pipeline).
Reads were mapped onto the reference genome N16961 (accession numbers NC_002505 and NC_002506 for both chromosomes) and peak were detected.
Genome_build: Reference genome (NC_002505, NC_002506)
Supplementary_files_format_and_content: tsv files for detected peaks

organism: Vibrio cholerae

source_name: bacterial in vitro culture

growth_protocol: Bacterial cultures were grown in 100 ml LB medium supplemented with 0.02% arabinose under shaking conditions.

extract_protocol:
Bacteria were lysed with Ready-Lyse lysozyme solution in presence of protease inhibitors. The lysates were sonicated to shear DNA. Diluted lysates were pre-cleared with Protein A Dynabeads and then incubated with an anti-QstR antibody.
The Illumina TruSeq ChIP library preparation was followed by sequencing on NextSeq 500, mid-output, 2x75bp; R1: forward read, R2: reverse read

tag: strain info

value: A1552ΔqstR (ΔqstR) with TntfoX transposon

tag: genotype/variation

tag: growth media


title: A1552-TntfoX (1626+ara), replicate 2

value: A1552 (WT) with TntfoX transposon

value: LB medium supplemented with 0.02% arabinose


title: NZ9000_pNZ_LLMGnc_082_A

tag: strain

tag: genotype


title: NZ9000_pNZ8048wt_B

description:
Control empty pNZ8048
02.RPKM_normalized.txt

value: Control empty pNZ8048


title: A1552ΔqstR-TntfoX (1631+ara), replicate 1


title: O_3h_3: 3 Hour Optimal Dengue

source_name: DENV2 JAM1409

value: Whole body

value: Optimal


title: N1


title: N2


title: O_3h_2: 3 Hour Optimal Dengue


title: A1552-TntfoX (1626+ara), replicate 1


title: O_3h_1: 3 Hour Optimal Dengue


title: O_3h_N2: 3 Hour Optimal Control


title: NZ9000_pNZ8048wt_A


title: SRSF2 P95H HITS-CLIP rep 1

status: Public on Jun 18 2018

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description:
SRSF2 HITS-CLIP from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 1
SRSF2_differential_RNA_interactome.txt
HITS-CLIP

data_processing:
HITS-CLIP: adapter removal and collapse of duplicate reads were performed with FASTX-Toolkit (0.0.14). Reads were aligned to the human genome (GRCh38.p3) with Tophat (version 2.0.14), using the Gencode 23 transcript annotation as transcriptome guide. Candidate binding sites were collected from genomic positions with at least 1 crosslinking induced deletion and coverage in at least two of the four replicates. Differential analysis of WT vs P95H binding sites was performed with edgeR.  RNA-seq: read pairs were aligned to the human genome (GRCh38.p3) with STAR (version 2.5.3a, --quantMode GeneCounts), using the Gencode 23 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package. Alternative splicing analysis was performed with rMATS.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: SRSF2_differential_RNA_interactome.txt: tab-delimited text file of SRSF2 differentially bound exonic RNA regions (P95H vs WT). The file contains the genomic coordinates (columns 1-4), differential binding analysis (columns 5-7) and annotation of the regions.  SRSF2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-7) and sample-specific counts of aligned reads.

source_name: Human Erythroleukemia Cell Line (HEL)

growth_protocol: RPMI 10% FBS

extract_protocol:
HITS-CLIP: cells were UV-crosslinked (400mJ, Stratalinker 2400, Stratagene). RNA–protein complexes were immunoprecipitated with anti-Flag M2 Agarose beads (Sigma). RNA was partially digested with RNase A (Affymetrix) and P32-labeled (Perkin Elmer). SRSF2-RNA complexes were isolated by SDS-PAGE, treated with proteinase K, followed by RNA linker ligation.   RNA_seq: QIAGEN RNeasy minikit protocol
HITS-CLIP: Ilumina small RNA library protocol for linker ligation.   RNA-seq: rRNA depletion

treatment_protocol: Doxycycline 1mcg/ml x 36 hours

tag: sequencing method

value: HITS-CLIP

tag: stable transfection

value: SRSF2 P95H


title: SRSF2 P95H HITS-CLIP rep 3

description:
SRSF2 HITS-CLIP from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 3
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: SRSF2 WT HITS-CLIP rep 4

description:
SRSF2 HITS-CLIP from HEL cells stably expressing wild type SRSF2, biological replicate 4
SRSF2_differential_RNA_interactome.txt
HITS-CLIP

value: SRSF2 wild type


title: SRSF2 WT HITS-CLIP rep 2

description:
SRSF2 HITS-CLIP from HEL cells stably expressing wild type SRSF2, biological replicate 2
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: SRSF2 WT HITS-CLIP rep 3

description:
SRSF2 HITS-CLIP from HEL cells stably expressing wild type SRSF2, biological replicate 3
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: SRSF2 WT HITS-CLIP rep 1

description:
SRSF2 HITS-CLIP from HEL cells stably expressing wild type SRSF2, biological replicate 1
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: SRSF2 P95H HITS-CLIP rep 4

description:
SRSF2 HITS-CLIP from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 4
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: 9589

city: Indianapolis

first: Simone

last: Gupta

address: Lilly Corporate Center

institute: Eli Lilly & Company

description: α-cells ectopically expressing PDX1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to Genome Reference Consortium Mouse build 38 (GRCm38) using GSNAP
RNA sequencing quality on each sample was assessed for overall coverage, base composition, presence of adaptors and 3’ bias, among other factors. A subset of samples were excluded from further analyses due to poor sequencing quality, 3’ bias, contamination, or outlier status for technical or biological reasons, including outliers on the first principal component of principal component analysis (PCA) across the entire sample set or samples with PDX-1 expression levels exceeding 3 SD from the mean of each respective experimental group. 30 samples were included for all downstream analyses.
ANOVA models were used to eliminate machine, flow-cell, and lane effects. Gene count data were quantile normalized and log2-transformed. For each gene, a two-way ANOVA model was fitted to identify differential gene expression.
Genome_build: Genome Reference Consortium Mouse build 38 (GRCm38)
Supplementary_files_format_and_content: gene count data (quantile normalized and log2-transformed)

source_name: α-cells ectopically expressing PDX1

extract_protocol:
Mature α-cells from 3-month-old Glucagon-Venus mice, α-cells 30 days after DT from Glucagon-Venus; RIP-DTR mice, mature β-cells from 3-month-old Insulin-mCherry mice,α-cells ectopically expressing PDX1 from 3-month-old Glucagon-rtTA; TetO-Cre; R26YFP;CAG-Pdx1, α-cells expressing PDX1 30 days after DT from Glucagon-rtTA; TetO-Cre; R26YFP; CAGPdx1;RIP-DTR mice. Mice were DT-injected at 2-months of age. RNA from cells isolated by FACS was assessed for quality by Agilent bioanalyzer prior to library generation.
RNA prepared using the Qiagen RNeasy Micro Kit. cDNA was prepared using the Qiagen QuantiTect Reverse Transcription Kit starting from 1μg of RNA

tag: transgenic

value: aPdx1OE noDT

tag: conditions

value: Glucagon-rtTA; TetO-Cre; R26YFP;CAG-Pdx1 mice

tag: cell type

value: D050416 - Pancreatic alpha cells


title: 9409

description: Mature α-cells

source_name: Mature α-cells

value: ctl noDT

value: Glucagon-Venus mice


title: 8840

description: α-cells ectopically expressing PDX1


title: 9002

description: Mature α-cells


title: 8984

description: Mature α-cells


title: 6320

description: α-cells expressing PDX1 30 days after DT

value: aPdx1OE DT

value: Glucagon-rtTA; TetO-Cre; R26YFP; CAGPdx1;RIP-DTR mice


title: 23801

description: α-cells 30 days after DT

source_name: α-cells 30 days after DT

value: ctl DT

value: Glucagon-Venus; RIP-DTR mice


title: 14879

description: α-cells 30 days after DT


title: 14876

description: α-cells 30 days after DT


title: 14873

source_name: α-cells expressing PDX1 30 days after DT


title: 9000

description: α-cells ectopically expressing PDX1


title: 14871

description: α-cells 30 days after DT


title: 4908_23896

description: Mature α-cells


title: 9001

description: Mature α-cells


title: SRSF2 P95H HITS-CLIP rep 2

description:
SRSF2 HITS-CLIP from HEL cells stably expressing mutant SRSF2 (P95H), biological replicate 2
SRSF2_differential_RNA_interactome.txt
HITS-CLIP


title: 9416

description: α-cells ectopically expressing PDX1


title: 9412

description: α-cells ectopically expressing PDX1


title: 7525


title: mucosa next to tumor bottom crypt fraction, px 23

city: Singapore

first: Peh Yean

last: Cheah

address: 20 College Road

department: Colorectal Surgery

country: Singapore

institute: Singapore General Hospital

description: gene expression data from MT bottom crypt fraction for px 23

hyb_protocol: Following fragmentation, target cRNAs were hybridized to GeneChip Human Gene 1.0 ST Arrays at 45C for 17hr. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000-7G.

data_processing: Signals were analysed with the GeneChip operating system (GCOS) software. Quality assessment of the arrays was performed with Affymetrix Expression Console v1.1.  The CEL files were imported into Partek for further analysis.

source_name: colonic mucosa next to tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA

extract_protocol: Total RNA was extracted from each specimen using Qiagen RNA (tissue) extraction kit according to manufacturer's instructions.

value: colonic mucosa next to tumor


title: mucosa next to tumor top crypt fraction, px 22

description: gene expression data from MT top crypt fraction for px 22


title: mucosa next to tumor top crypt fraction, px 23

description: gene expression data from MT top crypt fraction for px 23


title: mucosa next to tumor bottom crypt fraction, px 22

description: gene expression data from MT bottom crypt fraction for px 22


title: mucosa next to tumor bottom crypt fraction, px 21

description: gene expression data from MT bottom crypt fraction for px 21


title: mucosa bottom crypt fraction, px 22

description: gene expression data from M bottom crypt fraction for px 22

source_name: colonic mucosa

value: colonic mucosa


title: mucosa top crypt fraction, px 23

description: gene expression data from M top crypt fraction for px 23


title: 15635


title: mucosa bottom crypt fraction, px 23

description: gene expression data from M bottom crypt fraction for px 23


title: mucosa next to tumor top crypt fraction, px 21

description: gene expression data from MT top crypt fraction for px 21


title: mucosa top crypt fraction, px 22

description: gene expression data from M top crypt fraction for px 22


title: mucosa next to tumor bottom crypt fraction, px 20

description: gene expression data from MT bottom crypt fraction for px 20


title: mucosa top crypt fraction, px 19

description: gene expression data from M top crypt fraction for px 19


title: mucosa next to tumor top crypt fraction, px 20

description: gene expression data from MT top crypt fraction for px 20


title: mucosa next to tumor bottom crypt fraction, px 19

description: gene expression data from MT bottom crypt fraction for px 19


title: mucosa bottom crypt fraction, px 21

description: gene expression data from M bottom crypt fraction for px 21


title: mucosa bottom crypt fraction, px 20

description: gene expression data from M bottom crypt fraction for px 20


title: mucosa top crypt fraction, px 21

description: gene expression data from M top crypt fraction for px 21


title: mucosa next to tumor top crypt fraction, px 19

description: gene expression data from MT top crypt fraction for px 19


title: mucosa top crypt fraction, px 18

description: gene expression data from M top crypt fraction for px 18


title: mucosa top crypt fraction, px 20

description: gene expression data from M top crypt fraction for px 20


title: mucosa next to tumor top crypt fraction, px 18

description: gene expression data from MT top crypt fraction for px 18


title: ND 6, biological rep-2

city: Los Angeles

first: Lu

address: Room 706, 1985 Zonal Ave

department: School of Pharmacy

institute: University of Southern California

description: Small RNA data from hiPSC-derived cells toward neural progenitors.

hyb_protocol: Following fragmentation, mirRNA targets were hybridized for 20 hr at 48C on mirRNA-4_0 Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomics Suite.

source_name: hiPSC induced into neural progenitors at D6

label_protocol: After validation of the RNA quality with Bioanalyzer 2100, 500 ng of total RNA was biotin labelled following the FlashTag Biotin HSR RNA labelling kit (Affymetrix).

growth_protocol: The hiPSC line iBC 1.2 was induced to differentiate into representative lineages of the three germ layers, namely, hepatocytes for endoderm (HD), nephron progenitors for mesoderm (KD), and neural progenitors for ectoderm (ND), according to published protocols.

extract_protocol: Total RNA, including miRNAs, were extracted from cells using the RecoverAllTM Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Scientific, AM1975), according to the manufacturer's instruction.

tag: originating cell line

value: iBC 1.2

value: Neural progenitor (ND) differentiated cells

tag: time point

value: Day 6


title: ND 10, biological rep-2

source_name: hiPSC induced into neural progenitors at D10

value: Day 10


title: ND 6, biological rep-1


title: mucosa bottom crypt fraction, px 18

description: gene expression data from M bottom crypt fraction for px 18


title: mucosa next to tumor bottom crypt fraction, px 18

description: gene expression data from MT bottom crypt fraction for px 18


title: ND 3, biological rep-2

source_name: hiPSC induced into neural progenitors at D3

value: Day 3


title: mucosa bottom crypt fraction, px 19

description: gene expression data from M bottom crypt fraction for px 19


title: ND 10, biological rep-1


title: ND 3, biological rep-1


title: ND 0, biological rep-1

source_name: hiPSC induced into neural progenitors at D0

value: Day 0


title: mucosa top crypt fraction, px 17

description: gene expression data from M top crypt fraction for px 17


title: mucosa next to tumor bottom crypt fraction, px 17

description: gene expression data from MT bottom crypt fraction for px 17


title: KD 10, biological rep-2

description: Small RNA data from hiPSC-derived cells toward nephron progenitors.

source_name: hiPSC induced into nephron progenitors at D10

value: Nephron progenitor (KD) differentiated cells


title: mucosa bottom crypt fraction, px 16

description: gene expression data from M bottom crypt fraction for px 16


title: mucosa bottom crypt fraction, px 17

description: gene expression data from M bottom crypt fraction for px 17


title: mucosa next to tumor bottom crypt fraction, px 16

description: gene expression data from MT bottom crypt fraction for px 16


title: KD 10, biological rep-1


title: ND 0, biological rep-2


title: KD 6, biological rep-2

source_name: hiPSC induced into nephron progenitors at D6


title: KD 0, biological rep-2

source_name: hiPSC induced into nephron progenitors at D0


title: mucosa next to tumor top crypt fraction, px 15

description: gene expression data from MT top crypt fraction for px 15


title: KD 0, biological rep-1


title: mucosa top crypt fraction, px 16

description: gene expression data from M top crypt fraction for px 16


title: mucosa next to tumor top crypt fraction, px 17

description: gene expression data from MT top crypt fraction for px 17


title: mucosa next to tumor bottom crypt fraction, px 15

description: gene expression data from MT bottom crypt fraction for px 15


title: HD 6, biological rep-2

description: Small RNA data from hiPSC-derived cells toward hepatocytes.

source_name: hiPSC induced into hepatocytes at D6

value: Hepatocyte (HD) differentiated cells


title: HD 10, biological rep-2

source_name: hiPSC induced into hepatocytes at D10


title: mucosa top crypt fraction, px 15

description: gene expression data from M top crypt fraction for px 15


title: mucosa bottom crypt fraction, px 15

description: gene expression data from M bottom crypt fraction for px 15


title: HD 10, biological rep-1


title: KD 3, biological rep-2

source_name: hiPSC induced into nephron progenitors at D3


title: mucosa next to tumor bottom crypt fraction, px 14

description: gene expression data from MT bottom crypt fraction for px 14


title: KD 3, biological rep-1


title: mucosa next to tumor top crypt fraction, px 14

description: gene expression data from MT top crypt fraction for px 14


title: KD 6, biological rep-1


title: mucosa top crypt fraction, px 14

description: gene expression data from M top crypt fraction for px 14


title: HD 6, biological rep-1


title: mucosa bottom crypt fraction, px 14

description: gene expression data from M bottom crypt fraction for px 14


title: mucosa next to tumor bottom crypt fraction, px 13

description: gene expression data from MT bottom crypt fraction for px 13


title: HD 3, biological rep-2

source_name: hiPSC induced into hepatocytes at D3


title: mucosa next to tumor top crypt fraction, px 13

description: gene expression data from MT top crypt fraction for px 13


title: mucosa bottom crypt fraction, px 13

description: gene expression data from M bottom crypt fraction for px 13


title: HD 0, biological rep-1

source_name: hiPSC induced into hepatocytes at D0


title: mucosa next to tumor bottom crypt fraction, px 12

description: gene expression data from MT bottom crypt fraction for px 12


title: mucosa top crypt fraction, px 12

description: gene expression data from M top crypt fraction for px 12


title: Ctrl-T3

first: Tao

last: Shen

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from  Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Ctrl, T lymphocytes

growth_protocol: Human BxPC-3 cells were grown in RPMI 1640 medium supplemented with 10% FBS at 37°C in 5% CO2. Peripheral T lymphocytes were cultured at the density of 1 × 10^6/mL using the AIM-V Medium CTS supplementing with 100U/mL recombinant human interleukin 2 at 37°C in 5% CO2.

extract_protocol:
Treated T lymphocytes were washed twice with PBS and harvested, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from 6 healthy donors using Ficoll-Paque PLUS Medium density gradient centrifugation. Peripheral T lymphocytes were separated from PBMCs using CD3 MicroBeads. Peripheral T lymphocytes from three of all donors were adjusted to the density of 1 × 10^6/mL, and the isolated exosomes were added to each T lymphocytes sample at the concentration of 100μg/mL every 2 days (Exo-T). Isovolumetric PBS was added as a control (Ctrl-T). At days 5, the T lymphocytes were harvested for follow-up experiments.

tag: individual

value: peripheral T lymphocytes

value: PBS treated (Ctrl-T)


title: mucosa next to tumor top crypt fraction, px 12

description: gene expression data from MT top crypt fraction for px 12

tag: tissue


title: Exo-T2

source_name: Exo, T lymphocytes

value: exosomes treated (Exo-T)


title: Ctrl-T2


title: mucosa next to tumor bottom crypt fraction, px 11

description: gene expression data from MT bottom crypt fraction for px 11


title: mucosa bottom crypt fraction, px 12


title: Ctrl-T1


title: mucosa next to tumor top crypt fraction, px 11

description: gene expression data from MT top crypt fraction for px 11


title: mucosa next to tumor top crypt fraction, px 10

description: gene expression data from MT top crypt fraction for px 10


title: mucosa bottom crypt fraction, px 11

description: gene expression data from M bottom crypt fraction for px 11


title: HD 0, biological rep-2

description: Small RNA data from hiPSC-derived cells toward hepatocytes.


title: mucosa top crypt fraction, px 11

description: gene expression data from M top crypt fraction for px 11


title: ChIP_H3K36me3_ESC

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: GA7630-CGATGT-ChIP-Seq-Mouse-shLuc-ESC-H3K36me3-ChIP-rep1

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Chromatin IP against H3K36me3

growth_protocol: ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for reChIP and ChIP assays.
reChIP and ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: ESC

tag: antibody

value: Anti-H3K36me3 antibody (Abcam; ab9050)


title: mucosa next to tumor bottom crypt fraction, px 9

description: gene expression data from MT bottom crypt fraction for px 9

source_name: colonic mucosa next to tumor


title: mucosa next to tumor bottom crypt fraction, px 10

description: gene expression data from MT bottom crypt fraction for px 10


title: mucosa top crypt fraction, px 10

description: gene expression data from M top crypt fraction for px 10

source_name: colonic mucosa


title: HD 3, biological rep-1


title: ChIP_Input_ESC

description: GA7637-GATCAG-ChIP-Seq-Mouse-shLuc-ESC-Input-rep1

source_name: Direct sequencing following sonication of x-linked chromatin


title: mucosa bottom crypt, px 9

description: gene expression data from M bottom crypt fraction for px 9


title: mucosa top crypt fraction, px 13

description: gene expression data from M top crypt fraction for px 13


title: Exo-T3


title: Exo-T1


title: 9835

description: mature β-cells

source_name: mature β-cells

value: b-cell reference

value: Insulin-mCherry mice

value: D050417 - Pancreatic beta cells


title: 9834

description: mature β-cells


title: 9829

description: mature β-cells


title: 9570

description: Mature α-cells

source_name: Mature α-cells

value: ctl noDT

value: Glucagon-Venus mice

value: D050416 - Pancreatic alpha cells


title: 9827

description: mature β-cells


title: 9405

description: Mature α-cells


title: mucosa top crypt fraction, px 9

description: gene expression data from M top crypt fraction for px 9

value: colonic mucosa


title: mucosa next to tumor top crypt fraction, px 9

description: gene expression data from MT top crypt fraction for px 9

value: colonic mucosa next to tumor


title: mucosa next to tumor top crypt fraction, px 16

description: gene expression data from MT top crypt fraction for px 16


title: 3779

description: mature β-cells


title: 13890

description: α-cells expressing PDX1 30 days after DT

value: aPdx1OE DT

value: Glucagon-rtTA; TetO-Cre; R26YFP; CAGPdx1;RIP-DTR mice


title: 1807_15709

description: mature β-cells


title: 14887

source_name: α-cells expressing PDX1 30 days after DT


title: mucosa top crypt fraction, px 8

description: gene expression data from M top crypt fraction for px 8


title: mucosa next to tumor bottom crypt fraction, px8

description: gene expression data from MT bottom crypt fraction for px 8


title: 9830

description: mature β-cells


title: mucosa bottom crypt, px 8

description: gene expression data from M bottom crypt fraction for px 8


title: 9432

description: Mature α-cells


title: mucosa next to tumor top crypt fraction, px 8

description: gene expression data from MT top crypt fraction for px 8


title: mucosa next to tumor bottom crypt fraction, px 7

description: gene expression data from MT bottom crypt fraction for px 7

source_name: olonic mucosa next to tumor

value: olonic mucosa next to tumor


title: mucosa bottom crypt, px7

description: gene expression data from M bottom crypt fraction for px 7


title: mucosa top crypt fraction, px 7

description: gene expression data from M top crypt fraction for px 7


title: control #2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

hyb_protocol: Microarray hybridization was performed using the Affymetrix Fluidics Station 450 with  program FS450_0001.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were preprocessed in the R v3.2.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

organism: Chlorocebus sabaeus

source_name: control-treated Vero cells

label_protocol: 100ng total RNA from each sample was processed with the IVT Express reagent kit (Affymetrix, Santa Clara, CA) following the manufacturer's protocol.

growth_protocol: Cells were cultured in RPMI medium containing 10% fetal calf serum and standard antibiotics at 37°C and 5% CO2.

extract_protocol: RNA was extrated with Trizol reagent.

tag: cell line

value: Vero

tag: group

value: control


title: mucosa next to tumor top crypt fraction, px 6

description: gene expression data from MT top crypt fraction for px6


title: mucosa bottom crypt, px 10

description: gene expression data from M bottom crypt fraction for px 10


title: APOBEC3G #2

source_name: APOBEC3G-overexpressing Vero cells

value: overexpression