title: PCLS, RV+BRO 1:1000, exp3, rep2

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

description: Gene expression data from PCLS treated with RV+BRO 1:1000

hyb_protocol: Following fragmentation, 5.2 µg fragmented and labeled ss-cDNA were hybridized 16 hr at 45°C on GeneChip MTA 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0), using Affymetrix default settings and RMA normalization

source_name: precision cut lung slices (PCLS)

label_protocol: Fragmented and biotinylated ss-cDNA (5.5 µg) were prepared according to the GeneChip WT PLUS Reagent Kit Manual (Target Preparation for Gene Chip Whole Transkript (WT) Expression Arrays, ThermoFisher Scientific, 23 January 2017).

growth_protocol: Two PCLS per well were incubated in a volume of 500µl at 33°C, 5% CO2.

extract_protocol: RNA was isolated according to an optimized protocol for RNA isolation from PCLS from different species established by Niehof et al. 2017 [BMC Res Notes 10:121]. The protocol is based on a homogenisation and phenol extraction procedure coupled with a MagMax™ magnetic beads cleaning procedure.

treatment_protocol: Mouse PCLS were pre-incubated with BRO or BRO vehicle for 1h. After one hour, the incubation medium was removed, fresh treatment solutions added (250µl per well) and mPCLS were infected with 250µl HRV, replicative deficient UV-HRV or medium as sham infection. PCLS were incubated at 33 °C, 5% CO2 for 24h. After 24h mPCLS samples were snap frozen and stored at  80°C for potential further RNA isolation and gene expression analysis.

value: Balb/c

tag: gender

value: female

value: 8 - 12 weeks

value: lung


title: PCLS, RV+BRO 1:100, exp3, rep2

status: Public on Jun 10 2019

type: RNA

country: Germany

description: Gene expression data from PCLS treated with RV+BRO 1:100

label: biotin

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: tissue


title: PCLS, RV+BRO 1:1000, exp2, rep2


title: Parent_IFN_L_rep1

type: SRA

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

country: USA

institute: NIH/JHU

library_source: transcriptomic

data_processing:
Data were examined using Tuxedo pipeline for differential gene expression analysis. We used default parameters for these software programs and used a cutoff of 0.05 False Discovery Rate (FDR) by Benjamin-Hochberg method to determine differentially expressed genes with statistical significance.
We aligned to hg38 reference genome using HISAT2, version 2.0.5.
FPKM values were obtained using Cufflinks, patched version of 2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM abundance measurements

organism: Homo sapiens

growth_protocol: Cells were grown in Lonza's bronchial epithelial cell growth medium.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
To obtain the final sequencing library, 14 cycles of PCR were performed using Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes, Espoo, Finland). Three biological replicates were used and for each sample replicate we obtained ~50 million paired 50-mer reads (using Illumina HiSeq 2500 platform).

treatment_protocol: Cells were treated with IFNβ (0.2 ng/ml) and IFNλ1 (5ng/ml) for 24h.

tag: cell line

tag: cell type

value: respiratory epithelial cells

tag: genotype/variation

value: Wild type

tag: treated with

value: 5ng/ml IFNλ1 for 24h


title: PCLS, RV+BRO 1:100, exp3, rep1


title: PCLS, RV+BRO 1:100, exp2, rep2


title: PCLS, RV+BRO 1:1000, exp3, rep1


title: PCLS, RV+BRO 1:1000, exp1, rep2


title: skeletal muscle, 25(OH)D3 intervention, baseline sample, subject 3087

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).

source_name: m. vastus lateralis, 25(OH)D3 intervention, baseline sample, from subject 3087

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

growth_protocol: This study is part of a larger clinical trial [PMID: 30053278]. In  brief, a 6-month, double-blind, placebo-controlled trial was performed, that included subjects randomly allocated to treatment who received daily supplements with either 10 µg 25(OH)D3 or a placebo capsule. Measurements were performed at baseline and after 6 months  of intervention. The study was carried out at Wageningen University and Hospital Gelderse Vallei, Ede, Netherlands (latitude: 51°N), between December 2014 and December 2015. The Medical Ethics Committee of Wageningen University and Research approved the study protocol and Hospital Gelderse Vallei approved local feasibility. All of the participants gave their written informed consent. The study was registered at clinicaltrials.gov as NCT02349282. Study population: Participants were recruited via registries of municipalities in Wageningen and the surroundings. A total of 78 men and women volunteered to participate in the main. Participants were included if they were ≥65 y of age, had a serum 25(OH)D concentration between 20 and 50 nmol/L (to convert to nanograms per milliliter, divide by 2.496), a BMI (in kg/m2) between 18.5 and 35, and who were prefrail or frail based on the frailty criteria of Fried et al. [PMID: 11253156]. Exclusion criteria were as follows: a serum calcium concentration >2.6 nmol/L or uncontrolled hypocalcemia, diagnosed malabsorption disorders, sarcoidosis, lymphoma, primary hyperparathyroidism, kidney stones (in the past 10 y), renal insufficiency, cancer, or the use of medication that may influence vitamin D metabolism [e.g., bisphosphonates, parathyroid hormone (PTH) treatment, anti-tuberculosis medications, anti-epileptic medications, bile acid sequestrate, or lipase inhibitors]. Furthermore, participants were excluded if they consumed >21 servings of alcoholic beverages/wk, were not willing or able to stop the use of vitamin D–containing supplements during the study, expected to increase their sun exposure (e.g., planned holiday), or had a surgery planned. For the gene expression analysis, samples of a subset of 22 subjects were included.

extract_protocol: Total RNA was prepared from the muscle biopsies (50 mg) using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. 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: An independent investigator randomly allocated participants to 1 of the 2 intervention groups by a computer-generated list (SAS software 9.20; SAS Institute). Randomization was carried out in permuted blocks and stratified by sex and BMI (18.5–29.9 and 30–35). The 2 groups received daily supplements with either 10 µg 25(OH)D3, or placebo. Both the participants and investigators were blinded to treatment allocation, and study supplements were identical in appearance and taste. DSM Nutritional Products Ltd. provided the 25(OH)D3 (0.25% SD/S), vitamin D3, or placebo (microcrystalline cellulose; Avicel PH-102) in spray-dried form. Capsules were manufactured by Fisher Clinical Services GmbH. The actual content of the 25(OH)D3 capsules was 9.9 µg, which was tested by using HPLC. Participants were instructed to consume 1 capsule/d at breakfast. Treatment compliance was reported at 3 and 6 mo by capsule count of returned capsules, taking into account the number of days active in the study. Participants were considered compliant when ≥80% of the study supplements were taken. Before and after the intervention period, muscle biopsies were taken from the middle region of the vastus lateralis muscle under local anaesthesia (1% lidocaine, without epinephrine), ~15 cm above the patella and ~3 cm below entry through the fascia, using the percutaneous needle biopsy technique fromBergström [PMID: 5584523]. Samples were snap-frozen in liquid nitrogen, and stored at -80 degrees centigrade until RNA isolation.

value: muscle

tag: Sex

value: Male

tag: subject id

tag: intervention group

value: 25-hydroxycholecalciferol (25(OH)D3)

tag: time of sampling

value: before intervention (baseline)


title: PCLS, RV+BRO 1:1000, exp2, rep1


title: PCLS, RV+BRO 1:100, exp2, rep1


title: Aged_1_C72

city: Rochester

first: Laura

last: Calvi

state: New York

address: 601 Elmwood Ave

department: Medicine

institute: University of Rochester Medical Center

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: text file includes raw expression counts

source_name: Long-Term Hematopetic Stem Cell

growth_protocol: Mice were bred and mantained per standard rodent colony husbandry guidelines

extract_protocol:
Single long-term hematopoietuc stem cells (LT-HSC: Lineage-, Sca1+, cKit+, Flt3-, CD48-, CD150+) were captured on a 5–10 μm cell diameter integrated microfluidic chip (IFC) using the Fluidigm C1 Single-cell AutoPrep system (Fluidigm Corporation). Cells were pre-stained with Calcien AM/EthD-1 LIVE/DEAD cell viability assay (Life Technologies) and loaded onto the IFC at a concentration of 500–700 cells/ul.  Viable single cell confirmation was performed with phase-contrast fluorescence microscopy to assess the number and viability of cells per capture site. Only single, live cells were included in the analysis.
For RNA-seq analysis, cDNAs were prepared “on-IFC” using the SMARTer Ultra Low RNA kit for Illumina (Clontech) following fluidigm recomemdnations. Single-cell cDNA size distribution and concentration was assessed with PicoGreen (Life Technologies) and Agilent Bioanalyzer 2100 analysis (Agilent Technologies). Illumina libraries were constructed in 96-well plates using Illumina’s NexteraXT DNA Sample Preparation kit following the protocol supplied by Fluidigm. For each C1 experiment, a bulk RNA control and a negative control were processed in parallel, using the same reagent mixes as used on chip. Libraries were quantified by Agilent Bioanalyzer, using High Sensitivity DNA analysis kit, and also fluorometrically, using Qubit dsDNA HS Assay kits and a Qubit 2.0 Fluorometer (Technologies).
Fluidigm C1 full-length single-cell RNAseq

value: male

value: 24 Months

value: Long-Term Hematopetic Stem Cell


title: Aged_1_C71


title: Parent_no_IFN_rep2


title: PCLS, RV+BRO 1:10, exp3, rep2

description: Gene expression data from PCLS treated with RV+BRO 1:10


title: Aged_14_C11


title: PCLS, RV+BRO 1:100, exp1, rep1


title: PCLS, RV+BRO 1:1000, exp1, rep1


title: Aged_1_C51


title: Parent_IFN_B_rep1

value: 0.2 ng/ml IFNβ for 24h


title: Aged_1_C74


title: Parent_no_IFN_rep1


title: F2 RNA-Seq

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
RNA-seq reads were aligned to the UCSC human genes (hg19) using HISAT2 (version 2.1.0). Only concordantly mapped pairs were retained for analysis in this study.
We used Cuffdiff (version 2.2.1) to calculate the expression abundance of each gene as fragments per kilobase per million mapped reads (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file is a tab-delimited file showing gene expresssion levels with FPKM.

molecule: polyA RNA

source_name: liver cancer cell treated with ferroptosis

growth_protocol: Bel-7402 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) (Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS) (GIBCO, Carlsbad, CA, USA) and penicillin/streptomycin (GIBCO).

extract_protocol: Total RNA was isolated from cells using Trizol (Ambion, Carlsbad, CA, USA).

treatment_protocol: Cells in Erastin group was treated with 10uM erasin. Cells in Ferrostatin group was treated wth 1uM ferrostatin-1.

tag: cell

value: Bel-7402 cell

tag: reagent

value: Ferrostatin-1 (Selleck S7243)


title: F3 RNA-Seq


title: F1 RNA-Seq


title: PCLS, RV+BRO 1:100, exp1, rep2

value: Balb/c


title: Aged_1_C18


title: PCLS, RV+BRO 1:10, exp2, rep2

value: female


title: E3 RNA-Seq

source_name: liver cancer cell treated with erastin

value: Erastin (Selleck S7242)


title: PCLS, RV+BRO 1:10, exp3, rep1

value: 8 - 12 weeks

value: lung


title: PCLS, RV+BRO 1:10, exp1, rep1


title: Aged_14_C35


title: PCLS, RV+BRO 1:10, exp1, rep2


title: PCLS, RV+BRO 1:10, exp2, rep1


title: PCLS, infection vehicle control, exp3, rep1

description: Gene expression data from PCLS treated with infection vehicle control


title: PCLS, infection vehicle control, exp3, rep2


title: Aged_1_C92


title: Aged_1_C93


title: Aged_14_C96


title: Aged_1_C20


title: E2 RNA-Seq


title: E1 RNA-Seq


title: C3 RNA-Seq

source_name: liver cancer cell


title: C2 RNA-Seq


title: C1 RNA-Seq


title: PCLS, infection vehicle control, exp2, rep1


title: Aged_1_C69


title: PCLS, infection control, exp3, rep2

description: Gene expression data from PCLS treated with infection control


title: PCLS, BRO 1:10, exp3, rep2

description: Gene expression data from PCLS treated with BRO 1:10


title: PCLS, infection control, exp3, rep1


title: PCLS, infection control, exp2, rep1


title: PCLS, infection vehicle control, exp1, rep1


title: PCLS, infection vehicle control, exp1, rep2


title: PCLS, BRO 1:10, exp3, rep1


title: PCLS, infection control, exp2, rep2


title: PCLS, infection vehicle control, exp2, rep2


title: PCLS, infection control, exp1, rep2


title: Aged_1_C02


title: PCLS, BRO 1:10, exp2, rep2


title: PCLS, infection control, exp1, rep1


title: PCLS, BRO 1:10, exp2, rep1


title: Aged_1_C53


title: PCLS, BRO 1:10, exp1, rep2


title: FHSC04_RG6016_3 (in vivo)

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.2
Reads of low quality were filtered out prior to alignment to hg19 using TopHat v2.0.12. Reads were also independently aligned to mm9, and alignments to both genomes were compared, retaining reads which had fewer mismatches to hg19 than mm9.  Counts were generated from filtered alignments at the gene-level using “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: human SCLC PDX model RG6016/ORY1001 treated

extract_protocol:
Tumors were surgically excised from immunocompromised mouse host, with pieces of tumor frozen on dry ice and later used for total RNA extraction using TRIzol reagent. Tissue was minced with a scissors and then homogenized using a syringe/needle in 1mL Trizol reagent, with RNA isolated following manufacturers instructions.
RNA libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

treatment_protocol: Mice were treated with saline vehice or with 400ug/kg RG6016/ORY1001 orally on day 0,7 and also 4 hours before collection on Day 10

value: human PDX tumor that grew in mouse

tag: treatment

tag: tumor type

value: small cell lung cancer

tag: sample type

value: patient derived xenograft


title: FHSC04_RG6016_5 (in vivo)


title: Aged_1_C63


title: FHSC04_RG6016_4 (in vivo)


title: PCLS, UV control, exp3, rep2

description: Gene expression data from PCLS treated with UV control

tag: gender


title: Aged_1_C06

tag: strain


title: Aged_1_C26

tag: age


title: Aged_1_C27

tag: tissue


title: FHSC04_RG6016_2 (in vivo)


title: Aged_1_C91


title: Aged_1_C78


title: FHSC04_saline5 (in vivo)

source_name: human SCLC PDX model saline treated

value: saline


title: FHSC04_saline4 (in vivo)


title: FHSC04_saline3 (in vivo)


title: Aged_1_C60


title: FHSC04_RG6016_1 (in vivo)


title: FHSC04_saline1 (in vivo)


title: PCLS, UV control, exp2, rep1


title: PCLS, vehicle control, exp3, rep1

description: Gene expression data from PCLS treated with vehicle control


title: PCLS, vehicle control, exp2, rep1


title: PCLS, UV control, exp1, rep2


title: PCLS, BRO 1:10, exp1, rep1


title: PCLS, medium control, exp3, rep2

description: Gene expression data from PCLS treated with medium control


title: PCLS, vehicle control, exp2, rep2


title: PCLS, vehicle control, exp1, rep2


title: PCLS, vehicle control, exp1, rep1


title: PCLS, vehicle control, exp3, rep2


title: FHSC04_saline2 (in vivo)


title: PCLS, UV control, exp2, rep2


title: PCLS, UV control, exp3, rep1


title: Aged_1_C14


title: PCLS, medium control, exp2, rep2


title: PCLS, medium control, exp3, rep1


title: Aged_1_C58


title: PCLS, medium control, exp2, rep1


title: PCLS, UV control, exp1, rep1


title: Aged_1_C09


title: PCLS, medium control, exp1, rep2


title: LX227C_RG6016 (ex vivo)

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.2
Reads of low quality were filtered out prior to alignment to hg19 using TopHat v2.0.12.  Counts were generated from TopHat alignments at the gene-level  using the  “intersection-strict” overlap mode in HTSeq v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by HTSeq-count v0.6.1

source_name: human SCLC PDX model ex vivo RG6016/ORY1001 treated

extract_protocol:
Cells were lysed in TRIzol reagent with RNA isolated following manufacturers instructions.
RNA libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

treatment_protocol: 7 PDX models cultured ex vivo were treated with saline vehicle or 1nM RG6016/ORY1001 for 48 hours

tag: culture protocol

value: patient derived xenograft grown ex vivo


title: PCLS, medium control, exp1, rep1


title: LX108_RG6016 (ex vivo)


title: LX227C_control (ex vivo)

source_name: human SCLC PDX model ex vivo saline treated


title: Aged_1_C37


title: Aged_1_C83


title: Aged_14_C90


title: Aged_1_C28


title: Aged_1_C12


title: LX110_RG6016 (ex vivo)


title: LX108_control (ex vivo)


title: Aged_1_C94


title: LX110_control (ex vivo)


title: Aged_1_C07


title: LX48_RG6016 (ex vivo)


title: Aged_1_C61


title: LX48_control (ex vivo)


title: Aged_1_C21


title: LX33_control (ex vivo)


title: Aged_1_C40


title: Aged_1_C49


title: LX33_RG6016 (ex vivo)


title: Aged_1_C13


title: FHSC14_RG6016 (ex vivo)


title: FHSC14_control (ex vivo)


title: Aged_1_C23


title: FHSC04_RG6016 (ex vivo)


title: Liver genomic DNA from cirrhotic  AATD patient 13

type: genomic

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s90

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Infinium® MethylationEPIC Beadchip using standard Illumina protocol at the University of Minnesota Genomics Center.

scan_protocol: Arrays were imaged using BeadArray Reader Hi-Scan system.

data_processing: Resultant IDAT files were processed and normalized using the R Bioconductor package “minfi” using subset within-array quantile normalization (SWAN). CpGs that failed to reach significant detection (p<0.01) or were unreliable (0 or 1 value, 1 probe) in all samples were filtered out (45,921 probes) along with cross-reactive probes (43,255), leaving 779,088 CpGs for downstream analysis.

molecule: genomic DNA

source_name: Liver DNA 107

label_protocol: Standard Illumina Protocol

extract_protocol: Specimens were preserved in Qiagen Allprotect solution, Genomic DNA  were extracted from tissues using Qiagen Allprep isolation columns according to the manufacturer’s instructions.

tag: fib

value: liver biopsy

tag: disease state

value: Cirrhotic AATD


title: Liver genomic DNA from cirrhotic  AATD patient 7

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s334

source_name: Liver DNA 101

value: male


title: Liver genomic DNA from cirrhotic  AATD patient 2

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s218

source_name: Liver DNA 96


title: Aged_1_C04

value: 24 Months

value: Long-Term Hematopetic Stem Cell


title: Liver genomic DNA from cirrhotic  AATD patient 11

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s56

source_name: Liver DNA 105


title: Liver genomic DNA from AATD patient 94

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-109

source_name: Liver DNA 94

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: Liver genomic DNA from cirrhotic  AATD patient 8

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s43

source_name: Liver DNA 102


title: Liver genomic DNA from cirrhotic  AATD patient 5

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s276

source_name: Liver DNA 99


title: Liver genomic DNA from cirrhotic  AATD patient 14

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
sRM

source_name: Liver DNA 108


title: Liver genomic DNA from cirrhotic  AATD patient 4

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s263

source_name: Liver DNA 98


title: Liver genomic DNA from cirrhotic  AATD patient 3

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s23

source_name: Liver DNA 97


title: Liver genomic DNA from AATD patient 88

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-101

source_name: Liver DNA 88


title: Liver genomic DNA from cirrhotic  AATD patient 9

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s46

source_name: Liver DNA 103


title: Liver genomic DNA from AATD patient 91

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-104

source_name: Liver DNA 91


title: Liver genomic DNA from cirrhotic  AATD patient 12

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s77

source_name: Liver DNA 106


title: Liver genomic DNA from cirrhotic  AATD patient 1

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s216

source_name: Liver DNA 95


title: Liver genomic DNA from AATD patient 87

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-100

source_name: Liver DNA 87


title: Aged_1_C43

source_name: Long-Term Hematopetic Stem Cell


title: NBM_35M_CM_CD11b_HI

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCh38.p3 + Gencode-23 Annotation
Supplementary_files_format_and_content: text file includes raw expression counts

source_name: Young Bone Marrow Cells

growth_protocol: Marrow was isoalted from healthy volunteers.  Aspriates were isoalted from the illiac crest.

extract_protocol:
FACS with  CD45+, CD163b+, CD11b+, Side-scatter low, and DAPI- directly into Qiagen RLT PLUS buffer.  RNA extraction was performed with Qiagen Rneasy PLUS Micro kit following standard operating procedures.  RNA quality was assessed using Agilent Bioanalyzer 2100.
1 nanogram of high quality (RIN>8.0) total RNA from each sample was reverse transcribed into cDNA using the Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit.  Final Illumina libraries were constructed using 150pg of cDNA with the illumina Nextera XT DNA Library Preparation Kit.
Low input RNA-Seq using SMARTer (SMART-seq) chemistry.

value: Young Bone Marrow Cells


title: Liver genomic DNA from AATD patient 93

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-108

source_name: Liver DNA 93


title: Liver genomic DNA from AATD patient 89

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-102

source_name: Liver DNA 89


title: Liver genomic DNA from AATD patient 92

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-106

source_name: Liver DNA 92


title: Liver genomic DNA from AATD patient 90

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-103

source_name: Liver DNA 90


title: Aged_14_C08


title: FHSC04_control (ex vivo)

source_name: human SCLC PDX model ex vivo saline treated


title: NBM_34M_CM_CD11b_HI


title: Liver genomic DNA from cirrhotic  AATD patient 6

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s319

source_name: Liver DNA 100


title: Liver genomic DNA from AATD patient 85

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-098

source_name: Liver DNA 85


title: Aged_1_C46


title: Liver genomic DNA from AATD patient 84

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-096

source_name: Liver DNA 84


title: NBM_34M_BA_CD11b_HI

source_name: Young Bone Associated Cells

value: Young Bone Associated Cells


title: Liver genomic DNA from AATD patient 82

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-093

source_name: Liver DNA 82


title: Aged_1_C32


title: NBM_53M_SAC_CD11b_HI

source_name: Aged Bone Associated Cells

value: Aged Bone Associated Cells


title: Liver genomic DNA from cirrhotic  AATD patient 10

description:
liver cells of cirrhotic Alpha-1 Antitrypsin Deficiency patients
s537

source_name: Liver DNA 104


title: NBM_53M_BM_CD11b_HI

source_name: Aged Bone Marrow Cells

value: Aged Bone Marrow Cells


title: Aged_14_C48


title: Liver genomic DNA from AATD patient 81

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-092

source_name: Liver DNA 81

value: female


title: Liver genomic DNA from AATD patient 86

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-099

source_name: Liver DNA 86


title: Aged_1_C88

source_name: Long-Term Hematopetic Stem Cell


title: Aged_1_C57


title: NBM_57M_BM_CD11b_HI


title: Liver genomic DNA from AATD patient 83

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-095

source_name: Liver DNA 83


title: NBM_57M_SAC_CD11b_HI


title: Aged_1_C80


title: NBM_67M_SAC_CD11b_HI


title: Aged_1_C52


title: Aged_1_C15


title: NBM_67M_BM_CD11b_HI


title: Liver genomic DNA from AATD patient 80

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-091

source_name: Liver DNA 80


title: Aged_1_C68


title: NBM_35M_BA_CD11b_HI


title: Aged_1_C85


title: MCYT2_CD271POS

city: Merced

first: Fabian

middle: Volker

last: Filipp

state: California

address: 5200 North Lake Road

department: Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology

institute: University of California Merced

hyb_protocol: All RNA samples hybridized to the Human Genome U133 Plus 2.0 microarray (Affymetrix, Santa Clara, CA) chips.

scan_protocol: Following hybridization and scanning fluorescent signals were obtained for 54675 probes that were further processed and mapped to 20535 gene-coding transcripts.

data_processing: The RMA oligo package was used for normalization and background correction of transcriptomic data. We utilized melanoma and melanocyte specimens sorted for CD271 expression status and subjected the data to unsupervised clustering analysis. CD271+ and CD271- specimens are denoted as CD271+ and CD271-, respectively. Both, rows (genes) and columns (specimens) were clustered using Pearson correlation distance and average linkage of log-transformed, normalized transcriptome array values. Pathway and enrichment analysis was performed by Ingenuity Pathway Analysis (IPA) software (QIAGEN Bioinformatics, Germany) and mapped with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The enrichment study includes normalization of the enrichment score accounting for size of each gene set, yielding normalized enrichment score (NES). In addition to the calculated probability (p value) of hypothesis testing, there is adjustment for multiple hypothesis testing by controlling the proportion of false positives by calculating the false discovery rate (q values) corresponding to each NES, by comparing tails of the observed and the null distribution for the NES.

source_name: human skin cutaneous melanocyte CD271 positive

label_protocol: All RNA samples were processed using Ovation Pico WTA system V2.0 (NuGEN Technologies San Carlos, CA).

extract_protocol: Total RNA was extracted from CD271+ and CD271- cell populations using Trizol Reagent (T9424-Millipore-Sigma).

treatment_protocol: Prior to antibody staining, blocking reagent, mouse IgG (1 mg/ml) was added to the melanoma or adult melanocyte cell suspension and incubated on ice for 10 min. All stainings were performed in 100 μl volume of cold HBSS containing 2 percent FBS. The following lineage antibodies were added: CD45, CD31, CD2, CD3, glycophorin A, EpCAM (all conjugated to pacific blue) plus an antibody against CD271 (Alexa Fluor647-conjugated) at a 1:50 dilution. Cells were incubated on ice in the dark for 30 min. After washing and centrifugation, cells were resuspended in 0.5 ml Hank's balanced salt solution (HBSS) containing 2% FBS and propidium iodide to allow exclusion of nonviable cells. CD271+ and CD271- cell populations were gated based on the isotype control background signal. Isolation of CD271+ and CD271- cells was achieved using a FACSAria III (BD Biosciences, San Jose, CA) cell sorter instrument.

tag: tissue source

value: healthy human skin tissue

tag: cell type

value: epidermal melanocytes

tag: cell population


title: Liver genomic DNA from AATD patient 79

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-090

source_name: Liver DNA 79


title: Liver genomic DNA from AATD patient 77

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-088

source_name: Liver DNA 77


title: MCYT1_CD271POS


title: MCYT2_CD271NEG

source_name: human skin cutaneous melanocyte CD271 negative


title: Aged_1_C95

tag: Sex


title: Liver genomic DNA from AATD patient 71

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-078

source_name: Liver DNA 71


title: Liver genomic DNA from AATD patient 74

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-084

source_name: Liver DNA 74


title: Aged_1_C05


title: Liver genomic DNA from AATD patient 78

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-089

source_name: Liver DNA 78


title: Liver genomic DNA from AATD patient 75

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-085

source_name: Liver DNA 75


title: Aged_1_C47


title: Liver genomic DNA from AATD patient 68

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-074

source_name: Liver DNA 68


title: MCYT1_CD271NEG


title: MEL11409_CD271POS

source_name: human skin cutaneous melanoma CD271 positive

value: human melanoma tumor tissue

value: tumor cell subsets


title: Liver genomic DNA from AATD patient 69

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-076

source_name: Liver DNA 69


title: Liver genomic DNA from AATD patient 72

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-080

source_name: Liver DNA 72


title: Liver genomic DNA from AATD patient 76

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-086

source_name: Liver DNA 76


title: Liver genomic DNA from AATD patient 67

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-073

source_name: Liver DNA 67


title: Liver genomic DNA from AATD patient 63

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-069

source_name: Liver DNA 63


title: Liver genomic DNA from AATD patient 62

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-068

source_name: Liver DNA 62


title: Aged_1_C45

source_name: Long-Term Hematopetic Stem Cell


title: MEL11409_CD271NEG

source_name: human skin cutaneous melanoma CD271 negative


title: Liver genomic DNA from AATD patient 66

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-072

source_name: Liver DNA 66


title: Liver genomic DNA from AATD patient 70

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-077

source_name: Liver DNA 70


title: Liver genomic DNA from AATD patient 61

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-067

source_name: Liver DNA 61


title: Aged_1_C33


title: Liver genomic DNA from AATD patient 64

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-070

source_name: Liver DNA 64


title: Aged_1_C75


title: BMDM_acGM-0.2

city: Maucau

first: Feng

last: Yanxian

address: Tapai

department: Institute of Chinese Medical Sciences

country: Macau

institute: University of Maucau

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.  Text files on the series record include normalized expression signal, fold-change and gene annotation information.

source_name: after 24hr in acGM-0.2 induced BMDM

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: BMDM was tread with samples for 24h with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: 5 weeks

value: femur bone

value: bone marrow derived macrophages


title: MEL826_CD271POS


title: Liver genomic DNA from AATD patient 58

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-064

source_name: Liver DNA 58

value: liver biopsy


title: Aged_1_C64

value: male


title: Liver genomic DNA from AATD patient 60

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-066

source_name: Liver DNA 60


title: BMDM

description: BMDM

source_name: BMDM


title: Aged_1_C65

value: 24 Months


title: BMDM_acGM-1.8

source_name: after 24hr in acGM-1.8 induced BMDM


title: MEL826_CD271NEG


title: Liver genomic DNA from AATD patient 57

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-063

source_name: Liver DNA 57


title: Liver genomic DNA from AATD patient 56

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-062

source_name: Liver DNA 56


title: ipsilateral brain_PBS+4d_biological rep3

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Biotin-labelled aRNA was hybridized to the whole mouse genome HT MG-430 PM array plate (Affymetrix, CA, USA) using the GeneTitan multi-channel instrument (Affymetrix).

scan_protocol: Scanning was performed using the GeneTitan multi-channel instrument (Affymetrix)

data_processing:
Microarray datasets were normalised by the Robust Multiarray Averaging (RMA) method in Affymetrix Expression Console (Affymetrix, CA, USA) and analysis performed using the ht_mg-430_pm.na36 annotation release (Affymetrix).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HT_MG-430_PM
program-name = Expression Console
program-version = 1.3.0.187

source_name: Mouse brain ipsilateral to intrastriatal injection, 4 d after PBS injection

label_protocol: Total RNA was labelled using the IVT Express Kit (Affymetrix). First-strand cDNA was synthesised and converted to double-stranded DNA template for transcription and synthesis of aRNA incorporating a biotin-conjugated nucleotide. aRNA was purified and fragmented prior to hybridisation on Affymetrix arrays

growth_protocol: C57Bl/6J male mice 10-12 weeks old

extract_protocol: Qiagen miRNeasy isolation kit accoridng to manufacturer's instructions

treatment_protocol: Sterotaxic intrastriatal injection of lipopolysaccharide (LPS) or PBS followed by recovery for 1 d or 4 d, transcardiac saline perfusion, brain samples ipsilateral to injected hemisphere dissected for RNA extraction

tag: developmental stage

value: adult; 10-12 weeks

tag: time point

value: 4 d after PBS injection

value: brain


title: MEL425_CD271POS

source_name: human skin cutaneous melanoma CD271 positive


title: Liver genomic DNA from AATD patient 73

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-083

source_name: Liver DNA 73

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: ipsilateral brain_PBS+4d_biological rep2


title: Y3_BM_CD11b_Hi

data_processing:
DEMULTIPLEXING - bcltofastq-1.8.4
CLEANING - Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
MAPPING - STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - htseq-count v0.6.1 "-q -f bam -s no -r pos -i gene_name"
Genome_build: GRCm38.p4 + Gencode-M6 Annotation
Supplementary_files_format_and_content: text files include raw expression counts

source_name: Young Bone Marrow Cells

extract_protocol:
FACS with  CD11b+, LY6C-, F480+, and DAPI directly into Qiagen RLT PLUS buffer.  RNA extraction was performed with Qiagen Rneasy PLUS Micro kit following standard operating procedures.  RNA quality was assessed using Agilent Bioanalyzer 2100.
1 nanogram of high quality (RIN>8.0) total RNA from each sample was reverse transcribed into cDNA using the Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit.  Final Illumina libraries were constructed using 150pg of cDNA with the illumina Nextera XT DNA Library Preparation Kit.

value: 3 months; young

tag: cell type source

value: bone marrow cells

value: CD11b+ macrophages


title: ipsilateral brain_PBS+4d_biological rep1


title: MEL425_CD271NEG


title: Liver genomic DNA from AATD patient 52

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-057

source_name: Liver DNA 52


title: Liver genomic DNA from AATD patient 59

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-065

source_name: Liver DNA 59


title: MEL213_CD271POS


title: Liver genomic DNA from AATD patient 55

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-061

source_name: Liver DNA 55


title: Y2_BAC_CD11b_Hi

source_name: Young Bone Associated Cells

value: bone-associated cells


title: ipsilateral brain_LPS+4d_biological rep3

source_name: Mouse brain ipsilateral to intrastriatal injection, 4 d after LPS injection

value: 4 d after LPS injection


title: MEL213_CD271NEG

source_name: human skin cutaneous melanoma CD271 negative

value: human melanoma tumor tissue


title: Liver genomic DNA from AATD patient 65

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-071

source_name: Liver DNA 65


title: ipsilateral brain_LPS+4d_biological rep2


title: Y2_BM_CD11b_Hi


title: B10

city: jinan

first: yundong

last: sun

address: wenhua west road 44

institute: shanda university

library_source: genomic

data_processing:
Library strategy: 16s rDNA-sequencing
 Basecalls and quality filtering on Illumina MiSeq sequencer
Samples were seperated by barcode
After adaptor-trimming and low quality reads removing by Trimmomatic software, and paired-end merging by flash software, optimized reads were used for OTU clustering, and the OTU matrix of all samples were generated. The most abundant sequence in each OTU was selected as the representative sequence of that OTU.
Then these OTU representative sequences were aligned to greengene database, and generated the sample and taxonomy abundance matrix. mothur software and R enviroment were used to perform alpha diversity, beta diversity, statistics analysis and plotting.
Picrust software was used to perform function prediction.
Genome_build: greengene database

organism: mouse gut metagenome

source_name: Gastric flora

growth_protocol: Feeding mice with sterile feed for 4 weeks

extract_protocol:
Extracting DNA from mouse  gastric flora
The 16S rRNA gene comprising V3 and V4 regions was amplified by PCR, and the resulting amplicons were cleaned, quantified, and sequenced on the Illumina MiSeq platform.

treatment_protocol: CTL group was fed with normal salt diets for 4 weeks,Salt group were fed with high salt diets(5% NaCl)for 4 weeks,(S+B)group were fed with  high salt diets mixed with buckwheat (1:1)for 4 weeks ,B group: first fed high salt diets for 4 weeks and then fed with buckwheat for 4 weeks.

tag: mouse age

tag: mouse strain

tag: mouse sex

tag: mouse diet

value: B


title: Y1_BM_CD11b_Hi

tag: strain


title: B8


title: B7


title: B6


title: A3_BM_CD11b_Hi

source_name: Aged Bone Marrow Cells

tag: age

value: 24 Months; aged


title: A3_BAC_CD11b_Hi

source_name: Aged Bone Associated Cells


title: ipsilateral brain_LPS+1d_biological rep3

source_name: Mouse brain ipsilateral to intrastriatal injection, 1 d after LPS injection

value: 1 d after LPS injection

tag: tissue


title: Liver genomic DNA from AATD patient 54

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-060

source_name: Liver DNA 54

tag: gender

value: female

tag: sample type


title: B9


title: Y3_BAC_CD11b_Hi


title: ipsilateral brain_LPS+1d_biological rep2


title: B5


title: Y1_BAC_CD11b_Hi


title: SIRS patient 059 [NK cells]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
S_C_059
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: peripheral NK cells from SIRS patient on ICU admission

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

growth_protocol: Blood was collected in S-Monovette® K3E tubes (Sarstedt, Nümbrecht, Germany) by venipuncture with presurgical patients and from a central venous catheter with ICU patients.

extract_protocol: Total RNA was purified from isolated NK cells stored in RNAlater® (Ambion) using a modified version of the miRVana miRNA isolation kit protocol (Applied Biosystems) (Figueiredo et al., Data Brief. 2017 Oct; 14: 77–83).

treatment_protocol: For NK cells isolation, peripheral blood mononuclear cells (PBMCs) were extracted from 32 mL blood by a Ficoll gradient (GE Healthcare). PBMCs were subjected to depletion using a labeling cocktail composed of CD15, CD14, CD3 and CD19 MicroBeads on an LD column (Miltenyi Biotec) and subsequent enrichment with CD56 MicroBeads on an MS column (Miltenyi Biotec).

tag: diagnosis

value: SIRS

value: peripheral NK cells


title: Liver genomic DNA from AATD patient 46

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-050

source_name: Liver DNA 46

value: male

tag: fib

value: liver biopsy

tag: disease state


title: B2


title: Liver genomic DNA from AATD patient 53

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-058

source_name: Liver DNA 53


title: Liver genomic DNA from AATD patient 51

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-056

source_name: Liver DNA 51


title: SIRS patient 058 [NK cells]

description:
S_C_058
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

tag: cell type


title: ipsilateral brain_LPS+4d_biological rep1

tag: Sex

value: adult; 10-12 weeks


title: A2_BAC_CD11b_Hi


title: (S+B)10

value: high salt with buckwheat


title: Liver genomic DNA from AATD patient 50

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-055

source_name: Liver DNA 50

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: A1_BM_CD11b_Hi


title: (S+B)9


title: A1_BAC_CD11b_Hi


title: SIRS patient 057 [NK cells]

description:
S_C_057
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: A2_BM_CD11b_Hi_R


title: (S+B)8


title: Liver genomic DNA from AATD patient 44

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-048

source_name: Liver DNA 44


title: SIRS patient 055 [NK cells]

description:
S_C_055
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: Stroma2

city: Birmingham

first: Rob

last: Welner

state: AL

address: 1824 6th Ave S

department: Medicine - Hem/Onc

institute: University of Alabama at Birmingham

description:
bone_marrow_stroma.counts.tsv.gz
Libraries 2.1, 2.2, 2.3

data_processing:
R1: biological (all 54 bp)
R2: technical -- part 1 of cell barcode (all 8bp)
R3: technical -- library barcode (though files are already demultiplexed; all 8bp)
R4: technical -- part 2 of cell barcode (1-8bp) and UMI (9-14bp)
Raw sequencing data were processed using the previously described (Zilionis et al., Nature Protocols 2017) inDrops.py bioinformatics pipeline, available at https://github.com/indrops/indrops, using library version "v3".
The cDNA read was trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 200 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.90) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols 2017).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file for all samples. Each row corresponds to one cell barcode (unfiltered), and the columns are as follows:
Column 1 (barcode_id): Unique cell barcode ID.
Column 2 (barcode): Cell barcode sequence.
Column 3 (library): Library ID.
Column 4 (sample): Sample (mouse) ID.
Column 5 (n_genes): Number of genes detected.
Column 6 (n_counts): Number of transcript counts detected.
Column 7 (mito_frac): Fraction of counts from mitochondrial genes.
Column 8 (pass_filter): Flag for whether a barcode passed QC and cell type filters and was used in final analyses.
Column 9 (cluster): Cell cluster label for barcodes passing filters.
Column 10(SPRING_x): SPRING x-coordinate.
Column 11(SPRING_y): SPRING y-coordinate.
Column 12(PBA_Potential): PBA prediction of cell's differentiation potential.
Column 13(PBA_Pr_Adipo): PBA prediction of cell's probability of becoming an adipocyte.
Column 14(PBA_Pr_Osteo): PBA prediction of cell's probability of becoming an osteoblast.
Column 15(PBA_Pr_Chondro): PBA prediction of cell's probability of becoming an chondrocyte.
Column 16(PBA_Osteo_pseudotime): PBA-predicted pseudotime on osteoblast trajectory.
Column 17(PBA_Chondro_pseudotime): PBA-predicted pseudotime on chondrocyte trajectory.
Column 18(PBA_Adipo_pseudotime): PBA-predicted pseudotime on adipocyte trajectory.
Columns 19+ (gene names): counts for each gene.

source_name: Bone marrow

extract_protocol:
Using inDrops, cells were encapsulated into 4-nL droplets on ice and lysed using a final concentration of 0.4% NP-40. Single-cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 7 of Tusi et al., Nature 2018.

treatment_protocol: Tissue harvesting: Femurs, tibiae, and pelvic bones were harvested immediately following euthanasia, and placed in cold (4°C) PBS. Bones were crushed with a pestle and mortar to maximize cell recovery. Remaining bone fragments were treated with collagenase/dispase for 45min at 37°C, these were then washed to obtain additional bone adherent cells. Harvested bone marrow cells were lysed and then filtered through a 100µm strainer. FACS isolation of non-hematopoietic, non-endothelial cells: Bone marrow cell samples were stained for CD45, Ter119, and CD31, gating was set based on staining controls and viable, triple negative cells were sorted on a BDAria.

value: bone marrow

value: stromal cells

value: 8-16 weeks

tag: purification


title: SIRS patient 056 [NK cells]

description:
S_C_056
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: Stroma1

description:
bone_marrow_stroma.counts.tsv.gz
Libraries 1.1, 1.2


title: (S+B)7


title: Liver genomic DNA from AATD patient 45

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-049

source_name: Liver DNA 45


title: (S+B)6


title: zfCTT.CMA.2

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

data_processing:
Quality filtering was performed using the FASTX Toolkit v0.0.13
cutadapt v1.16 was used to trim adapters from original reads and to discard reads shorter than 15 nucleotides.
Reads were mapped to the mouse GRCm38 (mm10) genome assembly using HiSAT2 v2.1.0 with standard parameters
Gene-level quantification was performed using R/Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include sRPKM values for each sample

source_name: Sting-/- mouse macrophages stably expressing mSTING-zfCTT

growth_protocol: Mouse macrophages stably expressing different STING proteins were cultured in DMEM supplemented with 10% (v/v) FBS and seeded 4 × 106 cells per 10 cm dish one day prior to stimulation

extract_protocol:
RNAs were purified by phenol-chloroform extraction and ethanol precipitation.
Single-end Illumina sequencing libraries from polyadenylated mRNA were performed using a standard protocol (Lee et al., 2015).

treatment_protocol: Mouse macrophages were stimulated with 500 μg mL-1 CMA (10-carboxymethyl-9-acridanone from Sigma) for 4 h.

tag: transgene

value: zfCTT


title: SIRS patient 052 [NK cells]

description:
S_C_052
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: Liver genomic DNA from AATD patient 43

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-047

source_name: Liver DNA 43


title: Liver genomic DNA from AATD patient 48

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-053

source_name: Liver DNA 48


title: Liver genomic DNA from AATD patient 42

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-046

source_name: Liver DNA 42


title: Liver genomic DNA from AATD patient 49

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-054

source_name: Liver DNA 49


title: (S+B)4

source_name: Gastric flora


title: SIRS patient 051 [NK cells]

description:
S_C_051
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: SIRS patient 050 [NK cells]

description:
S_C_050
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: ipsilateral brain_LPS+1d_biological rep1

tag: developmental stage

tag: time point

value: brain


title: (S+B)5

tag: mouse age

tag: mouse strain


title: MSCV2.2.CMA.2

source_name: Sting-/- mouse macrophages


title: (S+B)1

tag: mouse sex

tag: mouse diet


title: (S+B)2


title: zfCTT.CMA.1


title: Liver genomic DNA from AATD patient 41

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-045

source_name: Liver DNA 41


title: Liver genomic DNA from AATD patient 47

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-051

source_name: Liver DNA 47


title: Liver genomic DNA from AATD patient 39

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-043

source_name: Liver DNA 39


title: Liver genomic DNA from AATD patient 40

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-044

source_name: Liver DNA 40


title: dCTT.CMA.2

source_name: Sting-/- mouse macrophages stably expressing mSTING-dCTT

value: dCTT


title: Salt10

value: high salt


title: SIRS patient 047 [NK cells]

description:
S_C_047
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

source_name: peripheral NK cells from SIRS patient on ICU admission

tag: age


title: mSTING.CMA.2

source_name: Sting-/- mouse macrophages stably expressing mSTING

value: mSTING


title: dCTT.CMA.1


title: Salt9


title: mSTING.CMA.1


title: Liver genomic DNA from AATD patient 35

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-038

source_name: Liver DNA 35


title: SIRS patient 044 [NK cells]

description:
S_C_044
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: SIRS patient 042 [NK cells]

description:
S_C_042
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: Salt7


title: SIRS patient 043 [NK cells]

description:
S_C_043
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: SIRS patient 041 [NK cells]

description:
S_C_041
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.


title: Transgenic_3

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

data_processing:
Quality control and Adpator trimming using Fastqc and cutadapt
Alignment using Tophat2
Read counts using HTSEQ-Count
Genome_build: mm10
Supplementary_files_format_and_content: Gene Count files

source_name: IMCD3 cell with stable PGC1a overexpression

growth_protocol: DMEM/F12 media

extract_protocol:
Rneasy
Illumina TruSeq kit  paired end

treatment_protocol: 10 micromolar cisplatin x 24 hrs

tag: genotype

value: PGC1a transgenic

tag: cell line


title: SIRS patient 054 [NK cells]

description:
S_C_054
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

tag: gender


title: Salt6


title: MSCV2.2.CMA.1


title: Liver genomic DNA from AATD patient 37

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-041

source_name: Liver DNA 37

value: female

tag: sample type


title: Transgenic_2


title: SIRS patient 033 [NK cells]

description:
S_C_033
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

tag: diagnosis

value: SIRS


title: Salt5


title: SIRS patient 031 [NK cells]

description:
S_C_031
Gene expression data from peripheral NK cells of SIRS patient on ICU admission.

value: peripheral NK cells


title: Transgenic_1


title: Salt8

value: male


title: Salt4


title: presurgical patient 040 [NK cells]

description:
S_B_040
Gene expression data from peripheral NK cells of presurgical patient.

source_name: peripheral NK cells from presurgical patient

value: presurgical


title: Liver genomic DNA from AATD patient 36

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-039

source_name: Liver DNA 36

tag: fib

value: liver biopsy

tag: disease state


title: Salt3


title: Transgenic Vector Control_3

source_name: IMCD3 cell with control lentivirus


title: presurgical patient 039 [NK cells]

description:
S_B_039
Gene expression data from peripheral NK cells of presurgical patient.

tag: cell type


title: Transgenic Vector Control_2


title: Liver genomic DNA from AATD patient 34

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-037

source_name: Liver DNA 34


title: presurgical patient 038 [NK cells]

description:
S_B_038
Gene expression data from peripheral NK cells of presurgical patient.


title: Transgenic Vector Control_1


title: presurgical patient 037 [NK cells]

description:
S_B_037
Gene expression data from peripheral NK cells of presurgical patient.


title: Knockout Control_3

source_name: IMCD3 cell control CRISPR


title: CTL10

source_name: Gastric flora

value: control


title: Liver genomic DNA from AATD patient 30

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-033

source_name: Liver DNA 30

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: presurgical patient 036 [NK cells]

description:
S_B_036
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 32

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-035

source_name: Liver DNA 32


title: Salt2


title: presurgical patient 028 [NK cells]

description:
S_B_028
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 38

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-042

source_name: Liver DNA 38


title: CTL9


title: presurgical patient 027 [NK cells]

description:
S_B_027
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 31

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-034

source_name: Liver DNA 31


title: Knockout Control_1


title: Liver genomic DNA from AATD patient 28

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-031

source_name: Liver DNA 28


title: Knockout_3

source_name: IMCD3 cell with PGC1a CRISPR KO


title: Liver genomic DNA from AATD patient 27

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-030

source_name: Liver DNA 27


title: CTL8


title: CTL7


title: Liver genomic DNA from AATD patient 26

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-029

source_name: Liver DNA 26


title: Liver genomic DNA from AATD patient 33

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-036

source_name: Liver DNA 33


title: presurgical patient 026 [NK cells]

description:
S_B_026
Gene expression data from peripheral NK cells of presurgical patient.


title: presurgical patient 025 [NK cells]

description:
S_B_025
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 29

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-032

source_name: Liver DNA 29


title: CTL6


title: Knockout_1


title: Knockout_2


title: Knockout Control_2


title: CTL5


title: Salt1


title: LK_MP4_Rep8

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

data_processing:
The generated raw reads were processed using FastQC 0.11.6 for assessing read quality, amount of duplicates and presence of adapter sequences.
After this, the Illumina TruSeq adaptors were cleaved using cutadapt (version 1.16) and resulting reads were further trimmed keeping a quality drop value below a mean of Q20.
Further, the processed sequences were mapped to the mouse genome using the short read aligner STAR (version-2.5.2b) with genome and annotation files retrieved from GENCODE (July 2017, GRCm38.p5, M12). For all the studied samples, the proportion of reads mapped to the mouse reference genome ranged between 81% and 83% in total.
The sequences aligning to specific genes were quantified using bedtools subcommand intersect (version 2.15.0).
Next, the differentially expressed genes were identified using DESeq2 (version 1.16.1). Only the genes having a Benjamini-Hochberg corrected p-value below 0.05 were classified as significantly differentially expressed (DEGs).
The data were visualized as MA plot using DESeq2’s function plotMA.
To compare the groups heatmaps were used to represent genes having p-adjusted values below 0.05 and an absolute log2 fold-change equal or above 2.
Supplementary_files_format_and_content: abundance

source_name: lymphoid follicle

extract_protocol:
RNeasy® Micro Kit (Qiagen, Hilden, Germany; REF: 74004) was used according to the manufacturer`s instructions.
Libraries for RNA sequencing were prepared from 8 - 28 ng of total RNA. From each sample, poly-A RNA was purified, converted to cDNA, and linked to Illumina adapters by using the Illumina TruSeq stranded mRNA Kit according to manufacturer instructions (Illumina, San Diego, CA, USA). Samples were multiplexed and sequenced on an Illumina NextSeq 500 in a 75-nt single-end setting using a high-output run mode.

tag: strain

tag: organ

value: lymph node

tag: eae model


title: Liver genomic DNA from AATD patient 25

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-028

source_name: Liver DNA 25


title: CTL4


title: presurgical patient 017 [NK cells]

description:
S_B_017
Gene expression data from peripheral NK cells of presurgical patient.

source_name: peripheral NK cells from presurgical patient


title: LK_MP4_Rep7


title: presurgical patient 024 [NK cells]

description:
S_B_024
Gene expression data from peripheral NK cells of presurgical patient.


title: presurgical patient 16 [NK cells]

description:
S_B_016
Gene expression data from peripheral NK cells of presurgical patient.


title: CTL3


title: LK_MP4_Rep6


title: CTL2


title: Liver genomic DNA from AATD patient 24

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-027

source_name: Liver DNA 24


title: LK_MP4_Rep5


title: CTL1


title: presurgical patient 014 [NK cells]

description:
S_B_014
Gene expression data from peripheral NK cells of presurgical patient.


title: presurgical patient 009 [NK cells]

description:
S_B_009
Gene expression data from peripheral NK cells of presurgical patient.


title: LK_MP4_Rep4


title: Liver genomic DNA from AATD patient 22

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-025

source_name: Liver DNA 22


title: VavCre; Jak2V617F; Cdk6+/+, Palbociclib treated, replicate 3

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

country: Austria

institute: Vetmeduni Vienna

data_processing:
Alignment to genome version GRCm38.p5 using STAR
Adapter trimming and removing of low quality bases was performed using Trimmomatic
FeatureCounts from the Subread package was used to obtain gene counts for union gene models
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: bone marrow

growth_protocol: not applicable, ex vivo data

extract_protocol:
RNA was extracted using the RNeasy Micro Kit according to the manufacturer’s instructions (Qiagen)
RNA-Seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer).

treatment_protocol: bone marrow cells were stained with antibodies for Lin-markers (Ter119, CD11b, Gr-1, CD19, CD3), Sca-1 and cKit and sorted for Lin-Sca-1+cKit+ cells with a BD Aria cell sorter

tag: tissue

value: bone marrow

value: bone marrow LSK cells

tag: treatment

value: Palbociclib

value: VavCre; Jak2V617F; Cdk6+/+


title: presurgical patient 015 [NK cells]

description:
S_B_015
Gene expression data from peripheral NK cells of presurgical patient.


title: VavCre; Jak2V617F; Cdk6+/+, Palbociclib treated, replicate 2


title: LK_MP4_Rep3


title: Liver genomic DNA from AATD patient 19

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-022

source_name: Liver DNA 19


title: LK_MP4_Rep2


title: Liver genomic DNA from AATD patient 23

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-026

source_name: Liver DNA 23


title: Liver genomic DNA from AATD patient 17

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-020

source_name: Liver DNA 17


title: presurgical patient 005 [NK cells]

description:
S_B_005
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 21

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-024

source_name: Liver DNA 21


title: LK_MP4_Rep1


title: VavCre; Jak2V617F; Cdk6+/+, Palbociclib treated, replicate 1


title: VavCre; Jak2V617F; Cdk6-/-, replicate 3

value: untreated

value: VavCre; Jak2V617F; Cdk6-/-


title: Liver genomic DNA from AATD patient 20

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-023

source_name: Liver DNA 20


title: presurgical patient 004 [NK cells]

description:
S_B_004
Gene expression data from peripheral NK cells of presurgical patient.


title: VavCre; Jak2V617F; Cdk6-/-, replicate 2


title: presurgical patient 006 [NK cells]

description:
S_B_006
Gene expression data from peripheral NK cells of presurgical patient.


title: Liver genomic DNA from AATD patient 18

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-021

source_name: Liver DNA 18


title: LK_MOG_Rep3


title: presurgical patient 003 [NK cells]

description:
S_B_003
Gene expression data from peripheral NK cells of presurgical patient.


title: SIRS patient 059 [granulocytes]

description:
S_C_059
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: peripheral granulocytes from SIRS patient on ICU admission

extract_protocol: Total RNA was purified from isolated granulocytes stored in RNAlater® (Ambion) using the miRVana miRNA isolation kit (Applied Biosystems).

treatment_protocol: Granulocytes were prepared from 2 mL blood by positive selection (StraightFrom™ Whole Blood CD15 MicroBeads, Miltenyi Biotec).

value: peripheral granulocytes


title: SIRS patient 058 [granulocytes]

description:
S_C_058
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: VavCre; Jak2V617F; Cdk6-/-, replicate 1


title: Liver genomic DNA from AATD patient 15

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-018

source_name: Liver DNA 15


title: septic shock patient 046 [NK cells]

description:
S_A_046
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.

source_name: peripheral NK cells from septic shock patient on ICU admission

value: septic shock


title: LK_MOG_Rep2


title: septic shock patient 045 [NK cells]

description:
S_A_045
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: Liver genomic DNA from AATD patient 14

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-017

source_name: Liver DNA 14

value: female


title: SIRS patient 057 [granulocytes]

description:
S_C_057
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.

value: SIRS


title: Liver genomic DNA from AATD patient 16

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-019

source_name: Liver DNA 16


title: KH_MOG_Rep5

source_name: infiltrate

value: cerebellum


title: VavCre; Jak2+/+; Cdk6-/-, replicate 1

value: VavCre; Jak2+/+; Cdk6-/-


title: KH_MOG_Rep4


title: LK_MOG_Rep1

source_name: lymphoid follicle


title: VavCre; Jak2V617F; Cdk6+/+, replicate 3


title: septic shock patient 021 [NK cells]

description:
S_A_021
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.

value: peripheral NK cells

value: male


title: SIRS patient 056 [granulocytes]

description:
S_C_056
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: LK_MOG_Rep4


title: SIRS patient 054 [granulocytes]

description:
S_C_054
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: Liver genomic DNA from AATD patient 11

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-014

source_name: Liver DNA 11

value: liver biopsy


title: VavCre; Jak2+/+; Cdk6-/-, replicate 3


title: septic shock patient 035 [NK cells]

description:
S_A_035
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: KH_MOG_Rep2


title: VavCre; Jak2V617F; Cdk6+/+, replicate 1


title: VavCre; Jak2+/+; Cdk6-/-, replicate 2


title: VavCre; Jak2+/+; Cdk6+/+, replicate 3

value: VavCre; Jak2+/+; Cdk6+/+


title: septic shock patient 034 [NK cells]

description:
S_A_034
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: Liver genomic DNA from AATD patient 12

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-015

source_name: Liver DNA 12

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: Liver genomic DNA from AATD patient 10

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-013

source_name: Liver DNA 10


title: Liver genomic DNA from AATD patient 7

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-009

source_name: Liver DNA 7


title: Liver genomic DNA from AATD patient 6

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-008

source_name: Liver DNA 6


title: VavCre; Jak2V617F; Cdk6+/+, replicate 2

source_name: bone marrow

value: bone marrow


title: Liver genomic DNA from AATD patient 8

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-010

source_name: Liver DNA 8


title: septic shock patient 032 [NK cells]

description:
S_A_032
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: SIRS patient 055 [granulocytes]

description:
S_C_055
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: SIRS patient 050 [granulocytes]

description:
S_C_050
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: SIRS patient 052 [granulocytes]

description:
S_C_052
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: Liver genomic DNA from AATD patient 9

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-012

source_name: Liver DNA 9


title: septic shock patient 008 [NK cells]

description:
S_A_008
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: SIRS patient 053 [granulocytes]

description:
S_C_053
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: septic shock patient 010 [NK cells]

description:
S_A_010
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: SIRS patient 051 [granulocytes]

description:
S_C_051
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: KH_Agg_MP4_Rep2

source_name: B-cell aggregate


title: KH_MOG_Rep3


title: VavCre; Jak2+/+; Cdk6+/+, replicate 1

value: bone marrow LSK cells


title: KH_MOG_Rep1


title: KH_Agg_MP4_Rep1


title: Mouse 10T1/2, Mutant 2 [ATAC-seq]

city: New York

first: Richard

last: Koche

state: NY

address: 430 East 67th Street

institute: Sloan Kettering Institute

data_processing:
ATAC-seq reads were trimmed and filtered for quality with trim_galore v0.4.5, backed by version 1.15 of cutadapt, with a quality setting of 15.
ATAC-seq reads were aligned to the mm9 genome assembly, using default settings in bowtie2, version 2.3.4.1.
Duplicate reads were removed with MarkDuplicates in Picard, version 2.16.0.
Peaks in ATAC-seq read density were called with version 2.1.1.20160309 of MACS2, using a setting of 0.001 for the p-value option.
For read density visualization, bigWig files were created with the bamToBed, slopBed, and genomeCoverageBed programs in version 2.27.1 of bedtools, and wigToBigWig in v359 of the UCSC utilities.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bw: Each bigWig file was generated from the corresponding aligned BAM by using bamToBed, slopBed, and genomeCoverageBed in version 2.27.1 of bedtools, and wigToBigWig in v359 of the UCSC utilities.

extract_protocol:
Extraction of material for sequencing was performed according to the Omni-ATAC-seq protocol from Corces et al., as in https://doi.org/10.1038/nmeth.4396
The NEBNext Q5 Hot Start HiFi PCR Master Mix with Nextera PCR primers was used for barcoding and library preparation, and purification was performed with AMPure XP beads.

tag: genotype/variation

value: IDH2 R172K


title: Mouse 10T1/2, Mutant 3 [ATAC-seq]


title: septic shock patient 020 [NK cells]

description:
S_A_020
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.


title: SIRS patient 047 [granulocytes]

description:
S_C_047
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: Mouse 10T1/2, Mutant 1 [ATAC-seq]


title: SIRS patient 043 [granulocytes]

description:
S_C_043
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: control cells, biological rep3

city: Changchun/Jilin

first: Ke

last: Wang

address: Ziqiang street

institute: The Second Hospital of Jilin University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip human Gene. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: control A549 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA

growth_protocol: A549 cells were cultured in RPMI-1640 supplemented with 10% foetal bovine serum at 37 °C in a humidified atmosphere containing 5% CO2.

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

treatment_protocol: IARS2 expression was stably knocked-down in A549 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.

value: lung cancer cell line

value: control


title: KH_Agg_MP4_Rep3


title: IARS2 knockdown cells, biological rep3

source_name: IARS2 knockdown A549 cells

value: IARS2 knockdown


title: 10X_day_8_H9_rep2

first: Ian

middle: R

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

description: Custom paired end, all reads informatiive. Read lengths: Read 1 = 26bp, Read 2 = 98bp, i7 index = 8bp

data_processing:
Raw reads were processed using the 10X Cell Ranger pipeline v2.1.1 ( 10X Genomics) in order to perform read alignment, filtering, barcode and UMI (unique molecular identifier) counting, and subsequently generate gene-cell matrices.
Genome_build: GRCh38

source_name: hESC derived cells from day8 of hESC-ECP differentiation protocol

growth_protocol: hES cells differentiatied to human embryonic stem cell derived endothelial product (hESC-ECP) using differentiation protocol from MacAskill et al.,Molecular Therapy, 2018. Cells detached at day 8 using TrypLE Express Enzyme (Thermo Fisher Scientific, Waltham, USA).

extract_protocol: Construction of single cell RNA-sequencing libraries was conducted using the Single Cell 3' Reagent Kit (10X Genomics, Pleasanton, USA) in accordance with the manufacturer’s protocol.

tag: passage number


title: 10X_HUVEC

source_name: human umbilical vein endothelial cell

growth_protocol: HPAECs (Lonza, Basel, Switzerland) maintained using endothelial growth media (EGM-2 BulletKit) (Lonza, Basel, Switzerland) supplemented with 10% FBS (Life Technologies, Paisley, UK) and P/S (100U/ml) (Gibco, Paisley, UK). Cells harvested using 1X Trypsin-EDTA.

value: HUVEC


title: RNA-seq-M3

city: Hangzhou

first: Yichen

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

department: College of Medicine

institute: Zhejiang University

description: MenSC therapy

data_processing:
After sequencing images generated, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: liver

growth_protocol: HepG2 cells were seeded in 6-well plates

extract_protocol:
Total RNA was isolated from cancer cells by using the AllPrep® DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
After assessment of the quantity, quality and integrity of RNA, the mRNA was enriched with Oligo(dT) beads and rRNA was removed using the Ribo-ZeroTM Magnetic Gold Kit (Epicentre, USA). The mRNA fragment library was prepared using the KAPA Stranded RNA-Seq Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. After mRNA amplification using qPCR, library quality was assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: HepG2 cells were cocultured with MenSC cells via transwell co-culture system.

value: hepatocellular carcinoma cell

value: liver


title: septic shock patient 019 [NK cells]

description:
S_A_019
Gene expression data from peripheral NK cells of septic shock patient on ICU admission.

source_name: peripheral NK cells from septic shock patient on ICU admission

value: septic shock

value: female


title: SIRS patient 044 [granulocytes]

description:
S_C_044
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.

source_name: peripheral granulocytes from SIRS patient on ICU admission

value: SIRS

value: peripheral granulocytes


title: Liver genomic DNA from AATD patient 4

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-006

data_processing: Resultant IDAT files were processed and normalized using the R Bioconductor package “minfi” using subset within-array quantile normalization (SWAN). CpGs that failed to reach significant detection (p<0.01) or were unreliable (0 or 1 value, 1 probe) in all samples were filtered out (45,921 probes) along with cross-reactive probes (43,255), leaving 779,088 CpGs for downstream analysis.

source_name: Liver DNA 4

extract_protocol: Specimens were preserved in Qiagen Allprotect solution, Genomic DNA  were extracted from tissues using Qiagen Allprep isolation columns according to the manufacturer’s instructions.


title: control cells, biological rep1


title: control cells, biological rep2


title: SIRS patient 049 [granulocytes]

description:
S_C_049
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: Mouse 10T1/2, Mutant + Tamoxifen 3 [ATAC-seq]

value: Tamoxifen


title: SIRS patient 042 [granulocytes]

description:
S_C_042
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: Liver genomic DNA from AATD patient 1

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-003

source_name: Liver DNA 1

value: liver biopsy


title: IARS2 knockdown cells, biological rep2


title: VavCre; Jak2+/+; Cdk6+/+, replicate 2

value: untreated

value: VavCre; Jak2+/+; Cdk6+/+


title: Mouse 10T1/2, Mutant + Tamoxifen 2 [ATAC-seq]


title: Liver genomic DNA from AATD patient 3

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-005

source_name: Liver DNA 3

value: male

value: Alpha-1 Antitrypsin Deficiency (AATD)


title: Liver genomic DNA from AATD patient 13

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-016

source_name: Liver DNA 13


title: RNA-seq-M2

description: MenSC therapy


title: RNA-seq-M1

description: MenSC therapy


title: Mouse 10T1/2, Wildtype 3 [ATAC-seq]

value: WT


title: Mouse 10T1/2, Wildtype 2 [ATAC-seq]


title: Liver genomic DNA from AATD patient 2

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-004

source_name: Liver DNA 2


title: RNA-seq-C3

description: control


title: RNA-seq-C2

description: control


title: Liver genomic DNA from AATD patient 5

description:
liver cells of Alpha-1 Antitrypsin Deficiency patients
63-2013-007

source_name: Liver DNA 5


title: SIRS patient 041 [granulocytes]

description:
S_C_041
Gene expression data from peripheral granulocytes of SIRS patient on ICU admission.


title: RNA-seq-C1

description: control


title: Mouse 10T1/2, Wildtype 1 [ATAC-seq]


title: Mouse 10T1/2, Wildtype + Tamoxifen 3 [ATAC-seq]


title: IARS2 knockdown cells, biological rep1

value: lung cancer cell line


title: Mouse 10T1/2, Wildtype + Tamoxifen 2 [ATAC-seq]


title: presurgical patient 040 [granulocytes]

description:
S_B_040
Gene expression data from peripheral granulocytes of presurgical patient.

source_name: peripheral granulocytes from presurgical patient

value: presurgical


title: stomach_normal_rep15

city: Xuzhou

first: Li

last: Li

state: Jiangsu

address: No. 99 West Huaihai Road, Xuzhou, Jiangsu 221002, P.R. China.

institute: the Affiliated Hospital of Xuzhou Medical University

description: Gene expression data from human normal stomach tissue

hyb_protocol: GeneChip Hybridization Wash and Stain Kit

scan_protocol: GeneChip Scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: human normal stomach tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: hMeDIP-seq-M5

description: MenSC therapy

data_processing:
the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human genome (UCSC HG19) using HISAT2 software (V2.1.0)
Aligned reads were used for peak calling, statistically significant hMeDIP enriched regions (peaks) were identified for each sample, using a q-value threshold of 10-4 by MACS v2. LncRNAs, mRNAs and Small ncRNAs associated hMeDIP enriched regions (peaks) were annotated by the nearest gene using the newest UCSC RefSeq database.
Statistically significant differentially hydroxymethylated regions (DhMRs) within promoters between two groups with statistically significant were identified by diffReps(Cut-off: log2FC=1.0, p-value=10-4).
Genome_build: hg19
Supplementary_files_format_and_content: The signal profiles in UCSC binary wig file format were generated from hMeDIP-seq data, which can be visualized using UCSC.

extract_protocol:
Genomic DNA was isolated from cancer cells by using the AllPrep® DNA/RNA Mini Kit (Qiagen, Germany).
Purified genomic DNA was sonicated to obtain fragments with a size range of 200-800 bp for hMeDIP-seq. Following end repair of the DNA samples with the addition of deoxyadenosine and adaptor ligation based on the Illumina paired-end protocol, the DNA fragments were immunoprecipitated with anti-5-hydroxymethylcytosine. Then, the precipitated fragments were amplified by PCR, and 300-900 bp DNA fragments were selected by using AMPure XP beads. The completed libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules, captured on an Illumina flow cell, an amplified in situ.

tag: antibody


title: MeDIP-seq C-input

description: control


title: presurgical patient 039 [granulocytes]

description:
S_B_039
Gene expression data from peripheral granulocytes of presurgical patient.


title: hMeDIP-seq-M3

description: MenSC therapy


title: stomach_normal_rep13


title: presurgical patient 038 [granulocytes]

description:
S_B_038
Gene expression data from peripheral granulocytes of presurgical patient.


title: Nascent_RNA-seq_kidney_biologicalRep1

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: RIKEN, Yokohama

data_processing:
For all our datasets we performed the following steps, (i) split reads by barcode, (ii) trimmed reads to remove barcode sequences and (iii) removed reads aligned to rRNA sequences (Human: GenBank U13369.1; Mouse: GenBank BK000964.3). These steps were performed using MOIRAI (Hasegawa et al., 2014) for human cell line data and using Trimmomatic v 0.36 (Bolger et al., 2014) and MOIRAI (Hasegawa et al., 2014) for mouse tissue data. For all CAGE based data and mouse RNA-seq data, sequences with base ‘N’ were also removed.
Non rRNA reads were mapped hg19 genome and human reference gene model Gencode v27lift37 comprehensive using  STAR v 2.5.0a with the following parameters for indexing: --runThreadN 12 --runMode genomeGenerate --genomeDir genome.fa --sjdbGTFfile Gencodeannotation.gtf and the following parameters for mapping: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1 --readFilesCommand zcat.
Transcription start sites for CAGE based data were identified using bedtools v 2.2.25 (Quinlan and Hall, 2010) as described here: http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment
Genome_build: Human: hg19 and Mouse:mm9
Supplementary_files_format_and_content: Bed 6 file for trasncription start sites. Scores represent aggregated tags with same starting position.

source_name: Kidney

growth_protocol: MCF-7, HeLa-S3 and HepG2 cells were cultured at 37 ˚C under 5% CO2 in DMEM with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS. GM12878 and K562 cells were cultured at 37 ˚C under 5% CO2 in RPMI 1640 with L-Gln supplemented with 1 mM sodium pyruvate and 10% FBS.

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Frozen mouse tissue samples were used for total and nascent RNA extraction. Tissue was homogenized using gentleMACS Dissociator (Miltenyi Biotec).  The sample was transferred to gentleMACS M tube (Miltenyi Biotec) and added with pre-chilled 2 ml of Buffer C (Nuclei PURE Lysis Buffer (Sigma-Aldrich), 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution, 20 units of SUPERase IN RNase Inhibitor, 1 mM DTT, Triton X-100). Lysate was then filtered through gentleMACS SmartStrainers (100 μm) (Miltenyi Biotec). 200 μL of the tissue lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction.
We added 2 ml of ice-cold Buffer D (10 ml of Sucrose Cushion solution (Sigma-Aldrich), 1.2 ml of Sucrose Cushion buffer (Sigma-Aldrich) and 11.2 μL of 1M DTT) to the bottom of a conical centrifuge tube on ice. Tissue lysate prepared above was gently mixed with 3.6 ml of Buffer D, and was carefully and slowly layered on top of the 2 ml of Buffer D in the conical centrifuge tube. Then, the tube was centrifuged at 13,000 G for 45 minutes at 4 ˚C to collect nuclei pellets. The pellets were washed once with 500 μL of Buffer C.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).

treatment_protocol: For the time course experiment, MCF-7 cells were serum-starved for 16 hours, and heregulin beta-1 was added to the medium at a final concentration of 10 nM. Cells were harvested at 0 (no treatment), 15, 30, 45, 60, 120, 180 and 360 minutes in triplicates.

value: kidney

tag: urea treatment

tag: age

value: 8 weeks

tag: molecule subtype

value: Nascent RNA


title: presurgical patient 017 [granulocytes]

description:
S_B_017
Gene expression data from peripheral granulocytes of presurgical patient.


title: MeDIP-seq M-input

description: MenSC therapy

value: hepatocellular carcinoma cell

value: liver

tag: cell line


title: stomach_normal_rep14

tag: gender

value: female


title: presurgical patient 037 [granulocytes]

description:
S_B_037
Gene expression data from peripheral granulocytes of presurgical patient.

tag: diagnosis


title: hMeDIP-seq-M2

description: MenSC therapy


title: Nascent_RNA-seq_brain_biologicalRep1

source_name: Brain

value: brain


title: stomach_normal_rep11


title: stomach_normal_rep10


title: presurgical patient 036 [granulocytes]

description:
S_B_036
Gene expression data from peripheral granulocytes of presurgical patient.

value: peripheral granulocytes


title: presurgical patient 016 [granulocytes]

description:
S_B_016
Gene expression data from peripheral granulocytes of presurgical patient.


title: hMeDIP-seq-C5

description: control


title: Mouse 10T1/2, Wildtype + Tamoxifen 1 [ATAC-seq]

value: Tamoxifen


title: presurgical patient 015 [granulocytes]

description:
S_B_015
Gene expression data from peripheral granulocytes of presurgical patient.


title: presurgical patient 012 [granulocytes]

description:
S_B_012
Gene expression data from peripheral granulocytes of presurgical patient.


title: stomach_normal_rep12


title: stomach_normal_rep9


title: 10X_HPAEC

description: Custom paired end, all reads informatiive. Read lengths: Read 1 = 26bp, Read 2 = 98bp, i7 index = 8bp

source_name: human pulmonary artery endothelial cell

growth_protocol: HUVECs (Lonza, Basel, Switzerland) maintained using endothelial growth media (EGM-2 BulletKit) (Lonza, Basel, Switzerland) supplemented with 10% FBS (Life Technologies, Paisley, UK) and P/S (100U/ml) (Gibco, Paisley, UK). Cells harvested using 1X Trypsin-EDTA.

value: HPAEC


title: stomach_normal_rep7


title: Nascent_RNA-seq_kidney_biologicalRep2

extract_protocol:
The cDNA synthesis was carried out using 5 μg of total and nascent RNA (A260/280 and 260/230 ratios > 1.7). CAGE libraries were generated based on no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) precisely as described in Murata et al. (Methods Mol Biol. 2014;1164:67-85.).
Frozen mouse tissue samples were used for total and nascent RNA extraction. Tissue was homogenized using PowerMasherII (FUJIFILM Wako Pure Chemical). The sample was transferred to BioMasherV (FUJIFILM Wako Pure Chemical) tube and added with pre-chilled 2 ml of Buffer C (Nuclei PURE Lysis Buffer (Sigma-Aldrich), 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution, 20 units of SUPERase IN RNase Inhibitor, 1 mM DTT, Triton X-100). 200 μL of the tissue lysate was sampled and mixed with 700 μL of QIAzol for total RNA extraction.
We added 2 ml of ice-cold Buffer D (10 ml of Sucrose Cushion solution (Sigma-Aldrich), 1.2 ml of Sucrose Cushion buffer (Sigma-Aldrich) and 11.2 μL of 1M DTT) to the bottom of a conical centrifuge tube on ice. Tissue lysate prepared above was gently mixed with 3.6 ml of Buffer D, and was carefully and slowly layered on top of the 2 ml of Buffer D in the conical centrifuge tube. Then, the tube was centrifuged at 13,000 G for 45 minutes at 4 ˚C to collect nuclei pellets. The pellets were washed once with 500 μL of Buffer C.
Washed pellets were resuspended in 200 μL of Buffer B (1% NP-40, 20 mM HEPES, 300 mM NaCl, 2 M Urea, 0.2 mM EDTA, 1 mM DTT, 25 μM alpha-amanitin, 1× cOmplete Protease Inhibitor solution and 20 units SUPERase IN RNase Inhibitor), and incubated for 10 minutes on ice. Then, nuclear insoluble fraction was collected by 3,000 G centrifuge for 2 minutes at 4 ˚C. The pellets were washed once with 100 μL of Buffer B.
50 μL of DNase I solution containing 10 units of DNase I (Thermo Fisher Scientific), 1× DNase I Buffer (Thermo Fisher Scientific) and 20 units of SUPERase IN RNase Inhibitor was added to the pellets. The solution was incubated for 30 minutes at 37 ˚C while pipetting up and down several times every 10 minutes. 700 μL of QIAzol was directly added to the solution and thoroughly mixed. RNA was extracted by miRNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. An “on-column DNase I digestion” was carried out using RNase-free DNase set (QIAGEN). RNA was eluted in 30 μL of RNase-free water, and quality and quantity were measured by NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2100 BioAnalyzer (Agilent).


title: RNA-seq_kidney_biologicalRep2

value: Total RNA


title: stomach_normal_rep8


title: hMeDIP-seq-C3

description: control


title: RNA-seq_kidney_biologicalRep1


title: presurgical patient 004 [granulocytes]

description:
S_B_004
Gene expression data from peripheral granulocytes of presurgical patient.


title: hMeDIP-seq-C2

description: control