title: 23    Aged    B


title: Non-cancer 3 [SH55L25_Cell4]

status: Public on Aug 03 2020

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

country: Japan

institute: Toray industries inc

description:
miRNA
XB0845

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: tissue

value: serum

tag: Sex

value: M

tag: age

tag: cstage

tag: child-pugh

tag: afp

value: unknown


title: Non-cancer 3 [SH55R30_Cell2]

description:
miRNA
XB0839


title: Non-cancer 3 [SH56407_Cell1]

description:
miRNA
XB0846


title: 20    Aged    B

type: SRA

city: Greenville

first: Michelle

middle: L

last: Ratliff

state: NC

address: 600 Moye Blvd, 132 Biotechnology Building

department: Microbiology and Immunology

country: USA

institute: East Carolina University

library_source: transcriptomic

data_processing:
Reads aligned to GrCh38 assembly of the human genome using STAR using default parameters
Partek Genomics Suite was run to align reads to perform differenital expression analyses
Genome_build: GrCh38
Supplementary_files_format_and_content: Abundance measurements

source_name: Aged B_peripheral blood HSC

extract_protocol:
Fluidigm C1 single cell platform
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

value: Aged B

value: Female

tag: race

value: Caucasian

value: peripheral blood

tag: cell type

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH56206_Cell2]

description:
miRNA
XB0827


title: Hs_H1_BG042_d3_445F12.1_16_RNAseq_1

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description:
BG42_445F12-1_d3_S4_L001
processed data file: lncrna_ko_rpkm.txt

data_processing:
Reads were aligned to hg38 using STAR (v2.5.3b) with the following parameters: --twopassMode Basic --outFilterMismatchNmax 6 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 3 --outFilterType BySJout --seedSearchStartLmax 50.
Reads per kilobase of transcript, per million mapped reads (RPKM) were calculated with Cufflinks (v2.2.1)
Count tables for differential gene expression analysis with DESeq2 (v1.10.1) were generated with htseq-count from the HTSeq Python library.
Genome_build: hg38
Supplementary_files_format_and_content: gene expression data table in text format

source_name: RP11-445F12.1 KO hESCs were differentiated to the definitive endoderm stage

growth_protocol: Pancreatic differentiation was performed as previously described (Rezania et al., 2012; Rezania et al., 2014), with minor modifications. Cells were grown either as a monolayer (RNA-seq of lncRNA KO hESC-derived tissues and corresponding WT controls) , or in suspension culture (Ribo-seq and matched RNA-seq).

extract_protocol:
Total RNA was extracted using either Trizol or the QIAGEN RNeasy Mini Kit. For cell fractionation experiments, the Paris Kit (Thermo Fisher Scientific) was used.
Libraries were prepared according to Illumina's (TruSeq Stranded Total RNA Library Prep Gold; TruSeq Stranded mRNA Library Prep; TruSeq Ribo Profile (Mammalian) or Roche's (KAPA mRNA HyperPrep Kit) instructions

treatment_protocol: Definitive endoderm and pancreatic progenitor stage cells were collected, and RNA was extracted for RNA-seq library preparation.

tag: cell line

value: H1 ES cells

value: ES-derived definitive endoderm cells

tag: genotype

tag: library

value: polyA, stranded


title: Hs_H1_BG73_d13_ctrl_RNAseq_4

description:
Hs_H1_BG73_d13_ctrl_RNAseq_4_S9_L003
processed data file: lncrna_ko_rpkm.txt

source_name: Unmodified hESCs were differentiated to the PP2 stage

value: ES-derived late pancreatic progenitor cells

value: WT


title: 19    Aged    B


title: 18    Aged    B


title: Non-cancer 3 [SH55L24_Cell1]

description:
miRNA
XB0822


title: 21    Aged    B


title: Hs_H1_BG058_d3_ctrl_RNAseq_1

description:
Hs_H1_BG058_d3_ctrl_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: Unmodified hESCs were differentiated to the definitive endoderm stage


title: Non-cancer 3 [SH56206_Cell4]

description:
miRNA
XB0829


title: Non-cancer 3 [SH55L25_Cell1]

description:
miRNA
XB0842


title: Non-cancer 3 [SH56829_Cell1]

description:
miRNA
XB0834


title: Non-cancer 3 [SH56829_Cell2]

description:
miRNA
XB0821


title: 17    Aged    B


title: 16    Aged    B


title: 15    Aged    B


title: Hs_H1_BG058_d3_GATA6-AS1_7_RNAseq_1

description:
Hs_H1_BG058_d3_GATA6-AS1_7_RNAseq_1_merged
processed data file: lncrna_ko_rpkm.txt

source_name: GATA6-AS1 KO hESCs were differentiated to the definitive endoderm stage


title: WT_L5_Rep4

city: San Francisco

first: Siavash

last: Fazel Darbandi

address: 1550 4th Street

department: Psychiatry

institute: University of California San Francisco

data_processing:
Sequenced reads were aligned to the mm9 mouse genome reference using STAR v2.5.2b with default parameters. Gene expression was quantified with HTSeq in intersection-strict mode.
Genes with less than or equal to one read in more than 50% of the samples were removed. Filtered genes were normalized for gene length, GC content, and sample library size using CQN R-package.
Gene length is obtained directly from the gene annotation file (.GTF) of mouse mm9 genome build reference. BedTools is used to compute the gene GC content.
Genome_build: mm9
Supplementary_files_format_and_content: raw gene counts for every gene and sample; normalized counts for all samples and genes passing filtering cut-offs

organism: Mus musculus

source_name: WT_L5_cortical neurons

growth_protocol: The cortices were dissected in HBSS from P5 mice. Cortices were dissociated and tdTomato+ cells were FACS sorted. Approximately 25,000 cells were collected from each sample.

extract_protocol:
RNeasy Plus Micro Kit (QIAGEN) following manufacturer’s protocol
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set A (Illumina). The amplification of adaptor-ligated fragments was carried out for 12 cycles during which individual index sequences were added to each distinct sample.

value: wild type

value: postnatal day 5

tag: tissue/cell type

value: cortical neurons

tag: cortical layer

value: FACS purified layer 5 Neurons

tag: sequencing batch

value: C


title: WT_L5_Rep3


title: Non-cancer 3 [SH56829_Cell4]

description:
miRNA
XB0819

value: serum

value: M


title: 14    Aged    B

value: Aged B


title: 11    Aged    B

value: Female


title: 13    Aged    B

value: Caucasian


title: 10    Aged    B

value: peripheral blood


title: 9    Aged    B

value: Hematopoietic Stem Cells (HSCs)


title: WT_L5_Rep1

value: B


title: WT_L5_Rep2


title: TBR1_NULL_L6_Rep4

source_name: TBR1_NULL_L6_cortical neurons

value: Tbr1 Layer 6 Null

value: FACS purified layer 6 Neurons

value: A


title: Non-cancer 3 [SH56830_Cell1]

description:
miRNA
XB0818

value: unknown


title: 6    Aged    B


title: 5    Aged    B


title: TBR1_NULL_L6_Rep3


title: 4    Aged    B


title: Non-cancer 3 [SH55C58_Cell4]

description:
miRNA
XB0769


title: Non-cancer 3 [SH55L15_Cell2]

description:
miRNA
XB0799


title: Non-cancer 3 [SH55C57_Cell2]

description:
miRNA
XB0763


title: Non-cancer 3 [SH56835_Cell1]

description:
miRNA
XB0778


title: 2    Aged    B


title: 96    Aged    A

source_name: Aged A_peripheral blood HSC

value: Aged A

value: Male


title: Non-cancer 3 [SH55C57_Cell1]

description:
miRNA
XB0762


title: 95    Aged    A


title: TBR1_NULL_L6_Rep1

value: postnatal day 5

value: cortical neurons


title: Non-cancer 3 [SH55C56_Cell3]

description:
miRNA
XB0760


title: 94    Aged    A


title: WT_L6_Rep4

source_name: WT_L6_cortical neurons

value: wild type


title: 7    Aged    B


title: 93    Aged    A


title: WT_L6_Rep3


title: WT_L6_Rep2


title: Non-cancer 3 [SH55C56_Cell2]

description:
miRNA
XB0759

value: serum


title: M8_10d_Exp2_M8_S7

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Samples taken at 10 days of culture

data_processing:
Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: ASM944v1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: bacterial culture

growth_protocol: Biofilms (which includes bacteria attached to the plastic wells and surface pellicles) for RNA extraction of BCG strains were cultured in Sauton media (containing the following g/L of anhydrous compounds from Sigma unless indicated otherwise): L-asparagine (4.0), citric acid (2.0), KH2PO4 (0.5), MgSO4 (0.5), ferric ammonium citrate (0.05), 1% ZnSO4 (1 mL), glycerol (60 mL), pH 7.0, and incubated at 37ºC, static, 5% CO2. All cultures were started at OD600nm 0.03. After 1, 7, and  10 days of incubation, two culture flasks were used to harvest the whole surface pellicle and biofilm attached to the wells (these samples are referred to as “biofilms”).

extract_protocol:
For each 1 mg of wet mass, 1 ml Trizol (Invitrogen) was added, and lysis was performed using 0.4 ml of 0.1 mm zirconia/silica beads by three cycles at full speed in a bead beater, including incubation in ice for 30 s between cycles of beating, followed by 1 min of centrifugation at 13,000 rpm, 4°C. Trizol supernatant was transferred to a heavy-lock phase tube (Eppendorf) containing 200 μl chloroform (Sigma), and vigorously shaken for 15 s, during 2 min. After 10 min at room temperature (RT), we centrifuged at 13,000 rpm, RT, for 5 min, and the supernatant (volume ∼540 μl) was transferred to 1.5 ml tubes, to which 270 μl of 2-propanol (Sigma) and 270 μl of 3 M sodium acetate pH 5.2 (Molecular biology grade, Sigma) were added, followed by mixing and incubation overnight at 4°C. Samples were centrifuged at 13,000 rpm, 4°C, 10 min, and the nucleic acids pellet was washed twice with 70% ethanol. After drying and dissolving in RNAse-free water (Sigma), we quantitated nucleic acids using a UV spectrophotometer. We performed genomic DNA digestion in solution using RQ1 DNase (Promega) following the manufacturer’s recommendation, and further clean-up was performed using RNeasy kit (Qiagen) according to their recommended protocol. RNA was eluted and quantitated
RNA was used to prepare cDNA using Nugen’s Ovation RNA-Seq System via single primer isothermal amplification (Catalogue # 7102-A01) and automated on the (BRAVO NGS liquid handler from Agilent). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific). Using Kapa Biosystem’s DNA Hyper Plus library preparation kit, (KK8514) cDNA was enzymatically sheared to approximately 150 bp fragments, end repaired and A-tailed. Illumina-compatible adapters with unique indexes (IDT #00989130v2) were ligated on each sample individually. The adapter ligated molecules were cleaned using Kapa pure beads (Kapa Biosciences, KK8002), and amplified with Kapa’s HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent’s Tapestation, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Thermo Fisher Scientific’s Quantstudio 5 before multiplex pooling and sequencing a 2x75 flow cell on the NextSeq500 platform (Illumina) at the ASU’s Genomics Core facility.

tag: strain

value: Pasteur ATCC 35734

tag: growth stage

value: Substrate attachment

value: 10 days


title: 92    Aged    A

value: Caucasian

tag: tissue


title: M7_10d_Exp1_M7_S6

description: Samples taken at 10 days of culture


title: M5A_1Wk_Exp1A_M5A_S9

description: Samples taken at 7 days of culture

value: Intercellular aggregation

value: 7 days


title: 3    Aged    B

value: Aged B

tag: Sex

value: Female

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH55C55_Cell2]

description:
miRNA
XB0755

value: M

tag: age

value: unknown


title: WT_L6_Rep1

value: FACS purified layer 6 Neurons

value: A


title: TBR1_NULL_L6_Rep2

value: Tbr1 Layer 6 Null

value: postnatal day 5

value: cortical neurons


title: 90    Aged    A

value: Aged A

value: Male


title: 89    Aged    A


title: M2_24h_Exp2_M2_S2

description: Samples taken at 24 h of culture

value: Pasteur ATCC 35734

value: Planktonic

value: 1 day


title: NAc3

first: Mazen

last: Kheirbek

address: 675 Nelson Rising Lane, Room 514D

institute: UCSF

description: We labeled ventral hippocampal neurons that projected to nucleus accumbens then used a translating ribosome affinity purification (TRAP) approach to profile translation in each of these populations

data_processing:
Sequencing type: Single End 50bp RNAseq
Library Kit: SmartSeq/NexteraXT
Aligner: STAR_2.5.2b
Differential Expression Test: DESeq2 v1.16.1
Genome_build: Alignment Genome: Ensembl Mouse GRCm38
Supplementary_files_format_and_content: counts.STAR.MOUSE.txt:  tab delimited text file containing samples and their raw (unnormalized) read counts per gene.
Supplementary_files_format_and_content: Log.STAR.MOUSE.txt:  tab delimited text file containing some summary information regarding the mapping of each sample.
Supplementary_files_format_and_content: stats.STAR.MOUSE txt: tab delimited text file containing some counts of alignment types (multimapping, no feature, unmapped, etc.)
Supplementary_files_format_and_content: All_genes.Kheirbek_Turner_0814.txt Contains all statistics for all pairwise comparisons as well as read counts for each sample (in counts per million reads).

source_name: ventral hippocampus

extract_protocol:
Ribosomal IP
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B6.129S4-Gt(ROSA)26Sortm1(CAG-EGFP/Rpl10a,-birA)Wtp/J (Jackson labs stock #022367)

value: ventral hippocampal neurons projection to the nucleus accumbens

tag: virus injection

value: retrograde traveling adeno-associated virus expressing Cre recombinase (AAV2-retro-Cre)

tag: viral injection site

value: nucleus accumbens


title: 88    Aged    A

value: Caucasian

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH55C55_Cell1]

description:
miRNA
XB0754

value: serum

value: M

tag: cstage

tag: child-pugh

tag: afp

value: unknown


title: M1_24h_Exp1_M1_S1

description: Samples taken at 24 h of culture


title: NAc2

tag: cell type


title: NAc1


title: 91    Aged    A

tag: subject id

tag: race


title: 87    Aged    A


title: Non-cancer 3 [SH55C53_Cell3]

description:
miRNA
XB0752


title: mPFC3

description: We labeled ventral hippocampal neurons that projected to medial prefrontal cortex then used a translating ribosome affinity purification (TRAP) approach to profile translation in each of these populations

tag: genotype

value: ventral hippocampal neurons projection to the medial prefrontal cortex

value: medial prefrontal cortex


title: M4A_1Wk_Exp1A_M4A_S8

description: Samples taken at 7 days of culture

value: Intercellular aggregation

value: 7 days


title: 84    Aged    A

value: Aged A

value: Male


title: mPFC1


title: 85    Aged    A


title: Non-cancer 3 [SH54P26_Cell1]

description:
miRNA
XB0715


title: Non-cancer 3 [SH55B48_Cell3]

description:
miRNA
XB0713


title: Non-cancer 3 [SH55C53_Cell4]

description:
miRNA
XB0753


title: 83    Aged    A


title: Ewing sarcoma_5

city: Bologna

first: Katia

last: Scotlandi

address: via di Barbiano 1/10

country: Italy

institute: IRCCS Istituto Ortopedico Rizzoli

data_processing:
After performing Fastqc quality check, Fastq files were aligned using TopHat (version 2.1.0) to hg19 version of human genome
HTSeq (version 0.6.0) was used to calculate counts for UCSC-annotated genes from aligned reads
EdgeR  package  (version 2.12.0) was used to normalize counts per million  (cpm) and to perform gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Log2CPM

source_name: Ewing sarcoma primary tumor

extract_protocol:
Total RNA was extracted using Trizol reagent.
250-1000 ng of total RNA was used as input for libraries preparation according to   Illumina TruSeq RNA Sample Prep Kit v2.

value: Ewing sarcoma primary tumor

tag: sample type

value: Snap-frozen tissue

tag: igf2bp3 expression

value: high


title: Ewing sarcoma_6


title: 82    Aged    A


title: 86    Aged    A


title: LH1

description: We labeled ventral hippocampal neurons that projected to lateral hypothalamus then used a translating ribosome affinity purification (TRAP) approach to profile translation in each of these populations

value: B6.129S4-Gt(ROSA)26Sortm1(CAG-EGFP/Rpl10a,-birA)Wtp/J (Jackson labs stock #022367)

value: ventral hippocampal neurons projection to the lateral hypothalamus

value: retrograde traveling adeno-associated virus expressing Cre recombinase (AAV2-retro-Cre)

value: lateral hypothalamus


title: Ewing sarcoma_4


title: 81    Aged    A

value: Caucasian

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: BMA3

description: We labeled ventral hippocampal neurons that projected to basomedial amygdala then used a translating ribosome affinity purification (TRAP) approach to profile translation in each of these populations

value: ventral hippocampal neurons projection to the basomedial amygdala

value: basomedial amygdala


title: Non-cancer 3 [SH55B36_Cell4]

description:
miRNA
XB0677

value: serum

value: M

value: unknown


title: 80    Aged    A

value: Aged A


title: Non-cancer 3 [SH56N16_Cell4]

description:
miRNA
XB0709


title: BMA2


title: MDA-MB-231_siTMPO-AS1_#2

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from MDA-MB-231 cells treated with siRNA targeting TMPO-AS1 (siTMPO-AS1 #2)

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Clariom D Assay, human). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

source_name: MDA-MB-231 cells treated with siTMPO-AS1 #2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human breast cancer MDA-MB-231 cells were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MDA-MB-231 cells were transfected with siRNAs targeting TMPO-AS1 (siTMPO-AS1 #1 and #2) or control siRNA (siControl) for 48 hours.

tag: cell line

tag: sirna


title: MDA-MB-231_siTMPO-AS1_#1

description: Gene expression data from MDA-MB-231 cells treated with siRNA targeting TMPO-AS1 (siTMPO-AS1 #1)

source_name: MDA-MB-231 cells treated with siTMPO-AS1 #1


title: MDA-MB-231_siControl

description: Gene expression data from MDA-MB-231 cells treated with control siRNA

source_name: MDA-MB-231 cells treated with siControl

value: siControl


title: LH2


title: 79    Aged    A

value: Male


title: Non-cancer 3 [SH56N22_Cell4]

description:
miRNA
XB0675


title: Non-cancer 3 [SH55B08_Cell2]

description:
miRNA
XB0651


title: Ewing sarcoma_1

value: Ewing sarcoma primary tumor

value: Snap-frozen tissue

value: low


title: Non-cancer 3 [SH55B32_Cell3]

description:
miRNA
XB0664


title: Non-cancer 3 [SH55B35_Cell2]

description:
miRNA
XB0671


title: BMA1

value: B6.129S4-Gt(ROSA)26Sortm1(CAG-EGFP/Rpl10a,-birA)Wtp/J (Jackson labs stock #022367)


title: Ewing sarcoma_2


title: 77    Aged    A


title: Ewing sarcoma_3


title: Day28_AT2_Tomato

city: Cambridge

first: Joo-Hyeon

last: Lee

address: Puddicombe Way, Cambridge Biomedical Campus

country: United Kingdom

institute: Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge

data_processing:
Droplet-based sequencing data was aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 2.0.2, 10x Genomics Inc) using the Mus musculus genome (mm9,GRCm38) (official Cell Ranger reference, version 1.2.0).  Cells were filtered by custom cutoff (more than 500 and less than 7000 detected genes, more than 2000 UMI count) to remove potential empty droplets and doublets.
Downstream analysis included data normalisation, highly variable gene detection, log transformation, principal component analysis, neighbourhood graph generation and Louvain graph-based clustering, which was done by python package scanpy (version 1.3.6) using default parameters.
Genome_build: Mus musculus, mm9/GRCm38
Supplementary_files_format_and_content: raw fastq files and raw gene quantifications, mtx/tsv format for matrix, barcode, and genes

source_name: Lineage labelled AT2 cells were collected at day 28 post injury

growth_protocol:
Lung organoids were co-culutured with stromal cells.
Mice for the lineage tracing and injury experiments were  bred and maintained under specific-pathogen-free conditions at the Cambridge Stem Cell Institute and Gurdon Institute of University of Cambridge.

extract_protocol:
Established organoids of control or IL-1β-treatment were incubated with dispase (BD Bioscience) for 30-60min. Then, cells were dissociated with TripLE  for 5min, followed by washing with buffer (PBS/0.01% BSA).
For SPC or Krt8 lineage-labelled cells, CD45–CD31–EpCAM+Tomato+ cells were sorted at specific time points (at day 14 and day 28 post damage) from PBS or Bleomycin-treated mice (2 mice were pooled for each experiment). For non-lineage-labelled cells isolated from SPCCreERT2;R26RtdTomato mice  in parallel with experiment of SPC lineage-labelled cells, we combined the cells of EpCAM+Tomato– and EpCAM– population with a ratio of 2:1, respectively.
The resulting cell suspension (~110,000 cells each) were submitted as separate samples to be barcoded for the droplet-encapsulation single- cell RNA-seq experiments using the Chromium Controller (10X Genomics). Single cell cDNA synthesis, amplification and sequencing libraries were generated using the Single Cell 3' Reagent Kit as per the 10x Genomics protocol.
10x libraries were multiplexed so that 2 libraries were sequenced per single lane of HiSeq 4000

treatment_protocol:
IL-1β or PBS were treated for organoid culture.
0.2mg/g body weight tamoxifen was given via intraperitoneal (IP) injection.
1.25U/kg of bleomycin, or PBS control, were delivered intratracheally.

value: lung progenitor cells

tag: strain

value: Lung


title: Day28_AT2_nonTomato

source_name: Unlineage labelled cells were collected at day 28 post injury

tag: tissue


title: 76    Aged    A

tag: Sex

value: Caucasian


title: Non-cancer 3 [SH54E18_Cell4]

description:
miRNA
XB0613

source_name: Serum

tag: age


title: Day14_AT2_nonTomato

source_name: Unlineage labelled cells were collected at day 14 post injury


title: 75    Aged    A

value: peripheral blood


title: 78    Aged    A

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH54E24_Cell2]

description:
miRNA
XB0627


title: Non-cancer 3 [SH54E23_Cell4]

description:
miRNA
XB0625


title: Day14_AT2_Tomato

source_name: Lineage labelled AT2 cells were collected at day 14 post injury


title: PBS_AT2_nonTomato

source_name: Unlineage labelled cells were collected at day 0


title: 73    Aged    A


title: 74    Aged    A


title: Non-cancer 3 [SH56N24_Cell3]

description:
miRNA
XB0609


title: Non-cancer 3 [SH54E18_Cell3]

description:
miRNA
XB0612


title: 72    Aged    A


title: PBS_AT2_Tomato

source_name: Lineage labelled AT2 cells were collected at day 0


title: HUVEC Transwell coculture + CD16+monocytes

city: Hannover

first: Sibylle

last: von Vietinghoff

address: Carl Neuberg Strasse 1

department: Internal Medicine

country: Germany

institute: Hannover Medical School

description:
M6709
The relative proportion of small fragments within the cRNA population turned out to be slightly elevated. This was compensated by a slight increase in the cRNA amount used for hybridization here (2500ng).

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2000-2500ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: Human umbilical vein endothelial cells

label_protocol: 150ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: HUVEC in passages 2-4 (appr. 90% confluent) were added directly or into PET membrane 0.4μm trans-wells (BRANDplates®InsertStrips, Brand GmbH&CoKG, Wertheim, Germany) to monocytes isolated using CD14 MicroBeads or CD16+ Monocyte Isolation Kit a QuadroMACS system according to manufacturer’s instructions (Miltenyi Biotec, Bergisch-Gladbach, Germany) after density gradient centrifugation using Biocoll 1.077 (Biochrom, Berlin, Germany). in a 1:1 mixture of full RPMI and EBM2 media for 24h.

extract_protocol: RNA was isolated using NucleoSpin RNA Plus Kit (Macherey-Nagel, Duren, Germany), yield and purity were determined in a Colibri Microvolume Spectrometer (Titertek-Berthold, Pforzheim, Germany).

treatment_protocol: After co-culture, HUVECs were sorted as live CD11b-CD45- population using a FACSAriaII.

value: endothelium


title: HUVEC Transwell coculture + CD14+monocytes

description:
M6710
The relative proportion of small fragments within the cRNA population turned out to be slightly elevated. This was compensated by a slight increase in the cRNA amount used for hybridization here (2500ng).


title: Non-cancer 3 [SH56N25_Cell2]

description:
miRNA
XB0602


title: Non-cancer 3 [SH54E22_Cell2]

description:
miRNA
XB0619


title: IL1r1+AT2_2

library_source: genomic

data_processing:
The quality of the generated sequencing data was checked using the FastQC program, followed by filtering of adapter and/or overrepresented sequences using Trimmomatic.
Filtered reads were next mapped to the mouse primary genome assembly (mm9/GRCm38) using STAR38, with parameters -outFilterMatchNminOverLread 0.4 -outFilterScoreMinOverLread 0.4, and a GTF annotation file of the latest mouse assembly (GCA_000001635.8) downloaded from ENSEMBL ftp.
MACS2 callpeak was used for ATAC-seq peak calling of the Il1r1+AT2 and bulk AT2 samples, using the options -nomodel-shift -100 -extsize 200. Differentially enriched peaks in Il1r1+AT2 and bulk AT2 populations were next inferred using the MACS2 bdgdiff with a log10 likelihood ratio score cutoff of 10. ATAC-seq heatmaps were plotted using deepTools2.
Annotation of ATAC-seq enriched peaks overlapping with promoter and other gene regions was performed using the ChIPseeker R/Bioconductor package, together with GO enrichment and pathway analyses. Finally, motif identification was performed using the findMotifsGenome.pl program of the HOMER software.
Genome_build: Mus musculus, GRCm38
Supplementary_files_format_and_content: raw fastq files and peak quantifications, bw format

molecule: genomic DNA

source_name: Il1r1 AT2

growth_protocol: Mice for the lineage tracing and injury experiments were  bred and maintained under specific-pathogen-free conditions at the Cambridge Stem Cell Institute and Gurdon Institute of University of Cambridge.

extract_protocol:
The ATAC-seq assay was performed on 50,000 FACS-purified
Purified cells were lysed in ATAC lysis buffer for 5 min to get nuclei and then transposed with Tn5 transposase (Illumina) for 30 min. Fractionated DNA was used for amplification and library preparation
Illumina, Illumina HiSeq 4000, 150 bp-paired end sequencing

treatment_protocol: 0.2mg/g body weight tamoxifen was given via intraperitoneal (IP) injection.

tag: strain background

value: lung pogenitor cells

tag: cell subtype

value: Alveolar type 2 progenitor cells (AT2)


title: Non-cancer 3 [SH56N24_Cell4]

description:
miRNA
XB0607

value: serum

value: M

tag: cstage


title: HUVEC Coculture + CD14+ monocytes

description:
M6708
Amount of cRNA used for hybridization was 2000ng.


title: 71    Aged    A

source_name: Aged A_peripheral blood HSC

value: Aged A


title: Il1r1+AT2_1


title: arota_diabetes_rep3 [miRNA]

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

description: miRNA expression data from diabetic rats

hyb_protocol: Labeled miRNA was hybridized to the array.

scan_protocol: After hybridization, the chips were scanned by using a Genechip Array Scanner 3000 (Affymetrix).

data_processing: The data were generated by Affymetrix Expression Console software v1.1.

organism: Rattus norvegicus

source_name: diabetic rats, 17week

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted by mirVanaTM RNA Isolation Kit (ABI)

value: arota

value: 17 weeks


title: arota_diabetes_rep2 [miRNA]


title: Non-cancer 3 [SH56N26_Cell1]

description:
miRNA
XB0599

tag: child-pugh

value: unknown


title: HUVEC Coculture CD16 + monocytes

description:
M6707
Amount of cRNA used for hybridization was 2000ng.


title: arota_vildagliptin-treated_rep3 [miRNA]

description: miRNA expression data from vildagliptin-treated rats

source_name: vildagliptin-treated rats, 17week


title: Control AT2_2

source_name: Control AT2


title: 70    Aged    A

value: Male


title: Non-cancer 3 [SH56N27_Cell1]

description:
miRNA
XB0595

tag: afp


title: arota_diabetes_rep1 [miRNA]


title: 69    Aged    A

tag: cell type


title: Control AT2_1


title: 68    Aged    A

tag: subject id


title: Non-cancer 3 [SH54E12_Cell4]

description:
miRNA
XB0593


title: Il1b_Organoids

description: IL-1b was treated in organoids

source_name: lung pogenitor cells


title: 67    Aged    A

tag: race


title: Non-cancer 3 [SH54E12_Cell2]

description:
miRNA
XB0591


title: dTHP-1_WT_6h_3rd

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Dual-RNA-Seq dataset
processed data file:
dTHP-1_human_log2cpm.xlsx
dTHP-1_vibrio_log2cpm.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 and Vibrio vulnificus whole genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_000186585.1) using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

organism:
Homo sapiens
Vibrio vulnificus MO6-24/O

source_name: Vibrio-infected dTHP-1 cell lines

growth_protocol: HT-29 and dTHP-1 cells were routinely cultured at 37 °C, 5% CO2 incubator

extract_protocol:
Total RNA was isolated from the samples using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: Either Phosphate buffered saline (PBS) or the bacterial suspension was treated on the cultured human cells

tag: host

value: Human monocytic cell line (dTHP-1)

tag: infection

value: Vibrio vulnificus (MO6-24) wild type


title: Non-cancer 3 [SH54E10_Cell3]

description:
miRNA
XB0588


title: 65    Aged    A


title: dTHP-1_WT_6h_1st


title: Control_Organoids

description: PBS was treated in organoids


title: 66    Aged    A


title: arota_vildagliptin-treated_rep2 [miRNA]


title: arota_vildagliptin-treated_rep1 [miRNA]


title: Non-cancer 3 [SH54E10_Cell2]

description:
miRNA
XB0587


title: dTHP-1_WT_6h_2nd


title: dTHP-1_WT_3h_3rd


title: Non-cancer 3 [SH54E09_Cell3]

description:
miRNA
XB0584


title: dTHP-1_WT_3h_2nd


title: 64    Aged    A


title: dTHP-1_WT_3h_1st


title: 63    Aged    A


title: 62    Aged    A


title: poor-prognosis group_B16

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: poor-prognosis group_B16

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

source_name: poor-prognosis group_B16

extract_protocol:
Total RNAs were extracted from the cells with miRNeasy FFPE Kit (QIAGEN), according to the manufacturer’s protocol.
NGS library preparation was performed using the TruSeq RNA Access Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Five 10-µm-thick FFPE sections from each case were subjected to RNA sequencing analysis.

tag: prognosis

value: poor

tag: subtype

value: aggressive subtype


title: dTHP-1_WT_0h_3rd


title: E1/R1

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

hyb_protocol: Two-colors Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version) were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: The cell lines OCI-Empty and OCI-RhoH were grown in alpha-MEM containing 20% (v/v) heat-activated FBS and supplemented with 150 µg/ml hygromycin B, in the presence of 100 Units/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: no treatment

tag: cell line

tag: genotype/variation

value: empty vector

value: RhoH sur-expressing vector


title: Non-cancer 3 [SH54E06_Cell3]

description:
miRNA
XB0572

tag: tissue


title: R2/E2


title: 61    Aged    A

tag: Sex

value: Caucasian

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH54960_Cell4]

description:
miRNA
XB0565

tag: age


title: poor-prognosis group_B15

description: poor-prognosis group_B15

source_name: poor-prognosis group_B15


title: mPFC2

source_name: ventral hippocampus

tag: genotype

value: B6.129S4-Gt(ROSA)26Sortm1(CAG-EGFP/Rpl10a,-birA)Wtp/J (Jackson labs stock #022367)

value: ventral hippocampal neurons projection to the medial prefrontal cortex

tag: virus injection

value: retrograde traveling adeno-associated virus expressing Cre recombinase (AAV2-retro-Cre)

tag: viral injection site

value: medial prefrontal cortex


title: dTHP-1_WT_0h_1st


title: poor-prognosis group_B14

description: poor-prognosis group_B14

source_name: poor-prognosis group_B14


title: 60    Aged    A

value: Aged A


title: dTHP-1_WT_0h_2nd


title: R4/E4


title: Non-cancer 3 [SH55B41_Cell2]

description:
miRNA
XB0696

source_name: Serum

value: serum

value: M

tag: cstage

tag: child-pugh


title: Non-cancer 3 [SH54953_Cell4]

description:
miRNA
XB0561

tag: afp

value: unknown


title: 59    Aged    A

tag: subject id

value: Male

tag: cell type


title: Non-cancer 3 [SH54949_Cell3]

description:
miRNA
XB0556


title: E3/R3


title: dTHP-1_BS1601_6h_3rd

tag: host

value: Human monocytic cell line (dTHP-1)

value: Vibrio vulnificus (MO6-24) ΔrtxA1


title: Non-cancer 3 [SH54929_Cell2]

description:
miRNA
XB0547


title: 58    Aged    A

tag: race


title: poor-prognosis group_B12

description: poor-prognosis group_B12

source_name: poor-prognosis group_B12

tag: prognosis

value: poor

value: aggressive subtype


title: Non-cancer 3 [SH54E07_Cell4]

description:
miRNA
XB0577


title: poor-prognosis group_B11

description: poor-prognosis group_B11

source_name: poor-prognosis group_B11

tag: subtype


title: Non-cancer 3 [SH54927_Cell3]

description:
miRNA
XB0540


title: dTHP-1_BS1601_6h_1st

tag: infection


title: 56    Aged    A


title: good-prognosis group_B10

description: good-prognosis group_B10

source_name: good-prognosis group_B10

value: good

value: indolent histological subtype


title: good-prognosis group_B13

description: good-prognosis group_B13

source_name: good-prognosis group_B13


title: dTHP-1_BS1601_3h_3rd


title: good-prognosis group_B9

description: good-prognosis group_B9

source_name: good-prognosis group_B9


title: 55    Aged    A

value: Caucasian

value: peripheral blood


title: dTHP-1_BS1601_3h_2nd


title: Non-cancer 3 [SH54929_Cell3]

description:
miRNA
XB0548


title: 53    Aged    A

value: Hematopoietic Stem Cells (HSCs)


title: dTHP-1_BS1601_3h_1st


title: dTHP-1_BS1601_6h_2nd


title: dTHP-1_BS1601_0h_3rd


title: 52    Aged    A


title: 54    Aged    A


title: Non-cancer 3 [SH54925_Cell3]

description:
miRNA
XB0536


title: Non-cancer 3 [SH54925_Cell2]

description:
miRNA
XB0535


title: Non-cancer 3 [SH54919_Cell3]

description:
miRNA
XB0528


title: Non-cancer 3 [SH54925_Cell1]

description:
miRNA
XB0534


title: 57    Aged    A


title: 51    Aged    A


title: Non-cancer 3 [SH54908_Cell4]

description:
miRNA
XB0517


title: poor-prognosis group_B2

description: poor-prognosis group_B2

source_name: poor-prognosis group_B2


title: Non-cancer 3 [SH54919_Cell2]

description:
miRNA
XB0527


title: dTHP-1_BS1601_0h_1st


title: poor-prognosis group_B1

description: poor-prognosis group_B1

source_name: poor-prognosis group_B1


title: dTHP-1_M_6h_3rd

source_name: Mock-treated dTHP-1 cell lines

value: Mock


title: 50    Aged    A

source_name: Aged A_peripheral blood HSC


title: 49    Aged    A


title: poor-prognosis group_B5

description: poor-prognosis group_B5

source_name: poor-prognosis group_B5


title: poor-prognosis group_B7

description: poor-prognosis group_B7

source_name: poor-prognosis group_B7


title: good-prognosis group_A18

description: good-prognosis group_A18

source_name: good-prognosis group_A18


title: dTHP-1_M_6h_2nd


title: Non-cancer 3 [SH54908_Cell3]

description:
miRNA
XB0516


title: dTHP-1_BS1601_0h_2nd

source_name: Vibrio-infected dTHP-1 cell lines


title: 47    Aged    A


title: 48    Aged    A


title: Non-cancer 3 [SH54901_Cell2]

description:
miRNA
XB0511


title: good-prognosis group_A17

description: good-prognosis group_A17

source_name: good-prognosis group_A17


title: dTHP-1_M_6h_1st


title: dTHP-1_M_3h_3rd


title: 46    Aged    A


title: dTHP-1_M_3h_2nd


title: 45    Aged    A


title: good-prognosis group_A15

description: good-prognosis group_A15

source_name: good-prognosis group_A15


title: Non-cancer 3 [SH54851_Cell1]

description:
miRNA
XB0502


title: good-prognosis group_A14

description: good-prognosis group_A14

source_name: good-prognosis group_A14


title: Non-cancer 3 [SH54819_Cell4]

description:
miRNA
XB0477

source_name: Serum


title: dTHP-1_M_3h_1st


title: 43    Aged    A


title: good-prognosis group_A16

description: good-prognosis group_A16

source_name: good-prognosis group_A16


title: Non-cancer 3 [SH54813_Cell3]

description:
miRNA
XB0472


title: poor-prognosis group_B4

description: poor-prognosis group_B4

source_name: poor-prognosis group_B4


title: dTHP-1_M_0h_3rd


title: Non-cancer 3 [SH54845_Cell1]

description:
miRNA
XB0490


title: 42    Aged    A


title: dTHP-1_M_0h_2nd


title: Non-cancer 3 [SH54805_Cell3]

description:
miRNA
XB0464


title: good-prognosis group_A12

description: good-prognosis group_A12

source_name: good-prognosis group_A12


title: good-prognosis group_A11

description: good-prognosis group_A11

source_name: good-prognosis group_A11


title: 41    Aged    A


title: Non-cancer 3 [SH53S19_Cell2]

description:
miRNA
XB0436


title: 39    Aged    A


title: dTHP-1_M_0h_1st


title: good-prognosis group_A9

description: good-prognosis group_A9

source_name: good-prognosis group_A9


title: good-prognosis group_A10

description: good-prognosis group_A10

source_name: good-prognosis group_A10


title: 40    Aged    A


title: HT-29_WT_6h_3rd

description:
Dual-RNA-Seq dataset
processed data file:
HT-29_human_log2cpm.xlsx
HT-29_vibrio_log2cpm.xlsx

source_name: Vibrio-infected HT-29 cell lines

value: Human colon cancer cell line (HT-29)

value: Vibrio vulnificus (MO6-24) wild type


title: Non-cancer 3 [SH53S17_Cell1]

description:
miRNA
XB0427


title: HT-29_WT_6h_2nd


title: 38    Aged    A

value: Aged A


title: good-prognosis group_A8

description: good-prognosis group_A8

source_name: good-prognosis group_A8


title: HT-29_WT_6h_1st


title: Non-cancer 3 [SH53S08_Cell1]

description:
miRNA
XB0419

value: serum


title: HT-29_WT_3h_3rd


title: good-prognosis group_A5

description: good-prognosis group_A5

source_name: good-prognosis group_A5


title: good-prognosis group_A13

description: good-prognosis group_A13

source_name: good-prognosis group_A13


title: 36    Aged    A

source_name: Aged A_peripheral blood HSC


title: HT-29_WT_3h_2nd


title: Non-cancer 3 [SH53S05_Cell1]

description:
miRNA
XB0411

value: M


title: Non-cancer 3 [SH53S02_Cell2]

description:
miRNA
XB0404

value: unknown


title: HT-29_WT_3h_1st


title: poor-prognosis group_A4

description: poor-prognosis group_A4

source_name: poor-prognosis group_A4


title: Non-cancer 3 [SH53S02_Cell1]

description:
miRNA
XB0403


title: 35    Aged    A

value: Male


title: good-prognosis group_A3

description: good-prognosis group_A3

source_name: good-prognosis group_A3


title: 33    Aged    A


title: Non-cancer 3 [SH53S15_Cell3]

description:
miRNA
XB0425


title: good-prognosis group_A2

description: good-prognosis group_A2

source_name: good-prognosis group_A2


title: good-prognosis group_A7

description: good-prognosis group_A7

source_name: good-prognosis group_A7


title: Non-cancer 3 [SH55B19_Cell3]

description:
miRNA
XB0398


title: HT-29_WT_0h_1st


title: Non-cancer 3 [SH53R31_Cell4]

description:
miRNA
XB0394


title: HT-29_Rtx_6h_3rd


title: Non-cancer 3 [SH53R31_Cell1]

description:
miRNA
XB0391


title: CTRL1_D15_T2C

city: Rotterdam

first: Andrea

last: Conidi

address: Dr. Molewaterplein 40

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Digested genomic DNA

data_processing:
bcl2fastq
bwa mem
T2C pipeline V3.beta
all fragments over 1kb were excluded due to the nature of the library (T2C). Otherwise the tlen fields do net reflect the insert sizes.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedpe file reporting 'chr_a', 'start_a', 'end_a', 'chr_b', 'start_b', 'end_b', 'signal'

source_name: WTC iPSCs line

growth_protocol: WTC cells were cultured feeder-cells free on 6-well-plates coated with 1% Geltrex in Essential-8 (E8) Basal Medium (ThermoFisher Scientific), and the medium was changed daily

extract_protocol:
2.5x10e6 cells were used for each time point; the cells were cross-linked using 1% formaldehyde at Room Temperature (RT, 24°C) for 10 min and quenched with 0.125 M Glycine. Subsequently, cells were lysed using cold lysis buffer containing 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.5% NP-40 and Complete Protease Inhibitors (Roche). Chromatin was digested with the ApoI restriction enzyme (New Englad Biolabs) (400 U/sample) overnight in a thermomixer (VWR) at 37°C at 900 rpm. The digested products were purified via Phenol:Chloroform. The diluted DNA fragments were ligated with T4 DNA Ligase High Concentration (100 U/sample; ThermoFisher Scientific) overnight at 16°C, and then 30 µl of 10 mg Proteinase K/ml (300 µg) were added and incubated at 65°C for 4 h, followed by 30 µl of 10 mg RNAse A/ml (300 µg) for 1h at 37°C, before proceeding to further purification with Phenol:Chloroform. In total, 6 µg of the resulting chromatin were then linearized using the frequent 4bp-cutting enzyme DpnII (New England Biolabs) (1U/µg of DNA) overnight at 37°C, whilst shaking in a thermomixer at 400 rpm. The day after, the material was precipitated by sodium acetate/ethanol before proceeding to T2C library preparation.
T2C Library was prepared using 250 ng of linearized chromatin. The samples were re-buffered to 10 mM Tris-HCl, pH8 by a standard AMPure XP (Agencourt) bead clean-up procedure. The chromatin was sheared to 300-400-bp fragments by a S220 Covaris (Covaris Inc.). Concentration was determined by Quant-it high sensitivity (ThermoFisher Scientific). For each sample 100 ng of sheared chromatin was end-repaired and A-tailed using the Kapa hyper prep kit (Roche) according to the manufacturer’s instructions. SeqCap library adaptors were ligated followed by AMPure bead clean up. The pre-capture library was amplified by PCR using KAPA HiFi hotstart readymix for 9 cycles. The amplified pre-capture library was purified by bead clean up and quantified by Bioanalyzer DNA1000 assay (Agilent) according to the manufacturer’s instructions.
A ZEB2 hg19 based design was ordered at NimbleGen (Roche) with baits located between 143270465 and 150642631 of chromosome 2. A hybridization mixture per sample was prepared with 2 µg pre-capture library, 1 mM HE-index-oligo, 1 mM HE universal oligo, COT Human DNA, AMPure XP reagent and added to 4.5 µl of pre-ordered baits and subsequently hybridized for 16 h at 47°C. Post hybridization the samples were washed according to the instructions in the Nimblegen SeqcapEZ Hypercap workflow (Roche), the  chromatin captured using capture beads. The captured library was amplified by PCR using Kapa HiFi mix and purified by AMPure XP beads. The captured library was quantified by Nanodrop spectrophotometer and the quality was assessed using a Bioanalyzer DNA1000 assay. Finally, the captured T2C libraries were denatured and sequenced on an Illumina HiSeq2500 sequencer as described for RNA-seq but with a custom recipe of 6 dark cycles, followed by paired end 101 sequencing with single index using the rapid v2 chemistry according to manufacturer’s instructions (Illumina).

treatment_protocol: For their neural induction,  70%-confluent cells were changed to Neural Induction Medium (NIM): DMEM/F12, supplemented with 20% knock-out serum replacement, 1 mM non-essential amino acids (NEAA) and 0.1 mM β-EtSH (all from ThermoFisher Scientific), and a mix of inhibitors (abbreviated as DAP), i.e. 2 µM dorsomorphin (BMP-inhibitor, Tocris Bioscience), 2 µM A83-01 (TGFβ-inhibitor, Tocris Bioscience) and 2 µM PNU-74654 (WNT-inhibitor, Sigma). After 6 days (D6) the medium was replaced with Neural Maturation Medium (NMM): DMEM/F12, 1mM NEAA, 0.1 mM β-EtSH, 1xN2 and 1x B27 without vitamin A (both ThermoFisher Scientific), and the medium was changed every day until D15 (NPC-state).

tag: cell line

value: WTC iPSCs line

tag: time

tag: differentiation stage

value: Neuro Progenitor Cells

tag: t2c digestion

value: ApoI/DpnII


title: CTRL1_D6_T2C

description: Digested genomic DNA

value: early Neuro Progenitor Cells


title: 30    Aged    A

tag: Sex

tag: age

tag: tissue


title: 29    Aged    A


title: Non-cancer 3 [SH53R29_Cell2]

description:
miRNA
XB0388

source_name: Serum

tag: cstage


title: Non-cancer 3 [SH53R29_Cell4]

description:
miRNA
XB0390

tag: child-pugh


title: 34    Aged    A


title: HT-29_Rtx_6h_2nd

value: Vibrio vulnificus (MO6-24) ΔrtxA1


title: HT-29_Rtx_6h_1st


title: HT-29_WT_0h_3rd


title: Non-cancer 3 [SH53R67_Cell4]

description:
miRNA
XB0402

tag: afp


title: CTRL1_D0_T2C

description: Digested genomic DNA

value: undifferentiated iPSCs


title: Non-cancer 3 [SH53R27_Cell4]

description:
miRNA
XB0386


title: 32    Aged    A

tag: subject id

value: Caucasian


title: HT-29_WT_0h_2nd


title: 27    Aged    A

value: peripheral blood

tag: cell type


title: HT-29_Rtx_3h_3rd

tag: host


title: 28    Aged    A

tag: race

value: Hematopoietic Stem Cells (HSCs)


title: Hs_H1_day13_SOX9-AS1-KO_RNAseq_1

description:
DSOX9-AS1_d13_TAGCTT
processed data file: lncrna_ko_rpkm.txt

source_name: SOX9-AS1 KO hESCs were differentiated to the PP2 stage

value: H1 ES cells

value: ES-derived late pancreatic progenitor cells

tag: genotype

tag: library

value: polyA, stranded


title: Non-cancer 3 [SH53R25_Cell2]

description:
miRNA
XB0380


title: 31    Aged    A

value: Aged A


title: HT-29_Rtx_3h_2nd

value: Human colon cancer cell line (HT-29)

tag: infection


title: good-prognosis group_A1

description: good-prognosis group_A1

source_name: good-prognosis group_A1

tag: prognosis

value: good

tag: subtype

value: indolent histological subtype


title: Hs_EndoC-bH1_RNASeq_1

description:
EndoC-bH1_GGCTAC
processed data file: 3d_pp2_riboseq_rpkm.txt

source_name: EndoC-bH1 cells grown under standard conditions.

tag: cell line

value: Human beta cell line

value: WT


title: 37    Aged    A

value: Male


title: Non-cancer 3 [SH53R19_Cell3]

description:
miRNA
XB0369

value: serum

value: M

value: unknown


title: HT-29_Rtx_0h_3rd

value: Vibrio vulnificus (MO6-24) ΔrtxA1


title: Hs_H1_day13_GATA6-AS1-KO_RNAseq_1

description:
DGATA6-AS1_d13_GCCAAT
processed data file: lncrna_ko_rpkm.txt

source_name: GATA6-AS1 KO hESCs were differentiated to the PP2 stage


title: 25    Aged    A

value: Caucasian


title: Hs_H1_day3_GATA6-AS1-KO_RNAseq_1

description:
DGATA6-AS1_d3_TGACCA
processed data file: lncrna_ko_rpkm.txt

source_name: GATA6-AS1 KO hESCs were differentiated to the definitive endoderm stage

value: ES-derived definitive endoderm cells


title: 23    Aged    A

value: peripheral blood

value: Hematopoietic Stem Cells (HSCs)


title: Non-cancer 3 [SH53Z49_Cell1]

description:
miRNA
XB0344


title: Hs_H1_day13_ctrl_RNAseq_1

description:
H1_ctrl_d13_ACAGTG
processed data file: lncrna_ko_rpkm.txt

source_name: Unmodified hESCs were differentiated to the PP2 stage

value: H1 ES cells

value: ES-derived late pancreatic progenitor cells


title: HT-29_Rtx_0h_2nd

source_name: Vibrio-infected HT-29 cell lines


title: HT-29_Rtx_0h_1st


title: Non-cancer 3 [SH53Z44_Cell2]

description:
miRNA
XB0337


title: Hs_H1_day3_ctrl_RNAseq_1

description:
H1_ctrl_d3_CGATGT
processed data file: lncrna_ko_rpkm.txt

source_name: Unmodified hESCs were differentiated to the definitive endoderm stage

value: polyA, stranded


title: 24    Aged    A

value: Aged A


title: Non-cancer 3 [SH53Z45_Cell2]

description:
miRNA
XB0341


title: HT-29_M_6h_3rd

source_name: Mock-treated HT-29 cell lines

value: Human colon cancer cell line (HT-29)

value: Mock


title: 22    Aged    A


title: Non-cancer 3 [SH53J35_Cell3]

description:
miRNA
XB0334


title: HT-29_Rtx_3h_1st


title: 21    Aged    A


title: 26    Aged    A


title: HT-29_M_6h_2nd


title: 20    Aged    A


title: Hs_H1_day13_5'Scar-KO_RNAseq_1

description:
D5_Scar_d13_CAGATC
processed data file: lncrna_ko_rpkm.txt

source_name: LHFPL3-AS2 KO hESCs were differentiated to the PP2 stage


title: 19    Aged    A

source_name: Aged A_peripheral blood HSC


title: HT-29_M_3h_3rd


title: Non-cancer 3 [SH53B18_Cell4]

description:
miRNA
XB0321


title: Non-cancer 3 [SH53B18_Cell1]

description:
miRNA
XB0318


title: HT-29_M_3h_2nd


title: 18    Aged    A


title: Non-cancer 3 [SH53J35_Cell1]

description:
miRNA
XB0332


title: He78: Vehicle

first: Mario

middle: J. Cabrero

last: Manresa

address: 9500 Gilman Dr

institute: University of California San Diego

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: Donor 3

growth_protocol: Cells grown and plated for experiments in smooth muscle cell medium supplemented with 2% FBS, 1% SMGS, 100u/ml penicilin and 100ug/ml streptomicin (ScienCell, CA)

extract_protocol:
Qiagen miRNeasy Micro Kit (Qiagen 217084)
200ng RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) prior to NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB E7760L)

treatment_protocol: Cells pre-starved to serum/growth factor free smooth muscle cell medium with 100u/ml penicilin and 100ug/ml streptomicin. After 16 hours pre-starvation, cells were treated with the specified doses of cytokine diluted on starvation medium, for 24 hours

value: Esophagus

value: Fibroblast

tag: treatment

value: Vehicle


title: He97: Vehicle

source_name: Donor 4


title: He78: TGF 5 ng/ml

value: TGF 5 ng/ml


title: HT-29_M_3h_1st


title: He78: LIGHT 50 ng/ml

value: LIGHT 50 ng/ml


title: He97: TGF 5 ng/ml


title: HT-29_M_0h_3rd


title: 15    Aged    A

tag: Sex

value: Male


title: Non-cancer 3 [SH54103_Cell4]

description:
miRNA
XB0272

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

value: M

tag: age

value: unknown


title: 17    Aged    A

data_processing:
Reads aligned to GrCh38 assembly of the human genome using STAR using default parameters
Partek Genomics Suite was run to align reads to perform differenital expression analyses
Genome_build: GrCh38
Supplementary_files_format_and_content: Abundance measurements

extract_protocol:
Fluidigm C1 single cell platform
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Caucasian

tag: tissue

value: peripheral blood


title: Non-cancer 3 [SH53B03_Cell3]

description:
miRNA
XB0260

tag: cstage


title: Non-cancer 3 [SH53B07_Cell1]

description:
miRNA
XB0274

tag: child-pugh


title: He109: Vehicle

source_name: Donor 2


title: HT-29_M_0h_2nd


title: He97: LIGHT 50 ng/ml


title: He109: TGF 5 ng/ml


title: 14    Aged    A

value: Hematopoietic Stem Cells (HSCs)


title: 13    Aged    A


title: HT-29_M_0h_1st


title: Non-cancer 3 [SH53B03_Cell1]

description:
miRNA
XB0258

tag: afp


title: Non-cancer 3 [SH53A66_Cell3]

description:
miRNA
XB0252


title: Non-cancer 3 [SH53B08_Cell4]

description:
miRNA
XB0281


title: He109: LIGHT 50 ng/ml


title: 16    Aged    A

tag: subject id


title: HD620_TPEX_unstim

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

institute: Humanitas Clinical and Research Center

data_processing:
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9 R version 3.4.4
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Peripheral blood mononuclear cells

extract_protocol:
RNA was extracted from T cell subsets FACS-sorted from the peripheral blood following stimulation in vitro with anti-CD3/CD28 + IL-2/IL-12 (4 days). 20-50,000 cells were washed twice in PBS–/– and RNA was immediately extracted using Direct-Zol RNA Microprep Kit (Zymo Research) according to manufacturer’s instructions, and stored at -80°C. RNA quality control was performed with the Agilent 4200 Tape Station system using the High Sensitivity RNA ScreenTape analysis kit (Agilent, Santa Clara, CA, USA).
Libraries for mRNA sequencing were prepared starting from 5 ng total-RNA for each sample by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). Full-length cDNAs were processed with the Nextera XT DNA Library Preparation Kits (Illumina, San Diego, CA, USA). Obtained libraries were checked using the Agilent TapeStation 4200 using the High Sensitivity DNA ScreenTape analysis kit. Afterwards, libraries were multiplexed in an equimolar pool and sequenced on a NextSeq-550 Illumina Platform.

tag: donor

value: healthy donor 620

tag: cell type

value: TPEX

tag: stimulation

value: unstimulated


title: He100: Vehicle

source_name: Donor 1


title: HD620_TSTEM_unstim

value: TSTEM


title: Wildtype5

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized using cuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: oocyte

extract_protocol:
The cell was lysed and the RNA was amplified according to Smart-seq2 procedures.
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later, they were euthanized, and their  20 oocytes were collected  in 4ul lysis buffer to release all RNAs.

tag: strain

value: 3 weeks

tag: genotype

value: WT


title: 12    Aged    A

first: Michelle

last: Ratliff

address: 600 Moye Blvd, 132 Biotechnology Building

institute: East Carolina University

value: Aged A

tag: race


title: 11    Aged    A


title: He100: TGF 5 ng/ml

value: Esophagus

value: Fibroblast


title: Wildtype6


title: HD620_TPEX_stim

value: anti-CD3/CD28 + IL-2/IL-12 (4 days)


title: 10    Aged    A

value: Male


title: Wildtype4


title: MUT3


title: 10uM-Heme-rep-4_S8

city: College Station

first: Zach

last: Adelman

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

description: 10µM Heme midgut replicate 4

data_processing:
Aligning reads to reference genome: Reads were aligned to the Ae. aegypti reference genome AaegL5 (www.vectorbase.org) using HISAT2 v2.1.0
Cleaning up mapped files: SAMtools view and SAMtools sort commands v1.7 were used to sort the mapped files and remove low quality mapping scores
Counting number of reads per transcript: BEDtools suite v2.19.1 used to calculate the number of reads per mRNA transcript
Merging Count tables: Counts data was merged from all samples into one file
EdgeR analysis: The counts table was analyzed in EdgeR (Robinson et al, 2010)
Genome_build: AaegL5 (www.vectorbase.org)
Supplementary_files_format_and_content: tab delimited text file containing the raw counts data

molecule: polyA RNA

organism: Aedes aegypti

source_name: 10µM Heme midgut

growth_protocol: Midguts dissected from 3-5 day old Aedes aegypti females were incubated at 28 degrees C in Schneider's Drosophila medium (Lonza BioWhittaker, Basel, Switzerland) supplemented with 1% penicillin-streptomycin, and 1% L-glutamine

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Invitrogen)
NEBNext Ultra RNA library preparation kit (New England Biolabs Ipswich, MA)

treatment_protocol: Midguts were incubated in culture media with 0µM or 10µM heme for 35hr with media changes occurring every 8-12hrs

value: female

value: 3-5 days

value: midgut

value: 10µM heme for 35hr


title: 9    Aged    A

value: Caucasian

value: peripheral blood


title: HD619_TPEX_unstim

value: healthy donor 619


title: MUT2


title: 10uM-Heme-rep-3_S7

description: 10µM Heme midgut replicate 3


title: 7    Aged    A

value: Hematopoietic Stem Cells (HSCs)


title: HD619_TSTEM_unstim

value: unstimulated


title: MUT1


title: 10uM-Heme-rep-2_S6

description: 10µM Heme midgut replicate 2


title: GCKO3

description: oocyte specfic knockout

value: Dpagt1F/F Gdf9CRE/+


title: HD619_TPEX_stim

value: TPEX


title: 5    Aged    A


title: 10uM-Heme-rep-1_S5

description: 10µM Heme midgut replicate 1


title: 6    Aged    A


title: He100: LIGHT 50 ng/ml

value: LIGHT 50 ng/ml


title: 4    Aged    A

value: Aged A


title: HD617_TPEX_stim

value: healthy donor 617


title: GCKO1

description: oocyte specfic knockout

value: 3 weeks


title: HD620_TSTEM_stim

value: healthy donor 620

value: TSTEM

value: anti-CD3/CD28 + IL-2/IL-12 (4 days)


title: No-FBS-rep-3_S3

description: 0µM Heme midgut replicate 3

source_name: 0µM Heme midgut

value: female

value: 3-5 days

value: 0µM heme for 35hr


title: HD617_TSTEM_stim


title: No-FBS-rep-4_S4

description: 0µM Heme midgut replicate 4

value: midgut


title: No-FBS-rep-2_S2

description: 0µM Heme midgut replicate 2


title: AmckO6

description: granulosa cell specific knockout

value: Dpagt1F/F Amhr2CRE/+


title: AmckO5

description: granulosa cell specific knockout


title: 2    Aged    A

value: Male

value: Caucasian

value: peripheral blood


title: HD616_TPEX_stim

value: healthy donor 616


title: 1    Aged    A

value: Hematopoietic Stem Cells (HSCs)


title: No-FBS-rep-1_S1

description: 0µM Heme midgut replicate 1


title: HT-29_M_6h_1st

tag: host

value: Human colon cancer cell line (HT-29)

tag: infection

value: Mock


title: HD616_TSTEM_stim


title: Non-cancer 3 [SH54851_Cell2]

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description:
miRNA
XB0503

source_name: Serum

value: serum

value: M

value: unknown


title: AmckO4

description: granulosa cell specific knockout

value: 3 weeks


title: HD619_TSTEM_stim

value: healthy donor 619

value: TSTEM

value: anti-CD3/CD28 + IL-2/IL-12 (4 days)


title: GCKO2

description: oocyte specfic knockout

value: Dpagt1F/F Gdf9CRE/+


title: 3    Aged    A

city: Greenville

value: Aged A


title: Mouse5_H04

status: Public on Aug 02 2020

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 for mouse, and for Pogona vitticeps pvi1.1 from http://georges.biomatix.org/genomics-uc, For annotation a synthetic chromosom. composed of al of Pogona vitticepsl transcript models extracted from  “Pogona_vitticeps.male.cds"  from http://georges.biomatix.org/genomics-uc, extended with 200bp to the 5’ end separated by 20 bp spacers.
Supplementary_files_format_and_content: Tab-delimited file of UMI counts

source_name: brain

extract_protocol:
Fresh frozen and O.C.T (Tissue-Tek) embedded brains were sectioned and 14 μm thick sections collected on agarose membranes. A metal frame was then placed on the slide and used to make a well, filled with O.C.T and quickly frozen on dry ice. The glass slide was removed and
replaced with a second metal frame and the created well was filled with O.C.T and frozen.  In order to mount the sample at a predefined angle we first use a scalpel to remove the sample from the metal frames and then angled using a custom made positioning device. After mounting in the correct angle, he sample was repositioned on the cryostat and 70 μm strips were sliced, collected with a forceps and transferred in a 96-wells plate kept inside the cryostat. The angle of the cryostat sample holder was not changed between samples

tag: slice id (cutting angle and slice index)


title: Mouse5_G08


title: Mouse5_G05


title: Mouse5_H08


title: Mouse5_H06


title: Mouse5_H10


title: Mouse5_G07


title: Mouse5_G11


title: Mouse5_G10


title: Mouse5_G06


title: Mouse5_H05


title: Mouse5_G12


title: Mouse5_H07


title: Mouse5_H12


title: Mouse5_H11


title: Mouse5_F12


title: Mouse5_G04


title: Mouse5_F11


title: Mouse5_F10


title: Mouse5_F06


title: Mouse5_F08


title: Mouse5_F07


title: Mouse5_F09


title: Mouse5_H09


title: Mouse5_F04


title: Mouse5_E12


title: Mouse5_E11


title: Mouse5_F05


title: Mouse5_E10


title: Mouse5_E09


title: Mouse5_E08


title: Mouse5_C11


title: Mouse5_E05


title: Mouse5_D07


title: Mouse5_D12


title: Mouse5_C10


title: Mouse5_G09


title: Mouse5_D08


title: Mouse5_C08


title: Mouse5_E04


title: Mouse5_E06


title: Mouse5_D06


title: Mouse5_D10


title: Mouse5_D11


title: Mouse5_C07


title: Mouse5_E07


title: Mouse5_D09


title: Mouse5_C09


title: Mouse5_C12


title: Mouse5_B12


title: Mouse5_C06


title: Mouse5_D05


title: Mouse5_C05


title: Mouse5_B09


title: Mouse5_B10


title: Mouse5_B11


title: Mouse5_B08


title: Mouse5_B07


title: Mouse5_B06


title: Mouse5_A12


title: Mouse5_A10


title: Mouse5_B05


title: Mouse5_A11


title: Mouse5_A07


title: Mouse5_A05


title: Mouse2_H10


title: Mouse2_H08


title: Mouse2_H07


title: Mouse5_A09


title: Mouse2_H05


title: Mouse2_G10


title: Mouse2_H02


title: Mouse2_H06


title: Mouse2_H09


title: Mouse5_A06


title: Mouse2_H03


title: Mouse2_G06


title: Mouse2_G08


title: Mouse2_H04


title: Mouse2_H01


title: Mouse2_G07


title: Mouse2_G04


title: Mouse2_G03


title: Mouse2_G05


title: Mouse2_G09


title: Mouse2_F10


title: Mouse2_G01


title: Mouse2_G02


title: Mouse5_A08


title: Mouse2_F09


title: Mouse2_F07


title: Mouse2_F08


title: Mouse2_F06


title: Mouse2_F05


title: Mouse2_F02


title: Mouse2_F04


title: Mouse2_F01


title: Mouse2_F03


title: Mouse2_E02


title: Mouse2_D10


title: Mouse2_E10


title: Mouse2_E08


title: Mouse2_E06


title: Mouse2_E07


title: Mouse2_E04


title: Mouse2_D08


title: Mouse2_E05


title: Mouse2_D06


title: Mouse2_E03


title: Mouse2_D05


title: Mouse2_D03


title: Mouse2_D01


title: Mouse2_D02


title: Mouse2_C10


title: Mouse2_C07


title: Mouse2_E09


title: Mouse2_C06


title: Mouse2_E01


title: Mouse2_C04


title: Mouse2_C03


title: Mouse2_C05


title: Mouse2_D07


title: Mouse2_D09


title: Mouse2_B06


title: Mouse2_C08


title: Mouse2_B10


title: Mouse2_B07


title: Mouse2_C01


title: Mouse2_B09


title: Mouse2_D04


title: Mouse2_B08


title: Mouse2_B03


title: Mouse2_B04


title: Mouse2_B05


title: Mouse2_B02


title: Mouse2_A09


title: Mouse2_A07


title: Mouse2_B01


title: Mouse2_C02


title: Mouse2_A08


title: Mouse2_A10


title: Mouse2_A06


title: Mouse2_C09


title: Mouse2_A05


title: Mouse2_A04


title: Mouse2_A03


title: Mouse2_A02


title: Mouse2_A01


title: Mouse8_H10


title: Mouse8_H11


title: Mouse8_H08


title: Mouse8_H03


title: Mouse8_G12


title: Mouse8_H06


title: Mouse8_H02


title: Mouse8_H04


title: Mouse8_G08


title: Mouse8_H05


title: Mouse8_G06


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title: Whole blood, MN.R.111742064.pre.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) or 3 time less than background signal in all samples were removed from further analysis.

source_name: Whole blood

label_protocol: amplified cRNA was generated from 100ng RNA using the TargetAmp Nano-g Biotin-aRNA Labeling Kit (Epicentre, Madison WI)

growth_protocol: Whole blood samples were collected in PAXgene Tubes (Qiagen) as recommended

extract_protocol: Total RNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) according to the manufacturer’s instructions

treatment_protocol: PAXgene tubes were transferred to Wistar Genomics facility for RNA extraction

tag: patient

tag: patient sample id

tag: nodule class

value: MN

tag: collection site

value: Roswell-Park

tag: cancer type

value: adenocarcinoma

tag: nodule histology

tag: gender

value: male

value: caucasian

tag: smoking

value: quit

tag: packyears

tag: nodule size, mm

tag: cancer stage

tag: post treatment sample

value: no

tag: post treatment days

tag: training set

value: yes

tag: validation set

value: whole blood


title: Whole blood, NN.R.112701401.pre.1

value: NN

tag: age

tag: race

value: never

tag: tissue


title: Whole blood, BN.R.112981219.pre.1

tag: patient

tag: patient sample id

value: BN

value: granuloma


title: Whole blood, NN.R.112492173.pre.1

tag: nodule class

tag: collection site

value: female

value: smoker


title: Whole blood, BN.R.111511647.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, BN.R.111721925.pre.1

tag: gender

tag: smoking


title: Whole blood, NN.R.111780211.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, BN.R.112001556.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, NN.R.112731315.pre.1

tag: post treatment days

tag: training set


title: Whole blood, BN.R.111651498.pre.1

tag: age

tag: validation set


title: Mouse9_B11

tag: slice id (cutting angle and slice index)


title: Whole blood, BN.R.111651586.pre.1

tag: patient

tag: race

tag: tissue


title: Whole blood, MN.R.112760264.pre.1

tag: patient sample id

tag: nodule class

tag: collection site


title: Whole blood, BN.R.112561255.pre.1

tag: cancer type

tag: nodule histology

tag: gender


title: Whole blood, MN.R.112580217.pre.1

value: other non-small cell

tag: smoking

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.R.112281500.pre.1

tag: cancer stage

tag: post treatment sample

tag: post treatment days


title: Whole blood, MN.R.112701470.pre.1

tag: age

tag: training set

tag: validation set


title: Whole blood, BN.R.112211431.pre.1

tag: patient

tag: race


title: Whole blood, MN.R.111541162.pre.1

tag: patient sample id

value: squamous cell carcinoma

tag: tissue


title: Whole blood, MN.R.113080126.pre.1

tag: nodule class

value: MN

tag: collection site


title: Whole blood, MN.R.112791841.pre.1

value: Roswell-Park

tag: cancer type

tag: nodule histology


title: Whole blood, MN.R.113121318.pre.1

tag: gender

tag: smoking


title: Whole blood, BN.R.112990273.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.R.112580837.pre.1

value: adenocarcinoma

tag: cancer stage

tag: post treatment sample


title: Whole blood, NN.R.112631585.pre.1

tag: age

tag: post treatment days


title: Whole blood, NN.R.113130598.pre.1

value: male

tag: training set

tag: validation set


title: Whole blood, MN.R.112841378.pre.1

tag: patient

tag: race

value: african american


title: Whole blood, BN.R.112771573.pre.1

tag: patient sample id

value: caucasian

value: quit

tag: tissue


title: Whole blood, BN.R.112001686.pre.1

tag: nodule class

tag: collection site

value: other

value: no

value: yes


title: Whole blood, MN.R.112491645.pre.1

tag: cancer type

tag: nodule histology

value: whole blood


title: Whole blood, MN.R.112151610.pre.1

tag: gender

tag: smoking


title: Whole blood, MN.R.113220342.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.R.112141797.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, BN.R.112421811.pre.1

value: BN

tag: age

tag: post treatment days


title: Whole blood, BN.R.112981220.pre.1

value: granuloma

tag: training set

tag: validation set


title: Whole blood, MN.R.112931491.pre.1

tag: patient

value: female

tag: race


title: Whole blood, BN.R.112981531.pre.1

tag: patient sample id

tag: tissue


title: Whole blood, MN.R.113201335.pre.1

tag: nodule class

tag: collection site


title: Whole blood, BN.R.112351978.pre.1

tag: cancer type

tag: nodule histology

value: never


title: Whole blood, MN.R.112381441.pre.1

tag: gender

tag: smoking


title: Whole blood, NN.R.111721926.pre.1

value: NN

value: smoker

tag: packyears

tag: nodule size, mm


title: Whole blood, NN.R.112771452.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, BN.R.113191734.pre.1

tag: age

tag: post treatment days


title: Whole blood, NN.R.111511463.pre.1

tag: training set

tag: validation set


title: Whole blood, MN.R.112871070.pre.1

tag: patient

value: MN

value: squamous cell carcinoma

tag: race


title: Whole blood, NN.R.112631738.pre.1

tag: patient sample id

value: Roswell-Park

tag: tissue


title: Whole blood, BN.R.111791965.pre.1

tag: nodule class

tag: collection site

value: male


title: Whole blood, BN.R.112211588.pre.1

tag: cancer type

tag: nodule histology


title: Mouse9_A07

tag: slice id (cutting angle and slice index)


title: Mouse9_A08


title: Whole blood, BN.R.111581879.pre.1

tag: gender

tag: smoking

tag: packyears


title: Whole blood, MN.R.113260164.pre.1

tag: nodule size, mm

tag: cancer stage

tag: post treatment sample


title: Mouse9_F02


title: Whole blood, MN.R.112221600.pre.1

value: adenocarcinoma

tag: age

tag: post treatment days

tag: training set


title: Whole blood, MN.R.112771060.pre.1

tag: patient

value: other non-small cell

tag: race

tag: validation set


title: Whole blood, MN.R.112421623.pre.1

tag: patient sample id

tag: nodule class

value: caucasian

tag: tissue


title: Whole blood, MN.R.112171143.pre.1

tag: collection site

tag: cancer type

tag: nodule histology


title: Whole blood, MN.R.112571342.pre.1

tag: gender

tag: smoking

value: quit


title: Whole blood, MN.H.WS006.pre.1

value: HFGCC

value: african american

tag: packyears

tag: nodule size, mm

value: no


title: Whole blood, BN.N.NYU1489.pre.1

value: BN

value: NYU

value: solid/ground glass opacity

tag: cancer stage

tag: post treatment sample

value: yes

value: whole blood


title: Whole blood, MN.R.113210875.pre.1

tag: age

tag: post treatment days


title: Whole blood, MN.R.112001255.pre.1

tag: patient

value: female

tag: training set


title: Whole blood, MN.H.WS004.pre.1

value: MN

tag: race

tag: validation set


title: Whole blood, MN.H.WS007.pre.1

tag: patient sample id

tag: nodule class

value: squamous cell carcinoma

value: smoker


title: Whole blood, MN.R.111740443.pre.1

tag: collection site

value: Roswell-Park

tag: tissue


title: Whole blood, MN.H.WS005.post.0

tag: cancer type

value: adenocarcinoma

tag: nodule histology


title: Whole blood, BN.N.NYU910.pre.1

value: ground glass opacity

tag: gender

value: male

tag: smoking


title: Whole blood, MN.H.WS003.pre.1

value: caucasian

value: quit

tag: packyears

tag: nodule size, mm


title: Whole blood, BN.N.NYU1372.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.R.113220508.pre.1

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU955.pre.1

tag: patient

tag: training set


title: Whole blood, BN.N.NYU1364.pre.1

tag: race

tag: validation set


title: Whole blood, MN.H.WS002.pre.1

tag: patient sample id

tag: nodule class

value: HFGCC


title: Whole blood, BN.N.NYU1576.pre.1

tag: collection site

value: other

value: no

tag: tissue


title: Whole blood, BN.N.NYU369.pre.1

value: BN

value: NYU

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU1187.pre.1

value: solid

tag: gender

value: african american

tag: smoking

value: yes


title: Whole blood, BN.N.NYU486.pre.1

value: female

tag: packyears

tag: nodule size, mm

value: whole blood


title: Whole blood, BN.N.NYU1488.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.R.112840353.pre.1

value: MN

value: squamous cell carcinoma

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU1367.pre.1

tag: patient

value: solid/ground glass opacity

tag: training set


title: Whole blood, BN.N.NYU255.pre.1

tag: race

tag: validation set


title: Whole blood, BN.N.NYU1419.pre.1

tag: patient sample id

tag: nodule class

value: smoker


title: Whole blood, BN.N.NYU1192.pre.1

tag: collection site

value: ground glass opacity

tag: tissue


title: Whole blood, BN.N.NYU1480.pre.1

tag: cancer type

tag: nodule histology

value: male


title: Whole blood, MN.H.WS011.post.19

tag: gender

value: caucasian

tag: smoking

value: quit


title: Whole blood, BN.N.NYU1206.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, BN.N.NYU1435.pre.1

value: other

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1855.pre.1

tag: age

value: no

tag: post treatment days


title: Whole blood, MN.N.NYU1877.pre.1

tag: patient

value: adenocarcinoma

value: never

tag: training set


title: Whole blood, MN.N.NYU1871.pre.1

value: NYU

tag: race

tag: validation set


title: Whole blood, MN.H.WS001.pre.1

tag: patient sample id

tag: nodule class

value: HFGCC


title: Whole blood, MN.N.NYU1862.pre.1

tag: collection site

value: yes

tag: tissue


title: Whole blood, BN.N.NYU409.pre.1

value: BN

tag: cancer type

tag: nodule histology

value: female


title: Whole blood, BN.N.NYU487.pre.1

tag: gender

tag: smoking

value: whole blood


title: Whole blood, MN.N.NYU1883.pre.1

value: MN

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1854.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1852.pre.1

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU1562.pre.1

tag: patient

value: solid

tag: training set


title: Whole blood, MN.N.NYU1783.pre.1

tag: race

tag: validation set


title: Whole blood, MN.N.NYU1825.pre.1

tag: patient sample id

tag: nodule class


title: Whole blood, MN.N.NYU1818.pre.1

tag: collection site

tag: tissue


title: Whole blood, MN.N.NYU1843.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1822.pre.1

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU1847.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1799.pre.1

value: squamous cell carcinoma

value: smoker

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1815.pre.1

value: male

tag: age

tag: post treatment days


title: Whole blood, MN.N.NYU1828.pre.1

tag: patient

value: caucasian

tag: training set


title: Whole blood, MN.N.NYU1777.pre.1

tag: race

value: quit

tag: validation set


title: Whole blood, MN.N.NYU1792.pre.1

tag: patient sample id

tag: nodule class


title: Whole blood, MN.N.NYU1816.pre.1

tag: collection site

tag: tissue


title: Whole blood, MN.N.NYU1787.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1798.pre.1

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU1774.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1782.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1748.pre.1

tag: age

value: african american

tag: post treatment days


title: Whole blood, MN.N.NYU1700.pre.1

tag: patient

value: no

tag: training set


title: Whole blood, MN.N.NYU1767.pre.1

value: adenocarcinoma

tag: race

tag: validation set


title: Whole blood, MN.N.NYU1760.pre.1

tag: patient sample id

tag: nodule class

value: other


title: Whole blood, MN.N.NYU1754.pre.1

tag: collection site

value: NYU

tag: tissue


title: Whole blood, MN.N.NYU1329S.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1690.pre.2

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU510S.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1683.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1743.pre.1

tag: age

tag: post treatment days


title: Whole blood, MN.N.NYU1680.pre.1

tag: patient

value: never

tag: training set


title: Whole blood, MN.N.NYU1669.pre.2

tag: race

tag: validation set

value: yes


title: Whole blood, MN.N.NYU1682.pre.1

tag: patient sample id

tag: nodule class


title: Whole blood, NN.R.112001840.pre.1

value: NN

tag: collection site

value: Roswell-Park

tag: tissue


title: Whole blood, MN.N.NYU1690.pre.3

tag: cancer type

tag: nodule histology

value: whole blood


title: Whole blood, MN.N.NYU251.post.3834

value: MN

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU1690.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1675.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1676.pre.1

value: female

tag: age

tag: post treatment days


title: Whole blood, MN.N.NYU1715.pre.2

tag: patient

tag: training set


title: Whole blood, MN.N.NYU1749.pre.1

tag: race

tag: validation set


title: Whole blood, MN.N.NYU1721.pre.1

tag: patient sample id

tag: nodule class


title: Whole blood, MN.N.NYU1675.pre.2

tag: collection site

tag: tissue


title: Whole blood, MN.N.NYU1672.pre.2

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1672.pre.1

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU1625.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, MN.N.NYU1715.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, BN.N.NYU994.pre.2

value: BN

value: solid/ground glass opacity

tag: age

tag: post treatment days


title: Whole blood, MN.N.NYU613.post.1807

tag: patient

tag: training set


title: Whole blood, BN.N.NYU83.pre.2

value: solid

value: male

tag: race

value: smoker

tag: validation set


title: Whole blood, MN.N.NYU1429.post.35

tag: patient sample id

tag: nodule class

value: caucasian

value: quit


title: Whole blood, MN.N.NYU1055.post.500

tag: collection site

value: adenocarcinoma

value: no

tag: tissue


title: Whole blood, BN.N.NYU1343.pre.2

value: NYU

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1625.pre.2

tag: gender

tag: smoking

value: never


title: Whole blood, MN.N.NYU1669.pre.1

tag: packyears

tag: nodule size, mm

value: yes


title: Whole blood, MN.N.NYU20.post.964

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1426.post.215

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU1331.pre.2

tag: patient

tag: training set


title: Whole blood, BN.N.NYU422.pre.1

tag: race

tag: validation set


title: Whole blood, BN.N.NYU634.pre.2

tag: patient sample id

tag: nodule class


title: Whole blood, MN.N.NYU697.post.1231

tag: collection site

tag: tissue


title: Whole blood, BN.N.NYU1615.pre.1

tag: cancer type

tag: nodule histology


title: Whole blood, MN.N.NYU1426.post.25

tag: gender

tag: smoking


title: Whole blood, MN.N.NYU524.post.298

tag: packyears

tag: nodule size, mm


title: Whole blood, BN.N.NYU819.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, MN.N.NYU1426.post.102

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU1632.pre.1

tag: patient

value: ground glass opacity

tag: training set


title: Whole blood, MN.N.NYU1426.pre.1

tag: race

tag: validation set


title: Whole blood, BN.N.NYU8.pre.3

tag: patient sample id

tag: nodule class


title: Whole blood, BN.N.NYU682.pre.1

tag: collection site

tag: tissue


title: Whole blood, BN.N.NYU377.pre.4

tag: cancer type

tag: nodule histology


title: Whole blood, BN.N.NYU1041.pre.1

tag: gender

tag: smoking


title: Whole blood, BN.N.NYU1309.pre.1

tag: packyears

tag: nodule size, mm


title: Whole blood, BN.N.NYU1545.pre.1

tag: cancer stage

tag: post treatment sample


title: Whole blood, BN.N.NYU634.pre.1

tag: age

tag: post treatment days


title: Whole blood, BN.N.NYU485.pre.2

tag: patient

tag: training set