title: MCC66

type: genomic

city: Ann Arbor

first: Arul

last: Chinnaiyan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description: cell line

hyb_protocol: 200-500 ng DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research). Genome-wide methylation at >850,000 CpG sites was then analyzed by Infinium Methylation EPIC arrays (Illumina Inc, San Diego CA) at the University of Michigan Advanced Genomics Core following standard manufacturer protocols.

scan_protocol: BeadArray Reader

data_processing: Raw IDAT files were processed using R package minfi with preprocessIllumina function

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: MKL1 and MKL2 cell lines (Rosen et al., 1987; Van Gele et al., 2002) were cultured in RPMI medium with 10% fetal bovine serum. The remaining MCC cell lines (UM-MCC9, 13, 29, 31, 32, 34, 35, 40, 565) originated at the University of Michigan and were cultured as previously described (Verhaegen et al., 2014). MCC cell lines UM-MCC47, 50, 52, 58, 66, and 68 were established at a later date (Choi et al., 2019) by the same approach and were confirmed to have comparable expression of KRT20 and ATOH1 to earlier established UM-MCC cell lines, and the cell lines were classified as virus-positive or virus-negative based on LT protein and transcript expression.

extract_protocol: DNA extraction from MCC cell pellets was performed using the DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: All MCC cell lines were screened for mycoplasma contamination using the Mycoprobe Kit (R&D Systems)

tag: cell type

value: MCC cell line


title: Intestine 104w

status: Public on Sep 15 2021

type: SRA

city: Münster

first: Monika

last: Stoll

country: Germany

institute: Institute for Human Genetics, Genetic Epidemiology, University of Muenster

library_source: genomic

data_processing:
FastQC quality control and read trimmed using trimmomatic
aligned to the mouse reference genome GRCm38 with BWA mem
marking duplicate reads with picard.2.11.0
GATK version 3.7 RNAseq variant calling pipeline: BaseRecalibrator, Haplotypecaller and VariantFiltration (FS > 30.0, QD < 2.0)
Filter for strain 129S1_SvImJ specific variants in hybrid strain mice
Genome_build: GRCm38
Supplementary_files_format_and_content: vcf files with called variants for each sample individually

molecule: genomic DNA

organism: Mus musculus

source_name: Small intestine

extract_protocol:
Total DNA was extracted from small intestine, liver and spleen tissues of naturally aged mice of 12 and 104 weeks of age. DNA was extracted using the Quick-DNATM Miniprep Plus Kit (Zymo Research) following the manufacturer’s protocol.
500 ng of the genomic DNA was sheared on the S220 instrument (Covaris) followed by NGS library preparation using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The size of the resulting library was controlled by use of a D1000 ScreenTape (Agilent 2200 TapeStation) and quantified using the NEBNext Library Quant Kit for Illumina (NEB). Equimolar pooled libraries were sequenced in a paired end mode (80 cycles) on the NextSeq 500 System (Illumina) using v2 chemistry yielding in an average QScore distribution of 85% >= Q30 score.

tag: strain

tag: age

value: 12 weeks

tag: tissue

value: Small intestine


title: 4W_KO_2_A31_1

city: Augusta

first: Xingguo

last: Zhu

state: Georgia

department: Cancer Center

country: USA

institute: Augusta University

library_source: transcriptomic

data_processing:
STAR v2.5: Read Alignment
htseq-count: fpkm
DESeq2: Differential expression analysis
Genome_build: mm10

molecule: total RNA

source_name: Liver tissue

extract_protocol: mouse liver tumors were removed, flash frozen on dry ice, and total RNA extracted using the PureLink™ RNA Mini Kit (Thermo Fisher) and subjected to library preparation using Illumina TrueSeq RNA kit V2 according to manufacturer’s protocol with 1 ug of total RNA for the construction of sequencing libraries.

value: mixed B6;129P2 background

value: 4-week post-DEN treatment

tag: genotype/variation

value: knockout


title: 4W_KO_1_A30_1


title: Spinalcord_Vehicle_mouse3

type: RNA

city: Barcelona

first: Carmen

last: Espejo

address: Passeig de la Vall d'Hebron, 119-129, Edifici Collserola, Laboratory 149-151

country: Spain

institute: Vall d'Hebron Institute of Research - Centre d'Esclerosi Múltiple de Catalunya

description: Gene expression data from EAE mice treated with vehicle (Clostridia strains culture medium)

hyb_protocol: Following fragmentation, 5.5ug of ds-cDNA were hybridized for 16 h at 45ºC on GeneChip Clariom S mouse array plate. Array plate was washed and stained in the Affymetrix Genetitan Instrument (GeneTitan Multichannel system)

scan_protocol: Array plate was scanned using the Genetitan instrument (GeneTitan Multichannel system)

data_processing: The data were processed and analyzed separately for each tissue. Raw expression values were obtained directly from .CEL files and were processed using the RMA method to get normalized expression values (log2 scale) summarized at the gene level. Different quality checks were performed before and after normalization to ensure that all samples were suitable for differential expression analysis. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis.  Statistical language R (version 3.6.1) and Bioconductor associated packages were used to process and analyze the data.

label: biotin

source_name: Spinal cord, Vehicle, 28 days post-immunization

label_protocol: Biotinylated ds-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 50 ng total RNA (GeneChip 3' IVT Pico Kit Manual Workflow, user guide).

extract_protocol: Spinal cord: Total RNA was isolated using QIAzol lysis reagent (79306, Qiagen) and RNeasy Mini Kit (74104, Qiagen) with on-column DNase digestion (79254, Qiagen) in order to remove any genomic DNA trace according to the manufacturer's instructions. Spleen: RNeasy Mini Kit together with on-column DNase digestion was also used to isolate splenocyte total RNA according to the manufacturer's instructions.

value: Spinal cord

tag: treatment

value: Vehicle (Clostridia strains culture medium)


title: HeLa cell culture - NT - Rep1 [NT_1]

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 microarray (8X60K, Design 039494) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 12 out of 15 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 32772 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 26516 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Homo sapiens

source_name: HeLa cell culture - NT

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: HeLa cells were were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies), supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco) and 1% antibiotics (penicillin/streptomycin). Cells were plated at a density of 150000 cells per well in 6 wells plate

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) mRNA were extracted and the quality of these samples was assessed (Agilent RNA 6000 Nano Kit Quick, Agilent Bioanalyzer 2100); RNA Integrity Number (RIN) of these mRNA was superior to 9.8.

treatment_protocol: One day after seeding, cells were exposed to 0.25 ng/ml of WT or HA CDT for 48 H. For chronic exposure, individual clones were selected, the rest of the cells were pooled. CDT was added at each passage (every 2-3 days) for 8 weeks.

tag: cell line

value: HeLa

tag: condition

value: NT

tag: exposure time

value: 8 weeks

tag: rna integrity number


title: MCC565

middle: M.

state: MICHIGAN

description: cell line


title: HI555-input

city: Madison

first: Shane

middle: P

last: Simonett

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

data_processing:
The raw reads from all samples were aligned to human reference genome (hg19) with Bowtie 2 (version 2.3.1).
We used Bowtie2 default reporting mode with the argument -X 550 --no-mixed --no-discordant being specified.
Picard MarkDuplicates tool (version 2.9.2) was used to remove duplicate reads from the alignment.
We performed peak calling from mapped and properly paired reads with Bioconductor package MOSAiCS (version 3.5).
The peak sets called from the six samples were merged and 8,635 peaks were retained based on the following criteria. We included (i) peaks reproducible in at least two samples and (ii) peaks identified in one sample, whose summit signals are higher than the third quantile of the summit signals of the reproducible peaks.
Peaks in ENCODE DAC blacklist regions were dropped from the peak list.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig files contain the Nfatc2 peaks identified from 6 human islet samples.
Supplementary_files_format_and_content: bigBed file contains the merged peaks used to determine Nfatc2 binding in human islets.

source_name: Human pancreatic islets

growth_protocol: All human islets were obtained through the IIDP (Integrated Islet Distribution Program). Upon receipt, all human islets were incubated overnight in RPMI 1640 supplemented with 8.0 mM glucose, 1% antibiotic/antimycotic (Gibco), 5 mM HEPES, and 10% FBS before performing experiments.

extract_protocol:
~17,000 human IEQs were incubated with 5 mL of 1% formaldehyde (Thermo Scientific, Cat. # 28906) in PBS for 5 minutes at room temperature. To quench the formaldehyde fixative, 256 uL of 2.5 mM glycine was added, incubated for 2 minutes, and then centrifuged (500 x g) to pellet the islets. Islets were washed with 1mL each of PBS, NCP buffer 1 (10 mM HEPES pH 6.5, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100) and NCP buffer 2 (200 mM NaCl, 10 mM HEPES pH 6.5, 1 mM EDTA, 0.5 mM EGTA). Islets were then lysed in 3 mL of lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% Empigen BB, 1% SDS, 1mM PMSF, and Roche cOmplete Mini EDTA-free Protease Inhibitor Cocktail Tablet). The islets were triturated with a 30-gauge needle ~20 times, and then sonicated using a Branson Digital Sonifier 250 with a double step microtip probe at 30% amplitude for 15 cycles (30 seconds on, 30 seconds off). The sample was then centrifuged (13000 x g, 10 minutes, 4˚C), and supernatant collected for immunoprecipitation. The supernatant was diluted with IP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100) at a ratio 5:2, IP buffer:supernatant; 10% of the supernatant was set aside for ChIP input determination. To the IP buffer/supernatant mixture, 10 uL of anti-HA antibody (Abcam, ab9110) was used to immunoprecipitate HA-tagged Nfatc2/chromatin complexes overnight at 4˚C. The following day 100 uL Protein A/G magnetic beads (Pierce) were supplied to the immunoprecipitated mixture for 2 hours. The magnetic bead complexes were then sequentially washed with 1 mL of wash buffer #1 (2 mM EDTA, 20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 150 mM NaCl), wash buffer #2 (2 mM EDTA, 20 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), and wash buffer #3 (1 mM EDTA, 10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% sodium deoxycholate, 1% NP-40 Alternative), followed by 5 washes in TE buffer. The Nfatc2/chromatin complexes were then eluted with elution buffer (200 mM NaCl, 100 mM NaHCO3, and 1% SDS) at 65˚C overnight. Eluted DNA was purified using MinElute PCR purification cleanup kit (Qiagen).
Samples were prepared according the TruSeq ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size-selected for an average insert size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit dsDNA HS Assay Kit, respectively. Libraries were standardized to 2 nM.

treatment_protocol: Isolated human islets were treated with an adenovirus to overexpress a constitutively active HA-tagged Nfatc2 protein. Islets were collected for ChIP-seq 48 hours later.

value: Human pancreatic islets

tag: Sex

value: M

tag: expression

value: constitutively active Nfatc2


title: Liver 104w

source_name: Liver

value: 104 weeks

value: Liver


title: HI556-HA-ChIP


title: MKL1

description: cell line


title: Spinalcord_Vehicle_mouse4


title: Spinalcord_Vehicle_mouse1


title: Spinalcord_Vehicle_mouse2


title: 4W_WT_2_A28_1

value: wild type


title: MCC47

description: cell line

value: MCC cell line


title: HCT116_shDHX30_NUTLIN_TOT_rep3

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: DHX30 silencing NUTLIN total replicate 3

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence and low-quality nucleotides, then quantified against the Gencode v25 transcriptome using Salmon 0.7.2 with default parameters
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

source_name: HCT116 cells

growth_protocol: HCT116 cells were maintained in RPMI (Gibco) supplemented with 10% FBS, antibiotics (100 units/mL penicillin plus 100 mg/mL streptomycin) and 2mM L-glutamine. Cultures were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Polysomal separation was performed as follows: samples were loaded in 15-50% linear sucrose gradients, ultra-centrifuged and fractionated with an automated fraction collector. All the fractions containing subpolysomal or polysomal RNA were identified and pooled in two separate tubes. RNA was purified by extraction with 1 volume of phenol-chloroform and, after isopropanol precipitation, a washing step in 70% v/v ethanol was performed in order to remove phenol contaminations.
RNA libraries were prepared for sequencing using standard Illumina protocols: Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA as input.

treatment_protocol: HCT116 cells were transduced with lentiviral vectors containing a pLK0.1 plasmid expressing shRNA sequences against DHX30 or PCBP2. A scramble sequence SHC206 was also used. Cells were allowed to reach 60-70% confluence before treatment with 10 mM Nutlin-3a (Nutlin) or only  DMSO at 0.1% (v/v).

tag: genotype

value: DHX30 silencing


title: Spinalcord_Clostridia_mouse6

description: Gene expression data from EAE mice treated with 17 Clostridia strains

source_name: Spinal cord, Clostridia, 28 days post-immunization

value: Clostridia strains


title: HI555-HA-ChIP


title: Intestine 12w

value: 12 weeks

value: Small intestine


title: HCT116_shDHX30_NUTLIN_TOT_rep4

description: DHX30 silencing NUTLIN total replicate 4


title: Liver 12w


title: 4W_WT_3_A29_1

value: mixed B6;129P2 background

value: 4-week post-DEN treatment


title: MCC68

description: cell line


title: MCC50

description: cell line


title: Spinalcord_Clostridia_mouse5

value: Spinal cord


title: MCC58

description: cell line


title: MCC52

description: cell line


title: MCC40

description: cell line


title: 36W_KO_3_A25_1

value: 36-week post-DEN treatment

value: knockout


title: MCC35

description: cell line


title: Spinalcord_Clostridia_mouse4


title: 36W_KO_2_A24_1


title: HCT116_shDHX30_DMSO_TOT_rep4

description: DHX30 silencing DMSO total replicate 4


title: Tert Rep4

data_processing:
FastQC quality control and read trimmed using trimmomatic
aligned to the mouse reference genome GRCm38 with hisat2 version 2.1.0
marking duplicate reads with picard.2.11.0
GATK version 3.7 RNAseq variant calling pipeline: SplitNCigarReads, IndelRealigner, BaseRecalibrator, Haplotypecaller and VariantFiltration (FS > 30.0, QD < 2.0)
Filter for strain (CBA and S129) specific variants in hybrid strain mice
Filter for variants introduced through model construction in Tert and Progeria models
Supplementary_files_format_and_content: vcf files with called variants for each sample individually
Genome_build: GRCm38

source_name: myocardial tissue

extract_protocol:
Total RNA was extracted from myocardial tissue of mice euthanized at the timepoints reported above using the Direct-zol™ RNA MiniPrep method (Thermofisher) following the manufacturer’s protocol.
Quality control of total RNA was performed using the RNA 6000 Pico Kit (Agilent Bioanalyzer) yielding RIN values of 6.3 and higher. Removal of rRNA was carried out using the NEBNext rRNA Depletion Kit Human/Mouse/Rat (NEB) followed by strand-specific cDNA NGS library preparation (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB). The size of the resulting library was controlled by use of a D1000 ScreenTape (Agilent 2200 TapeStation) und quantified using the NEBNext Library Quant Kit for Illumina (NEB). Equimolar pooled libraries were sequenced in a paired end mode (75 cycles) on the NextSeq 500 System (Illumina) using v2 chemistry yielding in an average QScore distribution of 84% >= Q30 score.

value: 16 weeks

value: myocardial tissue


title: MCC32

description: cell line


title: NA 104 w

data_processing:
FastQC quality control and read trimmed using trimmomatic
aligned to the mouse reference genome GRCm38 with BWA mem
marking duplicate reads with picard.2.11.0
GATK version 3.7 RNAseq variant calling pipeline: BaseRecalibrator, Haplotypecaller and VariantFiltration (FS > 30.0, QD < 2.0)
Filter for strain (CBA and S129) specific variants in hybrid strain mice
Genome_build: GRCm38
Supplementary_files_format_and_content: vcf files with called variants for each sample individually

extract_protocol:
Total DNA was extracted from heart tissues of naturally aged mice of 104 weeks of age and of mice with heart muscle-specific Ercc1 gene deletion: DNA was extracted using the Quick-DNATM Miniprep Plus Kit (Zymo Research) following the manufacturer’s protocol.
500 ng of the genomic DNA was sheared on the S220 instrument (Covaris) followed by NGS library preparation using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). The size of the resulting library was controlled by use of a D1000 ScreenTape (Agilent 2200 TapeStation) and quantified using the NEBNext Library Quant Kit for Illumina (NEB). Equimolar pooled libraries were sequenced in a paired end mode (80 cycles) on the NextSeq 500 System (Illumina) using v2 chemistry yielding in an average QScore distribution of 85% >= Q30 score.


title: 4W_WT_1_A27_1


title: HCT116_shDHX30_NUTLIN_TOT_rep2

description: DHX30 silencing NUTLIN total replicate 2


title: Tert Rep3


title: Ercc1


title: Spleen 12w

source_name: Spleen

value: Spleen


title: HCT116_shDHX30_DMSO_TOT_rep3

description: DHX30 silencing DMSO total replicate 3


title: MCC34

description: cell line


title: HCT116_shDHX30_NUTLIN_TOT_rep1

description: DHX30 silencing NUTLIN total replicate 1


title: MCC29

description: cell line


title: MCC31

description: cell line


title: 36W_KO_1_A23_1


title: MCC9

description: cell line


title: HCT116_shDHX30_DMSO_TOT_rep1

description: DHX30 silencing DMSO total replicate 1


title: MCC13

description: cell line


title: Tert Rep2


title: HCT116_shDHX30_DMSO_TOT_rep2

description: DHX30 silencing DMSO total replicate 2


title: 36W_WT_1_A19_1


title: Progeria Rep4


title: 36W_WT_3_A21_1


title: HCT116_scr_NUTLIN_TOT_rep4

description: scramble NUTLIN total replicate 4


title: 2D_KO_3_B14_1

source_name: Liver tumor

value: 2-day post-DEN treatment


title: Tert Rep1


title: 36W_WT_2_A20_1


title: Progeria Rep2


title: 2D_KO_2_B13_1


title: HCT116_scr_NUTLIN_TOT_rep1

description: scramble NUTLIN total replicate 1


title: Progeria Rep1


title: 2D_KO_1_B12_1


title: HCT116_scr_DMSO_TOT_rep4

description: scramble DMSO total replicate 4


title: 2D_WT_3_B11_1


title: 2D_WT_2_B10_1


title: HCT116_scr_DMSO_TOT_rep3

description: scramble DMSO total replicate 3


title: HCT116_scr_NUTLIN_TOT_rep3

description: scramble NUTLIN total replicate 3


title: Progeria Rep3


title: NA 104 w Rep3

value: 104 weeks


title: HCT116_scr_NUTLIN_TOT_rep2

description: scramble NUTLIN total replicate 2


title: NA 104 w Rep2


title: Spinalcord_Clostridia_mouse2


title: Spleen_Vehicle_mouse6

source_name: Spleen, Vehicle, 28 days post-immunization

value: Vehicle (Clostridia strains culture medium)


title: HCT116_scr_DMSO_TOT_rep2

description: scramble DMSO total replicate 2

value: wild type


title: Spleen_Vehicle_mouse4


title: 2D_WT_1_B9_1


title: NA 104 w Rep1


title: HCT116_scr_DMSO_TOT_rep1

description: scramble DMSO total replicate 1


title: Spinalcord_Clostridia_mouse1


title: Spleen_Vehicle_mouse5


title: Spleen_Vehicle_mouse3


title: Spinalcord_Clostridia_mouse3


title: Spleen_Vehicle_mouse2


title: NA 104 w Rep4


title: PR tumor 9

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: total RNA isolated from mammary gland tumors developing in PR/GAL4 mice

data_processing:
The RNA sequences were generated on an Illumina Nova 6000 Platform using a paired-end 2×150 bases.
RNA sequences were aligned against mouse genome mm10 by STAR (Version 2.7.3), and RNA expression was calculated by RSEM (RNA-Seq by Expectation Maximization).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mammary gland tumor

extract_protocol:
1 ug of RNA was used for cDNA library construction at Novogene using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (cat# E7420S, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB/n

tag: disease state

value: tumor

value: PR


title: NA 52 w Rep3

value: 52 weeks


title: PR tumor 8


title: NA 52 w Rep4


title: Spleen_Clostridia_mouse6

source_name: Spleen, Clostridia, 28 days post-immunization

value: Clostridia strains


title: NA 52 w Rep2


title: Spleen_Vehicle_mouse1


title: PR tumor 5


title: Spleen_Clostridia_mouse5


title: PR tumor 6


title: NA 12 w Rep3

value: 12 weeks


title: PR tumor 7


title: NA 52 w Rep1


title: NA 12 w Rep4


title: PR tumor 3


title: NA 12 w Rep2


title: Spleen_Clostridia_mouse2


title: NA 12 w Rep1


title: Patient 14 Fibroids

city: Baltimore

first: Crystal

last: Aguh

state: Maryland

address: 1500 Orleans St, CRB II Suite 200

department: Dermatology

institute: Johns Hopkins School of Medicine

hyb_protocol: Hybridized for 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization created quantile-normalized log2 transcript-level signal values, which were used in the subsequent ANOVA analysis.    Transcript annotation was subsequently updated.
Clariom_S_Human.r1.pgf
Clariom_S_Human.na36.hg38.transcript.csv

source_name: Scalp, vertex

label_protocol: Affymetrix 3’ IVT Pico Kit using standard protocol.

extract_protocol: RNA labeled with the miRNeasy Mini with DNase treatment kit and QiaCube Preparation using standard protocol.

treatment_protocol: Tissue samples were immersed in 2 mL of RNAlater immediately following collection, stored at 4 degrees Celsius for 24 hours, and then transferred to a -80 degree Celsius freezer for indefinite storage

tag: individual

value: Patient 14

value: Scalp, vertex

tag: fibroids

value: Fibroids

tag: ccca status

value: Moderate CCCA


title: Spleen_Clostridia_mouse3


title: Patient 16 Fibroids

value: Patient 16

value: Mild CCCA


title: Patient 12 No Fibroids

value: Patient 12

value: NoFibroids


title: Patient 15 No Fibroids

value: Patient 15


title: PR tumor 4


title: PR tumor 1


title: PR tumor 12


title: PR tumor 2


title: Healthy Control replicate3

city: Fuzhou

first: yunnan

last: Hu

state: Fujian

address: Xinquan Road No. 29

country: China

institute: fujian medical university union hospital

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The lncRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information. The lncRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed lncRNAs were annotated  in detail with the lncRNA/miRNA interaction information.

source_name: ascending aorta

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

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

treatment_protocol: Tissues from aortic dissection surgury and promptly cooled at -80℃ refrigerator.

value: tissue

tag: disease

value: Healthy Control


title: Patient 13 Fibroids

value: Patient 13


title: Healthy Control replicate1


title: Patient 11 No Fibroids

value: Patient 11


title: Hq Rep3

tag: strain

value: 17 - 20 weeks

value: myocardial tissue


title: Hq Rep4

tag: age


title: Spleen_Clostridia_mouse1

tag: tissue

value: Spleen

value: Clostridia strains


title: PR tumor 11

value: FVB/n

value: tumor

tag: genotype/variation

value: PR


title: Healthy Control replicate2


title: Patient 10 Fibroids

value: Patient 10

value: Scalp, vertex

value: Fibroids

value: Moderate CCCA


title: WT tumor 5

description: total RNA isolated from mammary gland tumors developing in control GAL4 mice

value: WT


title: Ercc1 Rep4

value: 16 weeks


title: PR tumor 10


title: Hq Rep1


title: Patient 6 Fibroids

value: Patient 6

value: Severe CCCA


title: Hq Rep2


title: Patient 9 Fibroids

value: Patient 9

value: Mild CCCA


title: WT tumor 4


title: Aortic Dissection replicate2

value: tissue

value: Aortic dissection


title: hippocampal DG Cav3.1 KO4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Intact brain

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: After decapitation of animals, brain tissue from hippocampal DG region was dissected and stored at −80 °C until assay.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Total RNA was purified from the mouse hippocampus using an RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: male

value: 8-12 weeks old

value: Cav3.1 KO

value: Dorsal hippocampal dentate gyrus (DG)


title: Aortic Dissection replicate1


title: Patient 7 No Fibroids

value: Patient 7

value: NoFibroids


title: hippocampal DG Cav3.1 KO3


title: Aortic Dissection replicate3


title: Patient 8 No Fibroids

value: Patient 8

value: Scalp, vertex


title: WT tumor 2

value: FVB/n

value: tumor


title: Ercc1 Rep2

value: 16 weeks

value: myocardial tissue


title: WT tumor 1

value: WT


title: Ercc1 Rep3


title: hippocampal DG Cav3.1 KO1


title: hippocampal DG WT4


title: hippocampal DG Cav3.1 KO2


title: Patient 5 No Fibroids

value: Patient 5

value: Moderate CCCA


title: Patient 4 Fibroids

value: Patient 4

value: Fibroids


title: Mat-IGTRE-del_Gtl2-VP_rep2

status: Public on Sep 14 2021

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

data_processing:
Library strategy: 4C-Seq
Read trimming: seqtk. Known adapter sequences were trimmed off the reads.
Read alignment: bowtie2 2.3.4.1. Reads were mapped against redcued mm10 reference sequence using bowtie2. Reduced reference genome only consists of sequences adjacent to DpnII/NlaIII cut-sites. Multi-mapped reads were discarded.
Read counts: custom script. The genome was binned in successively overlapping 5kb bins, with each bin overlapping by 500bp with the next bin. Reads were counted per bin, leading to multi-counts of each read.
Normalization: edgeR. Raw read counts were normalized with R library edgeR function cpm.
Genome_build: mm10
Supplementary_files_format_and_content: normalized bigwig tracks

organism:
Mus musculus
Mus musculus molossinus

source_name: Induced pluripotent stem cells

extract_protocol:
Cells were collected with trypsin and fixed with 1% formaldehyde
Cell pellets were lysed in 1ml Lysis Buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA; 1x complete protease inhibitor, 0.5% NP-40, 1% triton) and incubated on ice for 15 min. The samples were centrifuged at 2500xG for 5min at 4°C and the pellet was then resuspended in 360µl milli-Q, 60µl 10X DpnII restriction buffer and 15ul 10%SDS. After 1 hour incubation at 37ºC, 150ul of 10% Triton was added and samples were incubated again at 37ºC for 1 hour. 4ul DpnII enzyme (#R0543M, NEB) were added and samples were incubated at 37ºC over night while shaking in a thermomixer (9000rpm). After confirming the digestion efficiency, the enzyme was inactivated by adding 80ul 10% SDS and incubating at 65 ºC for 30 mins. The digested samples were then diluted with 4860ul Milli-Q, 700ul ligation buffer (500mM Tris pH 7.5, 100mM DTT, 100mM MgCl2,10mM ATP), and 750ul of Triton and incubated at 37ºC for 1 hour. Then 2ul Ligase (NEB M0202M) were added and samples were incubated over night at 16 ºC. Next morning, after testing the ligation efficiency, we reversed the crosslinks by adding 30ul of proteinase K (10mg/ml) and incubating over night at 65ºC. Subsequently the RNA was removed using 30ul of RNase A (10mg/ml) for 45mins at 37ºC. Extensive phenol/chloroform extraction was followed by EtOH precipitation and two washes with 70% EtOH. The pellets were dissolved in 150ul 10mM Tris pH 7.5 by incubating at 37 ºC. We then added 50ul 10x buffer B (Fermentas), 5ul Csp6I (Fermentas, ER0211) and 299ul milli-Q water and samples were digested at 37ºC over night. After determining digestion efficiency, the restriction enzyme was inactivated by incubating the tubes at 65ºC for 25 mins. Samples were diluted in 12ml milli-Q, 3ul ligase (NEB, M0202M) and 1.4ml 10X ligation buffer (500mM Tris pH7.5, 100mM DTT, 100mM MgCl2, 10mMATP) and incubated over night at 65ºC. Following phenol/chloroform and EtOH precipitation the pellets were dissolved in 300ul 10mM Tris pH7.5 and DNA was further purified using 4 Zymo columns per sample (Zymo, D4014). Each sample was eluted in 200ul total of 10mM Tris pH7.5
For allele-specific 4C-seq library preparation, primers were designed upstream of a SNP within IG-DMR. Due to lack of suitable restriction fragments on ΔMatTRE samples, non-allele specific libraries were prepared with the Gtl2 DMR as viewpoint. Library preparation was further performed by using a PCR strategy as previously described (Krijger et al., 2020). Briefly, 4x200 ng of 4C-template DNA was used to PCR amplify the libraries using the Roche Expand long template PCR system (Roche, 11681842001). Primers were removed using Ampure XP beads (Beckman Coulter, A63880). A second round of PCR was performed using the initial PCR library as a template, with overlapping primers to add the full adapters. The libraries were sequenced on a miSeq platform in SE150 mode.

tag: cell type

value: Induced pluripotent stem cells

tag: viewpoint

value: Gtl2 promoter

value: maternal IG-TRE deletion

tag: allele

value: non-allelespecific


title: C16 rep 3

city: Beijing

first: Hongxiu

last: XU

state: Beijing

address: Zhongguancun road

institute: PekingUniversity

description: wild type

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw sequence data were filtered with SeqPrep and Sickle software to obtain clean data.
Reference genome and gene model annotation files were downloaded from NCBI (Genbank No. CP046567.1, CP046568.1, and CP046569.1).
The clean reads were mapped to reference genome by Hisat2.
Genome_build: ASM974091v1
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Dietzia sp. DQ12-45-1b

source_name: Bacterial

growth_protocol: The Dietzia sp. DQ12-45-1b strain (CGMCC 1.10709) was first grown in GPY medium (10 g tryptone, 5 g yeast extract and 10 g glucose per liter deionized water) at 30 °C. For n-alkane-degrading experiments, cells of DQ12-45-1b cultured in GPY medium at 30 °C for 36 h (at mid exponential phase) were centrifuged and washed three times with the minimal medium (Bihari et al., 2011). Then cells were cultured in minimal medium with 0.1 % liquid n-alkane (C16) (v/v) or 0.1 % solid n-alkane (C28) (m/v) as the sole carbon source with the initial cell density of OD600 (0.1).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Waltham, USA) according to the manufacturer’s instructions. Then the RNA was treated with DNase I, and purified using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Then cells were cultured in 50 mL minimal medium with 0.1 % hexadecane (v/v) or 0.1 % octacosane (m/v) as the sole carbon source  and 0.2 % (m/v) glucose with the initial cell density of OD600 (0.1) in 250 mL Erlenmeyer flasks. The cells were harvested at mid-log phase, frozen in liquid nitrogen and stored at -80 °C.

tag: carbon source

value: hexadecane

tag: Stage

value: Mid log phase cells


title: Glu rep 1

description: wild type

value: glucose


title: Glu rep 3

description: wild type


title: C16 rep 2

description: wild type


title: Patient 3 No Fibroids

value: Patient 3

value: Scalp, vertex

value: NoFibroids

value: Severe CCCA


title: hippocampal DG WT2

tag: Sex

value: male

value: 8-12 weeks old

value: Dorsal hippocampal dentate gyrus (DG)


title: Glu rep 2

description: wild type


title: WT tumor 3

value: FVB/n

value: tumor

value: WT


title: hippocampal DG WT3


title: C28 rep 2

description: wild type

value: octacosane


title: MOI_Gtl2-VP_rep2

value: Induced pluripotent stem cells

value: Gtl2 promoter


title: C28 rep1

description: wild type


title: Patient 2 Fibroids

value: Patient 2

value: Fibroids

value: Moderate CCCA


title: Ercc1 Rep1

value: 16 weeks

value: myocardial tissue


title: Pat-IGCGI-del_paternal_IGDMR-VP_rep2

value: IG-DMR

value: paternal IG-CGI deletion

value: paternal


title: MOI_Gtl2-VP_rep1

value: non-allelespecific


title: hippocampal DG WT1

value: male

value: 8-12 weeks old


title: Mat-IGTRE-del_Gtl2-VP_rep1

value: maternal IG-TRE deletion


title: C28 rep 3

description: wild type

value: Mid log phase cells


title: C16 rep 1

description: wild type

value: hexadecane


title: Pat-IGCGI-del_maternal_IGDMR-VP_rep1

value: maternal


title: MOI_paternal_IGDMR-VP_rep2

value: Induced pluripotent stem cells

value: WT


title: MOI_paternal_IGDMR-VP_rep1


title: Patient 1 No Fibroids

value: Patient 1

value: Scalp, vertex

value: NoFibroids

value: Severe CCCA


title: MOI_maternal_IGDMR-VP_rep2


title: MOI_maternal_IGDMR-VP_rep1


title: Pat-IGCGI-del_maternal_IGDMR-VP_rep2


title: Pat-IGCGI-del_paternal_IGDMR-VP_rep1


title: liver_male_4days_mouse-M2

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Gene expression from primary hepatocytes of a male mouse after 96 hours of culture

hyb_protocol: Hybridizations of Clariom S Assays, mouse (Thermo Fisher Scientific Inc., Waltham, USA) were conducted according to the manufacturer’s instructions. 250 ng of total RNA was used for hybridization. Labeled samples were injected into arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized and quantile-normalized using RMA algorithm from oligo package.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps

source_name: Mus musculus, male, liver, 96 hours culture

label_protocol: Sample preparation for Clariom S Assays, mouse (Thermo Fisher Scientific Inc., Waltham, USA) was conducted according to the manufacturer’s instructions. Total RNA was used to synthesize double-stranded cDNA with random hexamer primers tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template and amplified by T7 RNA polymerase producing cRNA. In the second cycle of cDNA synthesis, random hexamers were used to prime reverse transcription of the cRNA and dUTP was incorporated to produce single-stranded DNA. This single-stranded DNA samples were then treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labeled by terminal eoxynucleotidyl transferase (TdT) with the proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: The mice were housed in a pathogen-free facility with a 12:12 h light:dark cycle. Animals were fed ad libitum with regular chow (Ssniff® V1534-300 composed of 24.0 kJ% protein, 67 kJ% carbohydrate, 9 kJ% fat; Ssniff® Spezialdiäten GmbH, Soest, Germany) and tap water throughout life.

extract_protocol: RNA was isolated from primary hepatocytes using the ReliaPrep RNA Miniprep Kit (Promega GmbH, Walldorf, Germany) according to the manufacturer’s instructions.

treatment_protocol: Mice were sacrificed during primary hepatocyte isolation procedure at the age of three months after administration of an anesthetic consisting of ketamine, xylazine and atropine between 8 and 11 am (zeitgeber time 2-5). Primary hepatocytes were isolated using a collagenase perfusion technique and subsequently cleared from other liver cells by differential centrifugation as previously described [Matz-Soja M, Aleithe S, Marbach E, et al. Hepatic Hedgehog signaling contributes to the regulation of IGF1 and IGFBP1 serum levels. Cell Commun Signal 2014; 12: 11 doi:10.1186/1478-811X-12-11 && Gebhardt R, Hengstler J G, Müller D, et al. New hepatocyte in vitro systems for drug metabolism: metabolic capacity and recommendations for application in basic research and drug development, standard operation procedures. Drug Metab Rev 2003; 35 (2-3): 145–213 doi:10.1081/dmr-120023684]. The hepatocytes from each individual mouse were suspended in Williams Medium E (Biochrom GmbH, Berlin, Germany, product No.: F1115) containing 10% foetal bovine serum (FBS) (PAA Laboratories GmbH, Pasching, Austria, Lot No.: A15111-3719), 20 µM glutamine (Carl Roth GmbH + Co. KG, Karlsruhe, Germany, Cat. No.: 3772.1), penicillin and streptomycin (Capricorn Scientific GmbH, Ebsdorfergrund, Germany, Cat. No. PS-B), and 90 pM dexamethasone (Sigma-Aldrich, St. Louis, USA, Cat. No. D1756) and seeded into cell culture plates coated with collagen type I. After 2 to 3 h, the medium was changed to serum-free medium. After 24, 48, and 72 h of culture, fresh sf medium was applied.

value: liver

value: 96 hours

value: wild type


title: liver_male_4days_mouse-M5


title: liver_male_3days_mouse-M7

description: Gene expression from primary hepatocytes of a male mouse after 72 hours of culture

source_name: Mus musculus, male, liver, 72 hours culture

value: 72 hours


title: liver_male_4days_mouse-M6


title: liver_male_1days_mouse-M5

description: Gene expression from primary hepatocytes of a male mouse after 24 hours of culture

source_name: Mus musculus, male, liver, 24 hours culture

value: 24 hours


title: liver_male_1days_mouse-M1

value: male


title: liver_male_2days_mouse-M7

description: Gene expression from primary hepatocytes of a male mouse after 48 hours of culture

source_name: Mus musculus, male, liver, 48 hours culture

value: 48 hours


title: liver_male_1days_mouse-M2


title: liver_male_2days_mouse-M6


title: liver_male_4days_mouse-M7


title: liver_male_3days_mouse-M1


title: liver_male_1days_mouse-M6


title: liver_male_3days_mouse-M2


title: liver_male_4days_mouse-M1


title: liver_male_1days_mouse-M7


title: liver_male_2days_mouse-M1


title: liver_male_0days_mouse-M7

description: Gene expression from primary hepatocytes of a male mouse before culture

source_name: Mus musculus, male, liver, 0 hours culture

value: 0 hours


title: liver_male_3days_mouse-M6


title: liver_male_3days_mouse-M5


title: liver_male_2days_mouse-M5


title: liver_male_2days_mouse-M2


title: liver_male_0days_mouse-M6


title: Spleen_Clostridia_mouse4

value: Spleen

tag: treatment

value: Clostridia strains


title: liver_male_0days_mouse-M5

tag: genotype


title: liver_female_4days_mouse-F6

description: Gene expression from primary hepatocytes of a female mouse after 96 hours of culture

source_name: Mus musculus, female, liver, 96 hours culture

value: female


title: liver_female_4days_mouse-F4


title: liver_male_0days_mouse-M1


title: liver_male_0days_mouse-M2


title: liver_female_4days_mouse-F7


title: liver_female_4days_mouse-F2


title: liver_female_4days_mouse-F3


title: liver_female_3days_mouse-F2

description: Gene expression from primary hepatocytes of a female mouse after 72 hours of culture

source_name: Mus musculus, female, liver, 72 hours culture


title: liver_female_2days_mouse-F7

description: Gene expression from primary hepatocytes of a female mouse after 48 hours of culture

source_name: Mus musculus, female, liver, 48 hours culture


title: liver_female_2days_mouse-F4


title: liver_female_3days_mouse-F3


title: JKD6009 rnc-HTF RNase III-CLASH replicate 5

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
Library strategy: CLASH
Trimming - BBTrim from BBTools
RNase III-CLASH: Merging paired reads: BBMerge from BBTools
RNase III-CLASH: Calling RNase III binding sites: pyCRAC (Webb et al Genome Biol 2014)
RNase III-CLASH: Calling RNA-RNA interactions: hyb (Travis et al Bioinformatics 2013)
dRNA-seq: Mapping, calling RNA 5' ends: ANNOgesic (Yu, Vogel, Forstner Gigascience, 2018)
Term-seq: Read mapping/alignment: bowtie2
Term-seq: 3' end mapping: bedtools genomecov
Term-seq: Statistical filtering: Custom R scripts inspired by Dar & Sorek Science 2016.
RNA-seq: Read mapping/alignment: bowtie2
RNA-seq: Statistical analysis: DESeq2 (Bioconductor)
Genome_build: NC_017341.1
Genome_build: NZ_LR027876.1
Supplementary_files_format_and_content: BEDGRAPH format, files contain mapped read depth representing RNase III-RNA interaction sites (binding sites)
Supplementary_files_format_and_content: BEDGRAPH, RNA 3' end depth (reverse complement read 5' ends)

organism: Staphylococcus aureus subsp. aureus str. JKD6009

source_name: whole bacterial cells

growth_protocol: Brain-Heart Infusion media, grown at 37C to an OD600 of 3.0

extract_protocol:
UV-crosslinking and RNase-RNA purification performed as per Waters et al EMBO J 2017
Library constructed as per Waters et al EMBO J 2017

tag: growth media

value: Brain-Heart infusion liquid media

tag: antibiotic

value: no antibiotic

value: rnc-HTF

tag: sequencing type

value: RNase III-CLASH

tag: 5' adapter sequence

value: NNNCACTAGC


title: liver_female_3days_mouse-F4


title: liver_female_1days_mouse-F6

description: Gene expression from primary hepatocytes of a female mouse after 24 hours of culture

source_name: Mus musculus, female, liver, 24 hours culture


title: liver_female_2days_mouse-F3


title: liver_female_2days_mouse-F6


title: RNase III-CLASH negative control 1

value: WT

value: NNNAGAGC


title: liver_female_1days_mouse-F2

value: liver


title: JKD6009 Term-seq 2

data_processing:
Trimming - BBTrim from BBTools
RNase III-CLASH: Merging paired reads: BBMerge from BBTools
RNase III-CLASH: Calling RNase III binding sites: pyCRAC (Webb et al Genome Biol 2014)
RNase III-CLASH: Calling RNA-RNA interactions: hyb (Travis et al Bioinformatics 2013)
dRNA-seq: Mapping, calling RNA 5' ends: ANNOgesic (Yu, Vogel, Forstner Gigascience, 2018)
Term-seq: Read mapping/alignment: bowtie2
Term-seq: 3' end mapping: bedtools genomecov
Term-seq: Statistical filtering: Custom R scripts inspired by Dar & Sorek Science 2016.
RNA-seq: Read mapping/alignment: bowtie2
RNA-seq: Statistical analysis: DESeq2 (Bioconductor)
Genome_build: NC_017341.1
Genome_build: NZ_LR027876.1
Supplementary_files_format_and_content: BEDGRAPH format, files contain mapped read depth representing RNase III-RNA interaction sites (binding sites)
Supplementary_files_format_and_content: BEDGRAPH, RNA 3' end depth (reverse complement read 5' ends)

growth_protocol: Muller-Hinton media, grown at 37C to an OD600 of 3.0

extract_protocol:
Total RNA was extracted using a GTC Phenol extraction protocol (Tollervey and Mattaj, EMBO J 1987)
Libraries were constructed at Veritis Biotechnology, Germany using the protocol described by Dar & Sorek Science, 2016

value: Muller-Hinton broth

value: Term-seq


title: liver_female_2days_mouse-F2

value: wild type


title: liver_female_0days_mouse-F3

description: Gene expression from primary hepatocytes of a female mouse before culture

source_name: Mus musculus, female, liver, 0 hours culture


title: RNase III-CLASH negative control 2

value: NNNGTGAGC


title: JKD6009 rnc-HTF RNase III-CLASH replicate 6


title: liver_female_3days_mouse-F7

value: 72 hours


title: liver_female_1days_mouse-F7

value: 24 hours


title: liver_female_0days_mouse-F4

value: 0 hours


title: liver_female_1days_mouse-F4


title: liver_female_0days_mouse-F6


title: liver_female_0days_mouse-F2


title: JKD6009 rnc-HTF RNase III-CLASH replicate 2

value: NNNTCTCTAGC


title: liver_female_3days_mouse-F6

value: female


title: liver_female_1days_mouse-F3


title: JKD6009 rnc-HTF RNase III-CLASH replicate 4

value: Brain-Heart infusion liquid media

value: NNNGCGCAGC


title: JKD6009 rnc-HTF RNase III-CLASH replicate 3

value: no antibiotic

value: rnc-HTF

value: NNNATTAGC


title: liver_female_0days_mouse-F7


title: JKD6009 Term-seq 1

value: WT


title: JKD6009 rnc-HTF RNase III-CLASH replicate 1

value: RNase III-CLASH

value: NNNCACTAGC


title: CI13

city: New York

first: Marina

last: Schernthanner

state: New York

address: 1230 York Ave.

institute: The Rockefeller University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using STAR version 2.5.3a
Reads falling on each gene are counted by HT-Seq
Genome_build: mm10
Supplementary_files_format_and_content: rawcount.txt

source_name: brain

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

treatment_protocol: Chronic social defeat stress

value: hippocampus

value: CTRL Input (CTRLIN)

tag: molecule type

value: translating RNA


title: CI12


title: CI14


title: S10

value: Susceptiable (STR)


title: R8

value: Resilient (RES)


title: S2


title: C9

value: CTRL


title: R5


title: C11


title: C6


title: Control day 15 wound skin replicate 2

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

institute: University of Ulm

description: fpkm_replicates_zero_values_removed_Co_db_db_6mm_wh_day_0_15_GEO_Upload.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Hisat2
Cufflinks was used to assemble the transcripts
Cuffmerge was used to merged all the transcripts
Cuffdiff was for differential expression analysis
Genome_build: mm10 and grch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: total skin

extract_protocol:
Total RNA from skin and macrophages was isolated using Rneasy kit (Qiagen)
rRNA removal was performed either by Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible NEBNext Ultra II Directional RNA Library Preparation kit (NEB).

tag: strain

value: total skin


title: db/db day 15 wound skin replicate 3

value: db/db


title: db/db day 15 wound skin replicate 1


title: R3


title: R7


title: db/db day 0 wound skin replicate 2


title: S4


title: db/db day 0 wound skin replicate 4


title: Control day 0 wound skin replicate 2


title: Control day 0 wound skin replicate 1


title: db/db day 0 wound skin replicate 1


title: Control day 15 wound skin replicate 1


title: db/db day 0 wound skin replicate 3


title: Vac+ZDC_rep_3

city: Saint Louis

first: Shabaana

middle: Abdul

last: Khader

state: Missouri

address: 660 South Euclid Avenue

department: Department of Molecular Microbiology

institute: Washington University in St. Louis

data_processing:
Illumina NextSeq 500
Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC. Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ
Paired end reads were mapped to the mouse genome (mm10) using STAR in a strand specific manner.
Pairwise differential expression was quantified using DESeq2 (version 1.24.0)
Genome_build: GrCm38 (mm10)
Supplementary_files_format_and_content: abundance_fpkm.txt

source_name: Lung CD4 T cells

growth_protocol: CD4 T cells are isolated from differently mice lung

extract_protocol:
Purified mouse lung CD4+ T cells were snap-frozen in RLT buffer, and DNase-treated total RNA was extracted using the Qiagen RNeasy Mini kit (Qiagen).
RNA-seq libraries were generated using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit for sequencing and the Illumina Nextera XT DNA Library preparation kit following the manufacturer’s protocol.

tag: cell

value: CD4 T cell

value: Vaccinated with BCG and received ZDC

tag: infection

value: Mtb


title: Vac_rep_5

value: Vaccinated with BCG


title: Vac+ZDC_rep_4


title: Control day 15 wound skin replicate 3

tag: tissue


title: C1


title: Control day 0 wound skin replicate 3


title: Vac_rep_3


title: Vac_rep_2


title: Vac_rep_1


title: Vac+ZDC_rep_5


title: PND21_XYF_O2_63

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

data_processing:
Reads were mapped to the UCSC mouse reference genome mm10 using HISAT2.
featureCounts was used to evaluate gene expression level as read counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

growth_protocol: This experiment was cinducted in neonatal mice prior to weaning

extract_protocol:
Total RNA from flash frozen lung samples was isolated using the ZYMO mRNA extraction kit. Sample concentration and quality was assayed using Nanodrop-8000 (Thermo Scientific, Wilmington, DE, USA) and further with the Agilent Bioanalyzer. The 260/280 and 260/230 ratios were greater than 1.8. and the RNA Integrity Number (RIN) were between 7-10 and with a range of 1 – 1.5.
RNA samples underwent quality control assessment using the RNA tape on Tapestation 4200 (Agilent) and were quantified with Qubit Fluorometer (Thermo Fisher). The RNA libraries were prepared and sequenced at the University of Houston Seq-N-Edit Core per standard protocols. RNA libraries were prepared with QIAseq Stranded Total RNA library Kit (Qiagen) using 1000 ng input RNA. mRNA was enriched with Oligo-dT probes attached to Pure mRNA beads (Qiagen). RNA was enzymatically fragmented for 15 minutes, reverse transcribed into cDNA, and ligated with Illumina sequencing adaptors. The size selection for libraries was performed using SPRIselect beads (Beckman Coulter) and purity of the libraries was analyzed using the DNA 1000 tape Tapestation 4200 (Agilent). The indexed libraries were pooled and sequenced using NextSeq 500 (Illumina); generating ~20million 2×76 bp paired-end reads per samples.

treatment_protocol: Neonatal mice from the four core genotypes model were exposed to hyperoxia (95% FiO2) and controls were maintained in normoxia

value: Lung

tag: age

value: Postnatal day 21

value: XYF

value: Hyperoxia


title: UnVac_rep_1

value: Unvaccinated


title: PND21_XYF_O2_64


title: Vac+ZDC_rep_2


title: Vac_rep_4


title: UnVac_rep_4


title: db/db day 15 wound skin replicate 2


title: PND21_XYM_O2_60

value: XYM


title: PND21_XXM_O2_55

value: XXM


title: UnVac_rep_3


title: PND21_XXM_O2_53


title: PND21_XXF_O2_52

value: XXF


title: PND21_XYM_O2_59


title: Vac+ZDC_rep_1


title: UnVac_rep_5


title: PND21_XYF_O2_61


title: PND21_XXF_O2_51


title: PND21_XYM_O2_58


title: UnVac_rep_2


title: PND21_XYF_RA_46

value: Room Air


title: PND21_XYF_RA_47


title: PND21_XXF_RA_34

value: Postnatal day 5


title: PND21_XXM_RA_37


title: PND21_XXM_O2_54


title: PND5_XYF_O2_29


title: PND21_XYM_RA_42


title: PND5_XYM_O2_27


title: PND5_XYM_O2_26


title: PND5_XYM_O2_25


title: PND21_XYM_RA_43


title: PND5_XXM_O2_22


title: PND21_XXF_O2_49


title: PND21_XYF_RA_48


title: PND5_XXM_O2_21


title: PND5_XXM_O2_23


title: PND5_XXF_O2_18


title: PND5_XYF_O2_30


title: PND21_XXM_RA_40


title: PND5_XXF_O2_17


title: PND21_XXF_RA_35


title: PND5_XYF_RA_14


title: PND21_XYM_RA_41


title: PND5_XYF_RA_15


title: PND21_XXM_RA_39


title: PND5_XXF_O2_19


title: PND21_XXF_RA_36


title: PND5_XYF_O2_31


title: PND5_XXM_RA_07


title: PND5_XYF_RA_13


title: PND5_XXF_RA_02


title: PND5_XYM_RA_11


title: Patient2U_GEX

city: Stanford

first: Emma

last: Tapp

email: etapp@stanford.edu, dgate@stanford.edu

state: California (CA)

address: 290 Jane Stanford Way

department: Neurology

institute: Stanford University

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped aligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples were merged into one seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: folders for each sample containing raw and filtered expression matrix, cellbarcodes, and genes

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD biosciences). RNA was extracted according to the 10x v2 5' Expression library kit
Libraries were prepared according to the 10x v2 5' Kit

tag: cell type

value: immune cells

tag: diagnosis

value: PD


title: Patient2S_GEX


title: PND5_XYM_RA_09


title: PND5_XYM_RA_10


title: Patient2U_TCR

data_processing:
Library strategy: single cell TCR-seq
Real-Time Analysis (RTA) software called RTA2 used for basecalling
Base call fles were demultiplexed using cellranger mkfastq version 3.0.2
TCR-seq reads were mapped aligned to the GRCh38 2.0.0 vdj genome assembly available from 10X Genomics using cellranger count version 3.0.2
T cell receptor sequences were generated using cellranger vdj version 3.0.2
Genome_build: GRCh38 vdj 2.0.0
Supplementary_files_format_and_content: two files for each sample; one file that indicates clonotypes and one file that has th sequence for each cell barcode

source_name: peripheral blood mononuclear cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD biosciences). RNA was extracted according to the 10x v2 5' Expression library kit
Libraries were prepared according to the 10x v2 5'V(D)J Kit

value: T cells


title: PND5_XXF_RA_01


title: PND5_XXF_RA_03


title: PND5_XXM_RA_06


title: PND5_XXM_RA_05


title: Patient1S_GEX


title: Patient1U_GEX


title: SNU16_5mC_Input

city: Singapore

first: TAOTAO

last: SHENG

address: 21 Lower Kent Ridge Rd, Singapore

country: Singapore

institute: NUS

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.7.0) ‘mem’ algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
Genome_build: hg19
Supplementary_files_format_and_content: Sequence coverage was computed using the R package “MEDIPS” (version 1.20.1) with a 50 bp bin size and read length extension to 200 bp. Peak density within a specific region was calculated by counting the total number of mapping reads normalized by the library size and the region length, an equivalence to the metric RPKM.
Supplementary_files_format_and_content: bigwig files

source_name: Gastric Cancer Line

extract_protocol:
For ChIP-seq, 1 million fresh harvested cells were fixed in 1% formaldehyde/medium buffer for 10 minutes (min) at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Fixed cells were washed 3 times with TBSE buffer, and centrifuged (5,000 r.p.m., 5 min). Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIP was performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam). For MeDIP-seq, DNA was sonicated using COVARIS S2 and peak fragment distribution between 100-500bp was verified on an Agilent Bioanalyzer (Agilent Technologies) using the DNA1000 chip.  Fragmented DNA was end-repaired, dA-tailed and adapter ligated using NEBNext® DNA Library Prep Master Mix Set for Illumina (E6040). Samples were then spiked with control DNAs that were unmethylated, methylated and hydroxymethylated (Diagenode C02040010) as a quality control measure.  For each sample, input DNA that was not exposed to the primary antibody was included.  Adapter-ligated DNA was subjected to immunoprecipitation with a primary monoclonal antibody against 5-methyl cytosine (Diagenode C15200081)
For ChIP-seq, 30ng of amplified DNA was used for each sequencing library preparation (New England Biolabs). 8 libraries were multiplexed (New England Biolabs) and sequenced on 2 lanes of a Hiseq2500 sequencer (Illumina) to an average depth of 20-30 million reads per library. For MeDIP-seq, Immunoprecipitated samples were amplified using Phusion® High-Fidelity DNA Polymerase (M0530) and NEBNext® Multiplex Oligos for Illumina® (E7335) for 10 cycles. Amplified libraries were run on the Agilent Bioanalyzer using the High sensitivity DNA kit prior to Illumina sequencing using a single-end 100 base pair configuration.

value: Gastric Cancer Line

tag: chip antibody

value: Input

tag: cell line


title: CHG210

data_processing:
Sequencing reads were trimmed (10bp from front and back) and mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.7.0) ‘mem’ algorithm.
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]
We filtered reads based on their mapping quality (MAPQ) and used uniquely mapped reads to perform peak calling using CCAT v3.0 [local FDR < 0.05]. ChIP enrichments for H3K27me3 and 185 H3K36me3 relative to input libraries were detected using macs2 (-q 0.05, --broad).
Genome_build: hg19
Supplementary_files_format_and_content: Sequence coverage was computed using the R package “MEDIPS” (version 1.20.1) with a 50 bp bin size and read length extension to 200 bp. Peak density within a specific region was calculated by counting the total number of mapping reads normalized by the library size and the region length, an equivalence to the metric RPKM.
Supplementary_files_format_and_content: bigwig files


title: CHG213


title: Patient1S_TCR


title: Patient1U_TCR


title: OCUM1_5mC


title: CHG234


title: CHG237


title: Patient2S_TCR


title: OCUM1_5mC_Input


title: SNU16_5mC


title: AKR02_T02

city: Bunkyo-ku

first: Yoichi

last: Kasahara

state: Tokyo

address: 1-1-1 Yayoi

department: Graduate school of Agricultural and life science

institute: Taste science

data_processing:
Sequence data were generated on a Genome analyzer IIx (Illumina).
Per sample, 3 × 107 reads (75 bp, single-ended) were obtained, and mapped using Bowtie 0.12.7 on the mouse genome (data assembly Jul. 2007, NCBI37/mm9)
The expression of protein coding genes was analysed using ERANGE software to obtain reads per kilobase (exon model) per million mapped reads (RPKM) values.
The steps after RNA extraction were carried out by Takara Bio, Shiga Japan.
Genome_build: data assembly Jul. 2007, NCBI37/mm9
Supplementary_files_format_and_content: files include RPKM values for each Sample .
Supplementary_files_format_and_content: The csv file for normalized RPKM value about every gene and sample

source_name: The epithelium without papillae of tongue

growth_protocol: Mice were fed a normal chow diet and housed at a constant temperature of 22 ± 1 °C under a 12-h light-dark cycle (lights on at 8 am.).

extract_protocol:
Total RNA was extracted from the CvP or Epi of C57BL/6J mice (n = 20 or more) and pooled for each (CLEA, Tokyo, Japan).
Poly (A)+ RNA was engineered into the DNA library using a TruSeq RNA sample preparation kit (Illumina, CA, USA).

value: epithelium without papillae of tongue

tag: developmental stage

value: 12-30 weeks old

tag: gender

value: male


title: AKR02_T01

source_name: The circumvallate papillae of tongue

value: circumvallate papillae of tongue


title: CHG226


title: CHG367


title: CHP-00029


title: CHP-00028


title: CHG365


title: CHG368


title: CHP-00024


title: CHP-00021

source_name: Gastric Normal Line

value: Gastric Normal Line


title: CHP-00020


title: CHP-00019


title: GCC046


title: GCC048


title: GCC045


title: GCC047


title: CHP-00027


title: CHG370


title: CHP-00026


title: CHP-00025


title: CHP-00016

value: SCH


title: CHP-00015


title: CHP-00023


title: CHP-00022


title: CHP-00011


title: YCC11_H3K4me3


title: CHP-00017


title: YCC11_Input


title: CHP-00018


title: CHP-00014


title: CHP-00012


title: CHP-00013


title: CHP-00010


title: CHG229


title: CHP-00009


title: SNU484_H3K4me1


title: YCC10_Input


title: YCC10_H3K4me3


title: SNU719_Input


title: HS746T_H3K4me3


title: SNU484_Input


title: SNU484_H3K4me3


title: SNU719_H3K4me3


title: NUGC4_H3K4me1


title: NUGC4_H3K4me3


title: NUGC4_H3K27ac


title: HGC27_Input


title: HsInt_H3K27ac

value: HsInt


title: HGC27_H3K27ac


title: NUGC4_Input


title: AGS_H3K27ac

value: AGS


title: LMSU_H3K4me3

value: LMSU


title: Ist1_H3K4me1


title: LMSU_Input


title: HS746T_H3K27ac


title: AGS_Input


title: LMSU_H3K4me1


title: HsInt_Input


title: HS746T_H3K4me1


title: Hs738_Input


title: HGC27_H3K4me1


title: HGC27_H3K4me3


title: Hs738_H3K4me3


title: HS746T_Input


title: AGS_H3K4me1


title: AGS_H3K4me3


title: fibroblasts_TGFβ_48h_rep1

first: Chang

last: Liu

address: 1 Xian Nong Tan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Gene expression data from TGFβ-stimulated primary lung fibroblasts
TGFB-1_(MoGene-2_0-st).rma-gene-full-Signal

hyb_protocol: The sample microarray hybridization and washing were performed based on the manufacturer's standard protocols.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix 7G).

data_processing: Array signal intensities were analyzed with Expression Console Software(version 1.4.1, Affymetrix). Raw data probes were normalized using robust multiarray analysis (RMA) for the background correction and quantile algorithm.

source_name: Primary lung fibroblasts, TGFβ, 48h

label_protocol: Total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Then 2nd cycle cDNAs were synthesized from cRNAs followed by fragmentation and biotin labeling. The sample labeling were performed on the manufacturer's standard protocols.

growth_protocol: Primary lung fibroblasts were cultured in DMEM medium with 10% FBS at 37℃ in 5% CO2 incubator.

extract_protocol: Total RNA was extracted using trizol according to the manufacturer's instructions.

treatment_protocol: Cells were incubated with 5ng/ml TGFβ or 50ng/ml CCL1 for 48 hours in incubator. Then the samples were collected in trizol for RNA extraction.

tag: tissue-derived primary cells

value: lung fibroblasts

tag: treatment

value: TGFβ 48h


title: fibroblasts_CCL1_48h_rep2

description:
Gene expression data from CCL1-stimulated primary lung fibroblasts
ccl1-2_(MoGene-2_0-st).rma-gene-full-Signal

source_name: Primary lung fibroblasts, CCL1, 48h

value: CCL1 48h


title: fibroblasts_CCL1_48h_rep3

description:
Gene expression data from CCL1-stimulated primary lung fibroblasts
ccl1-3_(MoGene-2_0-st).rma-gene-full-Signal


title: fibroblasts_untreated_rep1

description:
Gene expression data from untreated primary lung fibroblasts
con-1_(MoGene-2_0-st).rma-gene-full-Signal

source_name: Primary lung fibroblasts, untreated


title: fibroblasts_CCL1_48h_rep1

description:
Gene expression data from CCL1-stimulated primary lung fibroblasts
ccl1-1_(MoGene-2_0-st).rma-gene-full-Signal


title: smoker ground 33  (epithelial)

city: Oklahoma City

first: Susan

middle: Kasko

last: Munster

state: OK

address: 6500 S. MacArthur Blvd.

department: Office of Aerospace Medicine

institute: Federal Aviation Admininistration

hyb_protocol: All samples were hybridized using GeneChip® Hybridization, Wash, and Stain kit onto GeneChip® Human Transcript Array 2.0 microarrays

scan_protocol: Affymetrix 7G GeneChip® Scanner 3000

data_processing:
QC was performed in R using arrayQualityMetrics package.  Samples were normalized using oligo and pd.hta.2.0 packages in R. All non-core probesets were removed using genefilter in R. Differential expression analysis was carried out using the limma package in R
HTA-2_0.r3.pgf
HTA-2_0.na36.hg19.transcript.csv

source_name: bronchial epithelium derived RNA

label_protocol: All samples were fragmented and biotin labeled using WT Terminal Label Kit

extract_protocol: Bronchial Epithelial Cells were extracted with Qiagen RNeasy mini kit using a QIAcube® and samples were amplified using GeneChip® WT PLUS Reagent Kit.

treatment_protocol: Bronchial Epithelial cell samples collected during bronchial lavage, collected by centrifuge, suspended in Qiazol

value: female

tag: altitude

value: ground

tag: smoking status

value: smoker

tag: timepoint of collection

value: bronchial epithelial cells


title: fibroblasts_TGFβ_48h_rep2

description:
Gene expression data from TGFβ-stimulated primary lung fibroblasts
TGFB-2_(MoGene-2_0-st).rma-gene-full-Signal


title: smoker ground 20  (epithelial)


title: smoker ground 04  (epithelial)


title: smoker ground 10  (epithelial)


title: fibroblasts_untreated_rep3

description:
Gene expression data from untreated primary lung fibroblasts
con-3_(MoGene-2_0-st).rma-gene-full-Signal


title: smoker ground 28  (epithelial)


title: smoker ground 30  (epithelial)


title: smoker ground 26  (epithelial)


title: smoker flight 30  (epithelial)

value: flight


title: smoker flight 20  (epithelial)


title: fibroblasts_TGFβ_48h_rep3

description:
Gene expression data from TGFβ-stimulated primary lung fibroblasts
TGFB-3_(MoGene-2_0-st).rma-gene-full-Signal


title: nonsmoker ground 25  (epithelial)

value: nonsmoker


title: nonsmoker ground 27  (epithelial)


title: smoker ground 18  (epithelial)


title: smoker ground 15  (epithelial)


title: smoker flight 18  (epithelial)


title: smoker flight 23  (epithelial)


title: smoker flight 26  (epithelial)


title: smoker flight 28  (epithelial)


title: smoker flight 10  (epithelial)


title: smoker ground 23  (epithelial)


title: smoker flight 33  (epithelial)


title: smoker flight 15  (epithelial)


title: nonsmoker ground 32  (epithelial)


title: nonsmoker ground 24  (epithelial)


title: nonsmoker ground 19  (epithelial)


title: fibroblasts_untreated_rep2

description:
Gene expression data from untreated primary lung fibroblasts
con-2_(MoGene-2_0-st).rma-gene-full-Signal


title: smoker flight 04  (epithelial)


title: nonsmoker ground 16  (epithelial)


title: nonsmoker ground 09  (epithelial)


title: nonsmoker ground 01  (epithelial)


title: nonsmoker ground 07  (epithelial)


title: nonsmoker flight 24  (epithelial)


title: nonsmoker flight 25  (epithelial)


title: nonsmoker flight 19  (epithelial)


title: nonsmoker flight 27  (epithelial)


title: nonsmoker flight 16  (epithelial)


title: nonsmoker flight 07  (epithelial)


title: nonsmoker flight 21  (epithelial)


title: nonsmoker flight 09  (epithelial)


title: smoker ground 33 time 4 (blood)

source_name: blood-derived RNA

extract_protocol: Qiagen Blood RNA kit IVD using a QIAcube®, samples were amplified using GeneChip® WT PLUS Reagent Kit.

treatment_protocol: Samples collected in Paxgene® blood RNA tubes

value: blood


title: nonsmoker flight 32  (epithelial)

value: male


title: smoker ground 33 time 3 (blood)


title: nonsmoker flight 01  (epithelial)


title: nonsmoker ground 21  (epithelial)


title: smoker ground 33 time 1 (blood)


title: smoker ground 28 time 4 (blood)


title: smoker ground 30 time 4 (blood)


title: smoker ground 33 time 2 (blood)


title: smoker ground 28 time 3 (blood)


title: smoker ground 30 time 2 (blood)


title: smoker ground 26 time 4 (blood)


title: smoker ground 28 time 1 (blood)


title: smoker ground 30 time 1 (blood)


title: smoker ground 26 time 2 (blood)


title: smoker ground 28 time 2 (blood)


title: smoker ground 23 time 4 (blood)


title: smoker ground 26 time 3 (blood)


title: smoker ground 20 time 3 (blood)


title: smoker ground 26 time 1 (blood)


title: smoker ground 23 time 3 (blood)


title: smoker ground 20 time 4 (blood)


title: smoker ground 20 time 2 (blood)


title: smoker ground 23 time 2 (blood)


title: smoker ground 20 time 1 (blood)


title: smoker ground 23 time 1 (blood)


title: smoker ground 18 time 3 (blood)


title: smoker ground 15 time 4 (blood)


title: smoker ground 15 time 3 (blood)


title: smoker ground 18 time 1 (blood)


title: smoker ground 10 time 4 (blood)


title: smoker ground 15 time 1 (blood)


title: smoker ground 18 time 4 (blood)


title: smoker ground 10 time 3 (blood)


title: smoker ground 04 time 4 (blood)


title: smoker ground 04 time 3 (blood)


title: smoker ground 10 time 1 (blood)


title: smoker flight 30 time 4 (blood)


title: smoker ground 04 time 1 (blood)


title: smoker ground 04 time 2 (blood)


title: smoker ground 10 time 2 (blood)


title: smoker ground 18 time 2 (blood)


title: smoker flight 33 time 4 (blood)


title: smoker ground 15 time 2 (blood)


title: smoker flight 33 time 3 (blood)


title: smoker flight 28 time 4 (blood)


title: smoker flight 28 time 1 (blood)


title: smoker flight 30 time 3 (blood)


title: smoker flight 33 time 2 (blood)


title: smoker flight 28 time 3 (blood)


title: smoker flight 30 time 1 (blood)


title: smoker flight 30 time 2 (blood)


title: smoker flight 28 time 2 (blood)


title: smoker flight 23 time 3 (blood)


title: smoker flight 33 time 1 (blood)


title: smoker flight 26 time 4 (blood)


title: smoker flight 20 time 1 (blood)


title: smoker flight 23 time 1 (blood)


title: smoker flight 23 time 2 (blood)


title: smoker flight 26 time 1 (blood)


title: smoker flight 26 time 3 (blood)


title: smoker flight 20 time 2 (blood)


title: smoker flight 18 time 4 (blood)


title: smoker flight 18 time 3 (blood)


title: smoker flight 20 time 4 (blood)


title: smoker flight 20 time 3 (blood)


title: smoker flight 10 time 3 (blood)


title: smoker flight 18 time 2 (blood)


title: smoker flight 15 time 2 (blood)


title: smoker flight 15 time 3 (blood)


title: smoker flight 18 time 1 (blood)


title: smoker flight 04 time 3 (blood)


title: nonsmoker ground 32 time 4 (blood)


title: nonsmoker ground 32 time 1 (blood)


title: nonsmoker ground 27 time 4 (blood)


title: nonsmoker ground 32 time 2 (blood)


title: smoker flight 10 time 2 (blood)


title: nonsmoker ground 27 time 1 (blood)


title: nonsmoker ground 27 time 3 (blood)


title: smoker flight 15 time 1 (blood)


title: smoker flight 04 time 2 (blood)


title: nonsmoker ground 27 time 2 (blood)


title: smoker flight 04 time 4 (blood)


title: smoker flight 10 time 1 (blood)


title: smoker flight 04 time 1 (blood)


title: nonsmoker ground 25 time 3 (blood)


title: nonsmoker ground 32 time 3 (blood)


title: nonsmoker ground 25 time 2 (blood)


title: smoker flight 10 time 4 (blood)


title: nonsmoker ground 21 time 4 (blood)


title: nonsmoker ground 24 time 1 (blood)


title: nonsmoker ground 25 time 4 (blood)


title: nonsmoker ground 25 time 1 (blood)


title: nonsmoker ground 24 time 4 (blood)


title: nonsmoker ground 21 time 1 (blood)


title: nonsmoker ground 21 time 3 (blood)


title: smoker flight 26 time 2 (blood)


title: nonsmoker ground 19 time 2 (blood)


title: nonsmoker ground 24 time 2 (blood)


title: nonsmoker ground 01 time 1 (blood)


title: nonsmoker ground 21 time 2 (blood)


title: nonsmoker flight 32 time 2 (blood)


title: nonsmoker ground 01 time 4 (blood)


title: nonsmoker flight 32 time 4 (blood)


title: nonsmoker flight 27 time 3 (blood)


title: nonsmoker ground 09 time 3 (blood)


title: nonsmoker ground 16 time 3 (blood)


title: nonsmoker ground 01 time 2 (blood)


title: nonsmoker ground 07 time 3 (blood)


title: nonsmoker ground 19 time 4 (blood)


title: nonsmoker ground 09 time 2 (blood)


title: nonsmoker ground 16 time 2 (blood)


title: nonsmoker ground 19 time 3 (blood)


title: nonsmoker flight 32 time 3 (blood)


title: nonsmoker flight 27 time 2 (blood)


title: nonsmoker flight 25 time 4 (blood)


title: nonsmoker flight 24 time 3 (blood)


title: nonsmoker ground 19 time 1 (blood)


title: nonsmoker ground 24 time 3 (blood)


title: nonsmoker flight 32 time 1 (blood)


title: nonsmoker flight 25 time 1 (blood)


title: nonsmoker flight 21 time 4 (blood)


title: nonsmoker ground 09 time 1 (blood)


title: nonsmoker ground 16 time 1 (blood)


title: nonsmoker flight 27 time 4 (blood)


title: nonsmoker flight 24 time 2 (blood)


title: nonsmoker flight 25 time 2 (blood)


title: nonsmoker flight 27 time 1 (blood)


title: nonsmoker flight 21 time 1 (blood)


title: nonsmoker flight 19 time 4 (blood)


title: nonsmoker flight 19 time 2 (blood)


title: nonsmoker ground 07 time 1 (blood)


title: nonsmoker flight 19 time 1 (blood)


title: nonsmoker flight 25 time 3 (blood)


title: nonsmoker ground 07 time 2 (blood)


title: nonsmoker flight 21 time 3 (blood)


title: nonsmoker flight 16 time 2 (blood)


title: nonsmoker flight 24 time 4 (blood)


title: nonsmoker flight 19 time 3 (blood)


title: nonsmoker flight 16 time 1 (blood)


title: nonsmoker flight 16 time 4 (blood)


title: nonsmoker flight 24 time 1 (blood)


title: nonsmoker ground 16 time 4 (blood)


title: nonsmoker flight 16 time 3 (blood)


title: nonsmoker flight 09 time 3 (blood)


title: nonsmoker flight 21 time 2 (blood)


title: nonsmoker flight 09 time 1 (blood)


title: nonsmoker flight 09 time 2 (blood)


title: nonsmoker flight 07 time 1 (blood)


title: nonsmoker flight 01 time 2 (blood)


title: nonsmoker flight 07 time 3 (blood)


title: nonsmoker flight 01 time 3 (blood)


title: nonsmoker flight 01 time 4 (blood)


title: nonsmoker flight 01 time 1 (blood)


title: nonsmoker flight 07 time 2 (blood)


title: smoker ground 20  (alveolar)

source_name: bronchio-alveolar derived RNA

extract_protocol: Bronchio-Alveolar Cells were extracted with Qiagen RNeasy mini kit using a QIAcube® and samples were amplified using GeneChip® WT PLUS Reagent Kit.

treatment_protocol: Bronchio-Alveolar cell samples collected during bronchial lavage, collected by centrifuge, suspended in Qiazol

value: bronchio-alveolar cells


title: smoker ground 04  (alveolar)


title: smoker ground 33  (alveolar)


title: smoker flight 28  (alveolar)


title: smoker ground 26  (alveolar)


title: smoker flight 23  (alveolar)


title: smoker flight 26  (alveolar)


title: smoker ground 23  (alveolar)


title: smoker flight 15  (alveolar)


title: nonsmoker flight 07 time 4 (blood)


title: smoker ground 18  (alveolar)


title: smoker flight 10  (alveolar)


title: smoker ground 15  (alveolar)


title: smoker flight 33  (alveolar)


title: smoker ground 28  (alveolar)


title: smoker ground 10  (alveolar)


title: smoker ground 30  (alveolar)


title: smoker flight 18  (alveolar)


title: smoker flight 30  (alveolar)


title: GMP WT 3 [Cohort2]

first: Bongsoo

last: Park

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: RNA-sequencing

data_processing:
cutadapt
STAR alignment (RNA-seq)
featureCount, gene-level extraction (RNA-seq)
Genome_build: mm10
Supplementary_files_format_and_content: text file

source_name: Common myeloid progenitor

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard total RNA-seq kit v2

value: Control


title: GMP NR treated 4 [Cohort2]

description: RNA-sequencing

value: Nicotinamide reboside


title: GMP NR treated 1 [Cohort2]

description: RNA-sequencing


title: GMP WT 4 [Cohort2]

description: RNA-sequencing


title: GMP WT 1 [Cohort2]

description: RNA-sequencing


title: CLP NR treated 4 [Cohort2]

description: RNA-sequencing

source_name: Common lymphoid progenitor


title: smoker flight 20  (alveolar)


title: smoker flight 04  (alveolar)


title: nonsmoker ground 09  (alveolar)


title: nonsmoker ground 25  (alveolar)


title: GMP NR treated 3 [Cohort2]

description: RNA-sequencing


title: nonsmoker flight 32  (alveolar)


title: nonsmoker flight 27  (alveolar)


title: nonsmoker flight 16  (alveolar)


title: nonsmoker flight 25  (alveolar)


title: nonsmoker ground 24  (alveolar)


title: nonsmoker flight 07  (alveolar)


title: nonsmoker flight 09  (alveolar)


title: nonsmoker ground 01  (alveolar)


title: nonsmoker flight 01  (alveolar)


title: nonsmoker ground 21  (alveolar)


title: nonsmoker flight 24  (alveolar)


title: nonsmoker ground 16  (alveolar)


title: nonsmoker ground 32  (alveolar)


title: CLP NR treated 3 [Cohort2]

description: RNA-sequencing


title: CLP NR treated 1 [Cohort2]

description: RNA-sequencing


title: HSC NR treated 4 [Cohort2]

description: RNA-sequencing

source_name: Hematopoietic stem cell


title: GMP WT 2 [Cohort2]

description: RNA-sequencing


title: nonsmoker flight 21  (alveolar)


title: nonsmoker ground 27  (alveolar)


title: HSC NR treated 3 [Cohort2]

description: RNA-sequencing


title: nonsmoker flight 19  (alveolar)


title: HSC NR treated 2 [Cohort2]

description: RNA-sequencing


title: CLP WT 1 [Cohort2]

description: RNA-sequencing


title: HSC NR treated 1 [Cohort2]

description: RNA-sequencing


title: CLP WT 4 [Cohort2]

description: RNA-sequencing


title: HSC NR-RC2 [Cohort1]

data_processing:
cutadapt
STAR alignment (RNA-seq)
Genome_build: mm10
Supplementary_files_format_and_content: featureCount, gene-level extraction (RNA-seq)

value: Nicotinamide reboside, reversal

value: Hematopoietic stem cell


title: HSC WT 1 [Cohort1]


title: nonsmoker ground 07  (alveolar)


title: CLP WT 3 [Cohort2]

description: RNA-sequencing


title: CLP NR treated 2 [Cohort2]

description: RNA-sequencing


title: HSC WT 4 [Cohort2]

description: RNA-sequencing


title: HSC WT 3 [Cohort2]

description: RNA-sequencing


title: HSC WT 2 [Cohort2]

description: RNA-sequencing


title: HSC NR-RC3 [Cohort1]


title: HSC NR treated 3 [Cohort1]


title: HSC NR treated 2 [Cohort1]


title: HSC NR-RC1 [Cohort1]


title: H460 414

city: Halifax

first: Paola

last: Marignani

state: Nova Scotia

address: 5850 College Street, Tupper Medical Building

department: Biochemistry & Molecular Biology

country: Canada

institute: Dalhousie University

data_processing:
Basecalling performed using Real-Time Analysis (RTA) version 2.0
Fluidigm mRNA Sequencing High Throughput Demultiplexer Script (https://www.fluidigm.com/software) and Geneious Prime 2019.2.1 (https://www.geneious.com) were  used to demultiplex.
BBDuk Trimmer (a part of Bestus Bioinformatics Tools; RRID:SCR_016968) was used for quality trimming.
HISAT2 (RRID:SCR_015530) was used for read mapping to align processed reads to human reference genome (GRCh38.p13; NIH).
FeatureCounts (A part of Subread; RRID:SCR_009803) was used to count aligned reads per gene.
Genome_build: Human reference genome (GRCh38.p13; NIH)
Supplementary_files_format_and_content: Fastq containing 3'-end enriched scRNA-seq reads at single-end read

source_name: NSCLC

growth_protocol: Upon purchase, cells were stored at -80ºC freezer and then thawed just before directly loading to C1 HT mRNA-seq IFCs.

extract_protocol:
Individual cells were captured in chambers of Fluidigm HT mRNA-seq IFC. Total RNA extraction and preamplification of synthesized cDNAs were performed in Fluidigm C1 systems using the script of 'mRNA Seq HT:RT & Amp (1912x)’.
A total of 1,600 3'-end enriched scRNA-seq libraires (400 libraries per cell line) were constructed using Nextera XT index Kit v2 Set A/B and Nextera XT DNA library preparation kits.
3'-end enriched scRNA-seq using Fluidigm C1 system

treatment_protocol: Untreated

tag: tumour type

value: Lung adenocarcinoma

value: Epithelial


title: H460 421


title: H460 411


title: H460 412


title: H460 418


title: H460 416


title: H460 417


title: H460 423


title: H460 413


title: H460 419


title: HSC NR treated 4 [Cohort1]


title: HSC NR treated 1 [Cohort1]


title: H460 406


title: H460 422


title: H460 424


title: H460 425


title: HSC WT 1 [Cohort2]

description: RNA-sequencing


title: HSC WT 2 [Cohort1]


title: H460 415


title: H460 420


title: H460 408


title: H460 410


title: H460 404


title: H460 405


title: H460 407


title: H460 409


title: H460 403


title: H460 399


title: H460 398


title: H460 401


title: H460 400


title: H460 394


title: H460 392


title: H460 393


title: H460 402


title: H460 395


title: H460 397


title: H1299 1098


title: H1299 1102


title: H1299 1100


title: H1299 1099


title: H1299 1096


title: H1299 1095


title: H460 396


title: H1299 1101


title: H1299 1094


title: H1299 1093


title: H1299 1090


title: H1299 1092


title: H1299 1087


title: H1299 1091


title: H1299 1088


title: H1299 1089


title: GMP NR treated 2 [Cohort2]

description: RNA-sequencing


title: H1299 1086


title: H1299 1097


title: H1299 1085


title: H1299 1084


title: H1299 1082


title: H1299 1081


title: H1299 1083


title: H1299 1080


title: H1299 1077


title: H1299 1078


title: H1299 1079


title: H1299 1076


title: H1299 1074


title: H1299 1075


title: H1299 1073


title: H1299 1068


title: H1299 1070


title: H1299 1072


title: H1299 1066


title: H1299 1071


title: H1299 1069


title: H1299 1067


title: H1299 1065


title: H1299 1064


title: H1299 1063


title: H1299 1062


title: H1299 1061


title: H1299 1060


title: H1299 1059


title: H1299 1057


title: H1299 1056


title: H1299 1052


title: H1299 1053


title: H1299 1047


title: H1299 1051


title: H1299 1049


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title: H1299 1046


title: H1299 1054


title: H1299 1043


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title: H1299 1038


title: H1299 1036


title: H1299 1033


title: H1299 1034


title: H1299 1037


title: H1299 1032


title: H1299 1035


title: H1299 1055


title: CLP WT 2 [Cohort2]

description: RNA-sequencing


title: H1299 1058


title: H1299 1031


title: H1299 1029


title: H1299 1050


title: H1299 1030


title: H1299 1026


title: H1299 1017


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title: Calu 1451


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