title: 0.3 [140]

description: Sample name: 140

tag: treatment


title: Patient 10

status: Public on Mar 31 2018

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: 2565 miRNAs were spotted on each array.

hyb_protocol: Hybridized onto a human miRNA Oligo chip, version 21 (Toray, Tokyo).

scan_protocol: 3D-Gene 3000 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 quantile normalization (Bolstad BM, et al. Bioinformatics 2003; 19: 185-193). In short, the raw data of each spot was processed by substitution with a mean+2SD of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Any miRNAs which showed values equal to 0 or less than 0 after the substitution above were deleted, where 2555 miRNAs were narrowed down to 758 miRNAs. The quantile normalization was performed further on the data according to the literature above written by Bolstad, et al.

molecule: total RNA

organism: Homo sapiens

source_name: serum

label_protocol: Extracted total RNA was labeled with Hy3 using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy Serum/Plasma kit (Qiagen).

tag: diagnosis

value: HBeAg negative chronic hepatitis B

tag: tissue

value: serum

tag: peg-ifn dose (μg/week)

tag: weeks of peg-ifn treatment


title: 0.7 [37]

city: Aarhus C

first: Anders

middle: Riegels

last: Knudsen

address: Nørrebrogade 44, building 1c, LVN-research

department: Department of Surgery, Section for upper GI surgery

country: Denmark

institute: Aarhus University Hospital

description: Sample name: 37

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Rat Gene 2.0 ST Array (Thermo Fischer Scientific, Waltham, MA, USA) at 45C and 60 rpm for 16 hours.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7 G.

data_processing: Quality control of the array data was performed in Expression Console software (Affymetrix) with default RMA Gene analysis settings. Secondary analysis was performed in GeneSpring 13.0.

label: biotin

organism: Rattus norvegicus

source_name: Liver, 70% partial hepatectomy

label_protocol: Ambion® WT Expression Kit (Thermo Fischer Scientific, Waltham, MA, USA) was used for labelling 100 ng isolated RNA. Samples were hybridized to the Affymetrix GeneChip® Rat Gene 2.0 ST Array (Thermo Fischer Scientific, Waltham, MA, USA) at 45 °C and 60 rpm for 16 hours.

growth_protocol: Liver tissue removed 24 hours liver resection.

extract_protocol: Each cryopreserved liver tissue was cut in a 2 x 2 mm piece and immediately transferred into 5 mL polypropylene tubes (BD, Franklin Lakes, New Jersey, USA) containing 200 μL chilled homogenization solution and 4 μL lysis buffer (Maxwell 16 LEV simply RNA; Promega, Fitchburg, MA, USA). While kept on ice, each tube was thoroughly mixed using a homogenizer before adding 200 μL lysis buffer (Maxwell 16 LEV simply RNA; Promega, Fitchburg, MA, USA) and vortexed at a maximum speed for 15 seconds, before further processing according to the manufacturer's protocol. The isolated RNA was stored at 80°C.

treatment_protocol: Liver tissue was snap frozen in liquid nitrogen and stored at -80 Celsius until analysis.

tag: strain/background

value: Wistar

tag: genotype/variation

value: Wildtype

value: Liver

value: 70% partial hepatectomy


title: 0.7 [97]

description: Sample name: 97


title: 0.7 [139]

description: Sample name: 139


title: 0.3 [98]

description: Sample name: 98

source_name: Liver, 30% partial hepatectomy

value: 30% partial hepatectomy


title: Dusp9+/- 2 (24h)_b

type: SRA

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: CCGTCC | Sample 16 Dusp9+/- 2-2 (24h)

library_source: transcriptomic

data_processing:
Reads from all datasets (Dusp9+/-_ESCs, WT_XX_ESCs and WT_XY_ESCs) were aligned to mouse reference genome GRCm38/mm10 using STAR (v2.5.3a) with default parameters followed with conversion to BAM sorted by coordinate.
The featureCounts function from the R Bioconductor package “Rsubread” was used to assign mapped reads to genomic features. For downstream analyses, only the genes with CPM value (count-per-milion) higher than 0.5 in at least two libraries were kept.
A read count matrix was used as an input for differential expression analysis using the edgeR quasi-likelihood pipeline in R (Chen et al. 2016). The resulting p values were corrected for multiple testing with the Benjamini–Hochberg method to control the FDR. Genes were considered significantly differentially expressed on the basis of both FDR < 0.05 and fold difference = or greater than 1.5, a criteria necessary to assess small differences in gene expression between male and female ESCs.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with matrix for all samples with CPM values normalized by the library size

organism: Mus musculus musculus x Mus musculus castaneus

source_name: Embryonic Stem Cells

growth_protocol: ESCs (Wild type female and male ESCs, two independent female Dusp9+/- ESC lines) were grown in serum/LIF condition in the absence of feeders. Samples were collected at 0h and 24h of LIF withdrawal (LIF withdrawal was performed in mouse ESC media with 10% serum and without LIF) at a cell density of 4*10ˆ4 cells/cm2. Cells were harvested at 0h and 24h of LIF withdrawal.

extract_protocol:
Total RNA was isolated using TRIzol reagent following the manufacturer’s protocol.
4 µg of total RNA was used for library preparation with the KAPA stranded mRNA Library prep kit for Illumina platform (KAPA Biosystems). Library concentrations were quantified with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~20 million reads (range 16–23 million) of 36bp in length per sample.

tag: gender

value: female

tag: differentiation time

tag: cell type

value: ESC

tag: genotype


title: Patient 22

description: 2565 miRNAs were spotted on each array.


title: Patient 9

description: 2565 miRNAs were spotted on each array.


title: Patient 8

description: 2565 miRNAs were spotted on each array.


title: Patient 7

description: 2565 miRNAs were spotted on each array.


title: Patient 4

description: 2565 miRNAs were spotted on each array.


title: Patient 5

description: 2565 miRNAs were spotted on each array.


title: Patient 19

description: 2565 miRNAs were spotted on each array.


title: Patient 18

description: 2565 miRNAs were spotted on each array.


title: Patient 11

description: 2565 miRNAs were spotted on each array.


title: 0.9 [39]

description: Sample name: 39

source_name: Liver, 90% partial hepatectomy

value: 90% partial hepatectomy


title: Patient 6

description: 2565 miRNAs were spotted on each array.


title: 0.3 [99]

description: Sample name: 99


title: Patient 16

description: 2565 miRNAs were spotted on each array.


title: Patient 17

description: 2565 miRNAs were spotted on each array.


title: 0.7 [58]

description: Sample name: 58


title: Dusp9+/- 1 (0h)_b

description: AGTCAA | Sample 13 Dusp9+/- 1-2 (0h)


title: Dusp9+/- 2 (0h)_b

description: AGTTCC | Sample 14 Dusp9+/- 2-2 (0h)


title: F12,1 (24h)_b

description: CTTGTA | Sample 12 F12,1-1 (24h)

value: WT


title: F12,1 (0h)_b

description: TAGCTT | Sample 10 F12,1-1 (0h)


title: Patient 21

description: 2565 miRNAs were spotted on each array.


title: Dusp9+/- 1 (24h)

description: CAGATC | Sample 7 Dusp9+/- 1-2 (24h)


title: Dusp9+/- 2 (24h)

description: ACTTGA | Sample 8 Dusp9+/- 2-2 (24h)


title: Patient 2

description: 2565 miRNAs were spotted on each array.


title: Patient 20

description: 2565 miRNAs were spotted on each array.


title: Patient 1

description: 2565 miRNAs were spotted on each array.


title: 0.3 [65]

description: Sample name: 65


title: WT 1 (control)

type: genomic

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

description: WThTERT replicate one

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
BeadStudio software v3.2 and RnBeads through R.
Unmethylated and methylated signal intensities

molecule: genomic DNA

source_name: hTERT

label_protocol: Standard Illumina Protocol

growth_protocol: The parental or wild type (WT) adherent  hTERT1604 lung fibroblast cell line was cultured in 4.5g/l glucose DMEM  supplemented with 10% FBS and 2x NEAA. Knockdown (KD) cells (d8, d10 and d16) were maintained as for WT but media was supplemented with 150μg/ml hygromycin B, which was removed at least 48hrs before any experimental procedure.

extract_protocol:
Genomic DNA was harvested from cells in log phase of growth. Samples were incubated overnight at 55°C in lysis buffer (50 mM Tris pH 8, 0.1 M EDTA, 0.5% SDS, 0.2 mg/ml proteinase K ), with rotation, and DNA was subsequently isolated using the standard phenol:chloroform:isoamyl alcohol (25:24:1 pH8) extraction method. DNA quality was verified using gel electrophoresis and UV absorbance measurements at 260/280nm and 260/230nm using a Nanodrop UV spectrophotometer.
The genomic DNA isolated was assessed for purity and integrity prior to quantification using the Picogreen fluorescent assay.

treatment_protocol: The knockdown cell lines carrying an shRNA construct targeting DNMT1 were generated by transfecting the hTERT-immortalised human lung fibroblast cell line hTERT-1604 with pSilencer plasmid containing an shRNA

value: Male

value: WThTERT

tag: replicate

value: one


title: Gfi1b wt MxCretg NUP98/HOXD13_3

city: Essen

first: Cyrus

last: Khandanpour

state: NRW

address: Hufelandstr. 55

department: Department of Hematology

country: Germany

institute: University Hospital Of Essen

description: Gene expression data from Gfi1b wild-type bone marrow cells from NUP98/HOXD13 transgenic mice

hyb_protocol: Hybridization protocol not provided.

scan_protocol: The arrays were washed and stained according to the manufacturer's recommendation and finally scanned in a GeneChip scanner 3000 (Affymetrix) with G7 update.

data_processing: Signal summarization (RMA algorithm) and statistical analysis by ANOVA  was performed with AltAnalyze version 2.0.9 software (http://www.altanalyze.org/) applying quantile normalization, EnsMart72 database and default parameters.

organism: Mus musculus

source_name: leukemic bone marrow cells

label_protocol: For microarray analyses, we used the Affymetrix GeneChip platform employing the Express Kit protocol for sample preparation and microarray hybridization.  Total RNA (200 ng) was converted into biotinylated cRNA, purified, fragmented and hybridized MG-430_2.0 microarrays (Affymetrix).

growth_protocol: bone marrow cells were isolated from leukemic mice

extract_protocol: RNA extraction protocol not provided.

value: bone marrow

value: Gfi1b wildtype

tag: strain


title: Dusp9+/- 1 (24h)_b

description: ATGTCA | Sample 15 Dusp9+/- 1-2 (24h)


title: 0.3 [130]

description: Sample name: 130


title: P4x_1

city: Tianjin

first: Yiheng

last: Wang

address: 17km Jinjing Road

country: China

institute: Tianjin Academy of Agricultural Sciences

data_processing:
Illumina software used for base-calling.
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean reads were mapped to the reference genome. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq R package (1.18.0).
Genome_build: http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/
Supplementary_files_format_and_content: processed data file include FPKM values for genes in each sample.

organism: Brassica rapa subsp. pekinensis

source_name: autotetraploid petals

growth_protocol: Doubled haploids and autotetraploids were generated from a Chinese cabbage doubled haploid line ‘FT’ and grew under the same conditions.

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The integrity of the RNA samples was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
3 μg RNA per sample were used to generate the sequencing libraries using the NEBNext® Ultra™ RNA library prep kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: petal

tag: ploidy

value: autotetraploid

tag: sampling

value: fully expanded petals from flowering stage


title: P2x_3

source_name: doubled haploid petals

value: doubled haploid


title: P4x_3


title: P2x_2


title: P4x_2


title: F12,1 (24h)

description: TGACCA | Sample 4 F12,1-1 (24h)


title: 0.7 [59]

description: Sample name: 59

value: Wistar

value: Wildtype


title: Patient 3

description: 2565 miRNAs were spotted on each array.

value: HBeAg negative chronic hepatitis B

value: serum


title: P2x_1


title: Gfi1bfl/fl MxCretg NUP98/HOXD13_1

description: Gene expression data from Gfi1b deficient bone marrow cells from NUP98/HOXD13 transgenic mice

value: Gfi1b KO


title: F12,1 (0h)

description: CGATGT | Sample 2 F12,1-1 (0h)

value: female

value: ESC


title: P2x

data_processing:
Illumina software used for base-calling.
Raw data of fastq format were firstly processed through custom perl and python scripts. In this step, clean data were obtained by removing reads containing ploy-N, with 5' adapter containing ploy A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
miRNA expression levels were estimated by transcript per million (TPM)..
Differential expression analysis of two samples was performed using the DEGseq R package.
Genome_build: http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/
Supplementary_files_format_and_content: processed data file include TPM values for genes in each sample.


title: Dusp9+/- 2 (0h)

description: GGCTAC |Sample 6 Dusp9+/- 2-2 (0h)


title: Dusp9+/- 1 (0h)

description: ACAGTG | Sample 5 Dusp9+/- 1-2 (0h)


title: F-RCM v. F-RCM and stressed with 275µM Dipyridyl

city: Cork

first: Noreen

last: Lanigan

state: Cork

address: Biosciences Institute, University college Cork, cork, ireland.

department: Microbiology

country: Ireland

institute: University college cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: B. breve UCC2003 grown in filtered RCM until OD.600 of 0.6

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in filtered reinforced clostridial medium (RCM; Oxoid Ltd.) resuspended in deminerilised water. The RCM media was filtered to remove the agarose to allow cells to be collected by centrifugation this filtration was carried out with the aid of Watt man paper.  Iron limtiation was imposed by supplementing the medium with 85µM ciclopirox olamine or 100µM phenanthroline or 275µM Dipyridyl.   Bifidobacterial cultures were incubated at 37°C, anaerobically in a modular, atmosphere-controlled system (Davidson and Hardy, Belfast, Ireland) to an optical density OD600 of 0.6.

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Cells were collected by centrifugation at 10,000rpm for 2 minutes at room temperature prior to storage in the -80 degree freezer.

value: wild type

tag: growth condition

value: filtered RCM until OD.600 of 0.6

source_name: B. breve UCC2003 grown in filtered RCM supplemented with 275µM Dipyridyl until OD.600 of 0.6


title: P4x


title: LB controls compared to Csp_P treated samples rep 3

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N Wolfe St.

department: Molecular Microbiology and Immunology

country: USA

institute: Johns Hopkins School of Public Health

description: Biological replicate 3 of 4

hyb_protocol: Hybridization was performed according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol. RNA extracted from LB-fed individuals was hybridized to that of C.sp_P-fed individuals collected in the same replicate experiment, and samples were labeled in a dye-swap design to prevent dye bias.

scan_protocol: Scanning and feature extraction were performed using an Agilent Scanner and Agilent Feature Extraction Software.

data_processing: Background correction using the “normexp” method, signal normalization using global loess within array normalization. Differential transcript abundance between LB-fed and C.sp_P-fed female midguts was assessed using limma in R. Lists of genes with differential transcript abundance between treatments were then assessed for Gene Ontology term enrichment using DAVID.

organism: Anopheles gambiae

source_name: Csp_P treated

label_protocol: All samples were labeled using the Two-Color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. 200ng of RNA from each sample was used as input for the labeling reaction, and labeled cRNA was purified using the RNeasy Mini Kit (Qiagen).

growth_protocol: An. gambiae (Keele strain) were reared at 27°C and 80% RH with a 14:10 light:dark cycle. Csp_P biofilm culture: 1µL of pure freezer stock was added to to 5mL LB in a sterile 6-well cell culture plate and incubated without shaking at 30°C for 72 hours

extract_protocol: 20 females per treatment were dissected in sterile 1X PBS on a cold block and pooled in TRIzol (Invitrogen) reagent on ice. Midguts were stored at -80°C until RNA extraction. RNA was extracted following the manufacturer’s protocol and genomic DNA was removed using the TURBO DNA-free Kit (Invitrogen) according to the manufacturer’s instructions. Quality of RNA was verified using an Agilent Bioanalyzer 2100.

treatment_protocol: To collect biofilm supernatant, liquid media was removed from biofilm culture wells, transferred to centrifuge tubes and vortexed for one minute. To filter culture supernatant was pelleted at 5000rpm for 3-5 minutes and the liquid passed through a 0.2µm syringe filter. Six to seven day old adult An. gambiae females were starved overnight and provided sugar meals containing 3% sucrose mixed 1:1 with either LB or 72 hour C.sp_P biofilm supernatant. Both LB and C.sp_P supernatant were filter sterilized before being added to the sucrose solution. After 24 hours, midguts were dissected from 20 adult females and RNA extracted for analysis.

value: keele

value: midgut

tag: Sex

source_name: LB treated


title: NUGC4_untreated_6h_E3

status: Public on Mar 30 2018

city: melbourne

first: Liang

last: Yu

state: vic

address: 27-33 wright street

department: CIIID

country: Australia

institute: Hudson institute of medical research

description: mRNA gene expression

hyb_protocol: Affymatrix U133p2 follow the manufacturer's instructions.

data_processing: The data were RMA normalized with R (v.2.12.0) package affy. RMA normalization of 18 samples

source_name: cell line

growth_protocol: Human cell lines were grown in Gibco RPMI media containing 10% fetal calf serum (FCS), 1% penicillin-streptomycin and 1% L-glutamine (ThermoFisher Scientific, Waltham, MA, USA). Cell lines were characterized/authenticated via short tandem repeat profiling (PowerPlex HS16 System kit, Promega, Madison, WI, USA) and passaged for under 6 months after receipt.

extract_protocol: Total RNA was isolated from human GC cell lines using TRI Reagent Solution (Sigma, Castle Hill, NSW, Australia), followed by on-column RNeasy Mini Kit RNA clean-up and  DNase treatment (Qiagen, Hilden, Germany).

treatment_protocol: NUGC4, MKN1 and AZ521 cells were grown in 24-well plates in triplicate (1 × 105 cells/well) overnight before serum starvation for 24 h, following which cells in serum-free media were treated with 10ug Pam3Cys-Ser-(Lys)4 and FSL-1.

tag: cell line

tag: treatment

value: Saline control


title: Csp_P treated samples compared to LB controls rep 2

description: Biological replicate 2 of 4

tag: tissue


title: NUGC4_ligand treated_6h_E2

description: mRNA gene expression

scan_protocol: Affymatrix U133p2 follow the manufacturer's instructions.

value: 10ug P3C and FSL-1


title: LB controls compared to Csp_P treated samples rep 4

description: Biological replicate 4 of 4


title: PM4

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
Reads were mapped to the reference genome (Oar_v3.1) using the software package Tophat (v2.0.13).
Mapping sequencing reads: a maximum of 2 mismatches were allowed and reads that mapped equally well to more than 40 genomic locations were discarded.
Cufflinks (v2.2.1) was used to reconstruct transcript models from alignments.
The tool cuffmerge (Cufflinks v2.2.1) was used for merging together each of the assemblies with the reference ovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Sheep genome assembly: Oar_v3.1
Supplementary_files_format_and_content: Text files including locus, chromosome location, gene name, and number of mapped reads

organism: Ovis aries

source_name: Muscle

extract_protocol:
Total RNA was isolated and purified with TRIzol® Reagent in conjunction with PureLink RNA Mini Kit. To avoid genomic DNA contamination, eluted RNA was treated with DNase-free DNase Set (QIAGEN). RNA yield and quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
Libraries from individual samples were sequenced with Illumina's HiSeq 2000 at Macrogen (Korea) using 100-pb paired-end sequencing reads.

tag: muscle

value: Psoas major

tag: animal

value: cross-bred lamb

tag: id animal


title: PM2


title: PM1


title: MKN1_ligand treated_6h_E3

description: mRNA gene expression

label_protocol: Affymatrix U133p2 follow the manufacturer's instructions.


title: MKN1_untreated_6h_E2

description: mRNA gene expression


title: NUGC4_ligand treated_6h_E1

description: mRNA gene expression


title: MKN1_untreated_6h_E1

description: mRNA gene expression


title: MKN1_ligand treated_6h_E2

description: mRNA gene expression


title: AZ521_ligand treated_6h_E3

description: mRNA gene expression


title: NUGC4_ligand treated_6h_E3

description: mRNA gene expression


title: AZ521_untreated_6h_E1

description: mRNA gene expression


title: MKN1_ligand treated_6h_E1

description: mRNA gene expression


title: AZ521_untreated_6h_E3

description: mRNA gene expression


title: NUGC4_untreated_6h_E1

description: mRNA gene expression


title: PM3


title: MKN1_untreated_6h_E3

description: mRNA gene expression


title: AD4

value: Adductor


title: NUGC4_untreated_6h_E2

description: mRNA gene expression


title: AZ521_ligand treated_6h_E2

description: mRNA gene expression


title: AZ521_untreated_6h_E2

description: mRNA gene expression


title: AZ521_ligand treated_6h_E1

description: mRNA gene expression


title: AD2


title: AD1


title: LL4

value: Longissimus lumborum


title: LL2


title: LL3


title: LL1


title: P2-WKM_Scar

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

description:
Scarred GFP
each plate contains 384 sorted cells

data_processing:
In scar libraries, first read contains cell barcode (8 first nucleotides) and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries, first read contains UMI (6 first nucleotides) and cell barcode (from 7 to 14 nucleotides) and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome.
Genome_build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9, ensemble 74, extended with ERCC92
Supplementary_files_format_and_content: *scarclones.txt: tabular separated files, with scar percentage (columns) per cell (rows). Cells from the same fish have been named according to barcode ID, plate and organ of origin.  Last column (hclust) referes to ID for the clone (cells sharing hclust label have the same scar pattern). *transcriptome.txt.gz: tabular separated files, with transcript count (rows) per cell (columns). Cells in each file are labeled according to barcode ID, plate, organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained after running RaceID (Grun, D. et al. Nature 525, 251-255, 2015) and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.

organism: Danio rerio

source_name: WKM single cells

extract_protocol:
After organ isolation, live single cells are sorted into 384 well plates containing mineral oil, uniquely barcoded cell specific primers for independent scar and mRNA detection, Spike-in controls and and RNAse inhibitor.
Scartrace
Illumina TruSeq adapaters

tag: cas9 injection

value: protein

tag: FISH id

tag: organ

value: WKM

tag: sorted plates


title: P2_forebrain_Scar

source_name: forebrain single cells

value: forebrain


title: P2_right_eye_Scar

source_name: right eye single cells

value: right eye


title: P2_left_midbrain_Scar

source_name: left midbrain single cells

value: left midbrain


title: P2_right_midbrain_Scar

source_name: right midbrain single cells

value: right midbrain


title: P2_cfin_vent_Scar

source_name: primary fin single cells

value: primary fin


title: P1_cfin_dorsal_Scar


title: SS4

value: Supraspinatus


title: SS3


title: SS2


title: SS1


title: P2_left_eye_Scar

source_name: left eye single cells

value: left eye


title: RF4

value: Rectus femoris


title: GM4

value: Gluteus medius


title: RF2


title: RF3


title: GM3


title: SAMPLE 16_Genomic DNA from healthy donor CD34+CD15- cells

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

description:
healthy donor CD34+CD15- cells
SAMPLE 16

hyb_protocol: Hybridisation on the arrays was performed by Integragen. SA following the Illumina Infinium HD methylation protocol.

scan_protocol: Standard protocol defined by Illumina for HM450K

data_processing:
GenomeStudio V2011.1
The non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: Apheresis product

label_protocol: Bisulfite conversion was performed by Integragen. SA.

growth_protocol: Primary cells from G-CSF mobilized peripheral blood progenitor cells (PBPC) apheresis products and from patients with chronic phase CML were used for this study.

extract_protocol: Genomic DNA was extracted using Macherey Nagel DNA Tissue XS Kit according to standard instructions.

treatment_protocol: Fresh sample were used. mature (CD34-CD15+) and immature (CD34+CD15-) cells were sorted using flow cytometry (BD FACSAria SORP. Becton Dickinson).

tag: disease state

value: normal hematopoietic cells

tag: cell type type


title: genomic DNA from cord blood 72

city: Little Rock

first: Yuetkin

last: Leung

state: AR

address: 323 Jack Stephens Dr

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences

description: cord blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: minfi and Enmix, 21 samples (samples 2, 3, 4, 6, 12, 13, 15, 17, 18,  24, 30, 32, 33, 34, 40, 42, 43, 44, 46, 68 and 71) were removed from the final analysis due to poor quality

source_name: cord blood 72

extract_protocol: genomic DNA was extracted and purified from cord blood samples using Maxwell 16 system DNA purification kit (Promega) according to standard instructions

tag: gender

value: female

value: cord blood


title: SAMPLE 23_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 23

source_name: CP-CML patient

value: CML cells


title: SAMPLE 22_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 22


title: genomic DNA from cord blood 71

description: cord blood sample

source_name: cord blood 71

value: male


title: GM2

value: cross-bred lamb


title: GM1


title: GB4

value: Gluteobiceps


title: GB3


title: genomic DNA from cord blood 70

description: cord blood sample

source_name: cord blood 70


title: SAMPLE 19_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 19


title: AD3

value: Adductor


title: SAMPLE 11_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 11


title: SAMPLE 14_Genomic DNA from healthy donor CD34+CD15- cells

description:
healthy donor CD34+CD15- cells
SAMPLE 14


title: SAMPLE 17_Genomic DNA from healthy donor CD34+CD15- cells

description:
healthy donor CD34+CD15- cells
SAMPLE 17


title: genomic DNA from cord blood 68

description: cord blood sample

source_name: cord blood 68


title: genomic DNA from cord blood 69

description: cord blood sample

source_name: cord blood 69


title: GB1


title: ST4

value: Semitendinosus


title: genomic DNA from cord blood 67

description: cord blood sample

source_name: cord blood 67


title: SAMPLE 21_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 21


title: GB2


title: SAMPLE 20_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 20


title: SAMPLE 15_Genomic DNA from healthy donor CD34+CD15- cells

description:
healthy donor CD34+CD15- cells
SAMPLE 15


title: genomic DNA from cord blood 66

description: cord blood sample

source_name: cord blood 66


title: ST2

source_name: Muscle


title: ST3


title: SAMPLE 13_Genomic DNA from healthy donor CD34+CD15- cells

description:
healthy donor CD34+CD15- cells
SAMPLE 13


title: genomic DNA from cord blood 63

description: cord blood sample

source_name: cord blood 63


title: SM2

value: Semimembranosus


title: SM3


title: SM4


title: SAMPLE 18_Genomic DNA from CML CD34+CD15- cells

description:
CML CD34+CD15- cells
SAMPLE 18


title: genomic DNA from cord blood 61

description: cord blood sample

source_name: cord blood 61


title: Csp_P treated samples compared to LB controls rep 1

description: Biological replicate 1 of 4

source_name: LB treated

tag: strain

value: keele

value: midgut

source_name: Csp_P treated


title: genomic DNA from cord blood 60

description: cord blood sample

source_name: cord blood 60


title: SM1


title: genomic DNA from cord blood 59

description: cord blood sample

source_name: cord blood 59


title: genomic DNA from cord blood 64

description: cord blood sample

source_name: cord blood 64


title: ST1


title: RF1


title: genomic DNA from cord blood 57

description: cord blood sample

source_name: cord blood 57


title: genomic DNA from cord blood 56

description: cord blood sample

source_name: cord blood 56


title: genomic DNA from cord blood 62

description: cord blood sample

source_name: cord blood 62


title: genomic DNA from cord blood 54

description: cord blood sample

source_name: cord blood 54


title: SAMPLE 10_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 10

source_name: CP-CML patient


title: genomic DNA from cord blood 52

description: cord blood sample

source_name: cord blood 52


title: genomic DNA from cord blood 49

description: cord blood sample

source_name: cord blood 49


title: SAMPLE 12_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 12


title: genomic DNA from cord blood 46

description: cord blood sample

source_name: cord blood 46


title: genomic DNA from cord blood 47

description: cord blood sample

source_name: cord blood 47


title: genomic DNA from cord blood 48

description: cord blood sample

source_name: cord blood 48


title: genomic DNA from cord blood 43

description: cord blood sample

source_name: cord blood 43


title: genomic DNA from cord blood 45

description: cord blood sample

source_name: cord blood 45


title: genomic DNA from cord blood 42

description: cord blood sample

source_name: cord blood 42


title: genomic DNA from cord blood 50

description: cord blood sample

source_name: cord blood 50


title: HT29_2D2

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description:
HT29 2D cell culture replicate 2
Biological replicate 2 of 2. HT29 cells were cultivated under 2D monolayer forming growth conditions

data_processing:
Basecalls were performed and FASTQ files were generated using Casava pipeline version 1.8.3.
Initial quality assessment was based on data passing the Illumina Chastity filtering. Subsequently, reads containing PhiX control signal were removed.
Sequenced reads were trimmed for adaptor sequence (TGGAATTCTCGGGTGCCAAGG) using Cutadapt 1.11. Additionaly for DLD1, 4 random, miRNA sequence flanking nucleotides, that were introduced in library building process, were cut. Sequences that  quality score was less than 25 and sequences shorter than 15 nt were excluded.
Trimmed and filtered reads were aligned to human genome hg19 (UCSC) using bowtie2 2.1.0 using –end-to-end alignment
Human genome aligned reads were further aligned to mirbase.org miRNA sequences (release 21)  using bowtie2 2.1.0 using parameters --local -N 0 -L 16
miRNA mapped reads were counted and written to tab delimited abundance measurement text files.  Abundance measurements were used for differential expression analysis using EdgeR package 3.4.2. First, abundance measurements containing miRNA counts were normalized using upper-quartile method. Secondly, fold changes of miRNA expression were calculated and miRNA with fold changes >1.5, p>0.05 and at least 10 miRNA counts  per million were considered differentially expressed.
Genome_build: hg19 (UCSC); miRBAse release 21
Supplementary_files_format_and_content: tab delimited text files contain abundance measurements of miRNAs that mapped to annotated miRNA sequences. Data are provided as miRNA IDs in first collumn and miRNA counts in second collumn.

source_name: Colorectal adenocarcinoma cell line HT29

growth_protocol: For the monolayer (2D) culture, colorectal adenocarcinoma DLD1 (ATCC, Rockville, Maryland, USA) and HT29 (ATCC) cells were plated in 25 cm2 tissue culture flasks at cell densities of 35000 and 100000 cells, respectively. For multicellular spheroid culture, 7000 and 3500 cells, for DLD1 and HT29 cells, accordingly, were plated in 96 round-bottom well plates precoated with a layer of 1% agarose gel. DLD1 cells were cultured in RPMI (Gibco, Germany), meanwhile HT29 cells - in DMEM (Gibco) cell culture medium, which were supplemented with 10% fetal bovine serum (Gibco), 2mM glutamine (Gibco), 1mM sodium pyruvate (Gibco), 100 UI/mL penicillin (Sigma-Aldrich, USA) and 0.1 mg/mL streptomycin (Sigma-Aldrich). Cell cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2.  Total RNA was extracted from cells following 6 days of cell growth in 2D or 3D conditions.

extract_protocol:
Total RNA was isolated using MirVana miRNA isolation kit according to manufacturer's instructions.
2 μg of total RNA were used for the library construction using NEXTflex small RNA sequencing kit V3 (Bioo Scientific, USA) for DLD1 cells, and NEXTflex small RNA sequencing kit V2 for HT29 cells according to the manufacturer’s instructions.

tag: cell culture

value: 2D monolayer


title: genomic DNA from cord blood 44

description: cord blood sample

source_name: cord blood 44


title: SAMPLE 6_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 6

source_name: Apheresis product


title: HT29_SF2

description:
HT29 3D cell culture replicate 2
Biological replicate 2 of 2. HT29 cells were cultivated under 3D multicellular spheroid growth conditions

value: Colorectal adenocarcinoma cell line HT29

value: 3D multicellular spheroids


title: HT29_SF1

description:
HT29 3D cell culture replicate 1
Biological replicate 1 of 2. HT29 cells were cultivated under 3D multicellular spheroid growth conditions


title: SAMPLE 5_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 5


title: SAMPLE 8_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 8


title: SAMPLE 3_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 3


title: DLD1_SF2

description:
DLD1 3D cell culture replicate 2
Biological replicate 2 of 2. DLD1 cells were cultivated under 3D multicellular spheroid growth conditions

source_name: Colorectal adenocarcinoma cell line DLD1


title: SAMPLE 7_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 7


title: genomic DNA from cord blood 40

description: cord blood sample

source_name: cord blood 40


title: genomic DNA from cord blood 41

description: cord blood sample

source_name: cord blood 41


title: genomic DNA from cord blood 51

description: cord blood sample

source_name: cord blood 51


title: SAMPLE 2_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 2


title: genomic DNA from cord blood 39

description: cord blood sample

source_name: cord blood 39


title: genomic DNA from cord blood 58

description: cord blood sample

source_name: cord blood 58


title: genomic DNA from cord blood 65

description: cord blood sample

source_name: cord blood 65


title: genomic DNA from cord blood 55

description: cord blood sample

source_name: cord blood 55


title: HT29_2D1

description:
HT29 2D cell culture replicate 1
Biological replicate 1 of 2. HT29 cells were cultivated under 2D monolayer forming growth conditions.


title: SAMPLE 4_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 4


title: genomic DNA from cord blood 37

description: cord blood sample

source_name: cord blood 37


title: genomic DNA from cord blood 38

description: cord blood sample

source_name: cord blood 38


title: genomic DNA from cord blood 36

description: cord blood sample

source_name: cord blood 36


title: genomic DNA from cord blood 35

description: cord blood sample

source_name: cord blood 35


title: DLD1_SF1

description:
DLD1 3D cell culture replicate 1
Biological replicate 1 of 2. DLD1 cells were cultivated under 3D multicellular spheroid growth conditions

value: Colorectal adenocarcinoma cell line DLD1


title: genomic DNA from cord blood 34

description: cord blood sample

source_name: cord blood 34


title: DLD1_2D1

description:
DLD1 2D cell culture replicate 1
Biological replicate 1 of 2. DLD1 cells were cultivated under 2D monolayer forming growth conditions.


title: DLD1_2D2

description:
DLD1 2D cell culture replicate 2
Biological replicate 2 of 2. DLD1 cells were cultivated under 2D monolayer forming growth conditions


title: genomic DNA from cord blood 33

description: cord blood sample

source_name: cord blood 33


title: genomic DNA from cord blood 32

description: cord blood sample

source_name: cord blood 32


title: SAMPLE 9_Genomic DNA from CML CD34-CD15+ cells

description:
CML CD34-CD15+ cells
SAMPLE 9

source_name: CP-CML patient


title: SAMPLE 1_Genomic DNA from healthy donor CD34-CD15+ cells

description:
healthy donor CD34-CD15+ cells
SAMPLE 1

source_name: Apheresis product


title: genomic DNA from cord blood 53

description: cord blood sample

source_name: cord blood 53


title: genomic DNA from cord blood 30

description: cord blood sample

source_name: cord blood 30


title: genomic DNA from cord blood 31

description: cord blood sample

source_name: cord blood 31


title: genomic DNA from cord blood 29

description: cord blood sample

source_name: cord blood 29


title: genomic DNA from cord blood 28

description: cord blood sample

source_name: cord blood 28


title: P7358_1581

city: Uppsala

first: Bryndis

last: Birnir

address: Husargatan 3

department: Department of Medical Cell Biology

country: Sweden

institute: Uppsala University

data_processing:
Single-end 43 bp reads were generated and mapped to human reference genome GRCh38 by employing STAR (version 2.4.1) with parameter outSAMstrandField intronMotif
Reads per kilobase transcript per million mapped reads (RPKM) from RefSeq gene annotations were calculated using RPKM for genes
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: CD3+ T cells

extract_protocol:
Total RNA was extracted from CD3+ T cells using Direct-zol™ RNA MicroPrep (Zymo Research, Irvine, CA, USA) according to manufacturer’s recommendation.
cDNA libraries were prepared according to Smart-seq2 protocol

tag: cell type

value: CD3+ T cells

tag: condition

value: Type 1 diabetes


title: P7358_1621


title: P7358_1612


title: P7358_1615


title: P7358_1613


title: P7358_1616


title: P7358_1580


title: P7358_1574


title: P7358_1618


title: P7358_1620


title: genomic DNA from cord blood 27

description: cord blood sample

source_name: cord blood 27

value: female


title: genomic DNA from cord blood 24

description: cord blood sample

source_name: cord blood 24

value: cord blood


title: genomic DNA from cord blood 26

description: cord blood sample

source_name: cord blood 26


title: genomic DNA from cord blood 25

description: cord blood sample

source_name: cord blood 25


title: CD8+CAR-_Rep2.ATAC

city: Philadelphia

first: J

middle: Joseph

last: Melenhorst

state: PA

address: SPE 9-105, 3400 Civic Center Blvd.

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

description: Transposase-accessible DNA

library_source: genomic

data_processing:
Raw paired-end reads were uniquely aligned to human reference genome hg19 using bowtie2 allowing for 1 mismatch
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: CD8+ T cells

extract_protocol:
Nuclei were extracted from sorted CD8+ T cells and transposed with Tn5 transposase (Illumina Nextera) as per Buenrostro et al. Nature Methods, 2013 (PMID: 24097267)
Libraries were generated using a single PCR-based addition of Illumina compatible 5' and 3' ends with 8bp, dual indeces

tag: genotype

value: CAR-


title: CD8+CAR+_Rep2.ATAC

description: Transposase-accessible DNA

value: CAR+


title: CD8+CAR+_Rep1.ATAC

description: Transposase-accessible DNA


title: P7358_1606


title: P7358_1604


title: P7358_1608


title: P7358_1603


title: genomic DNA from cord blood 23

description: cord blood sample

source_name: cord blood 23


title: P7358_1600


title: CD8+CAR-_Rep1.ATAC

description: Transposase-accessible DNA


title: P7358_1607


title: genomic DNA from cord blood 21

description: cord blood sample

source_name: cord blood 21


title: P7358_1599


title: P7358_1596


title: genomic DNA from cord blood 22

description: cord blood sample

source_name: cord blood 22


title: MM231 cells tfxn HDAC5 shRNA, biological rep1

city: Pittsburgh

first: Yi

last: Huang

state: Pennsylvania

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

hyb_protocol: cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA)

scan_protocol: cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility

data_processing: The data is RMA normalized using 'affy' package in R-Bioconductor

source_name: MM231_HDAC5 shRNA

label_protocol: cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies)

growth_protocol: normal culturing conditions for MDA-MB-231

extract_protocol: QIAgen RNeasy Mini (Animal Cells Spin protocol, w/DNase I digest performed on homogenized lysate prior to applying lysate to column for purification)

treatment_protocol: shRNA Lentiviral Particles were purchased from Santa Cruz Biotecnology and transduced according to manufacturer's protocol (http://www.scbt.com/protocols.html?protocol=shrna_lentiviral_particles_transduction)

tag: cell line

value: breast cancer cell line

tag: transfected with

value: HDAC5 shRNA


title: MM231 cells tfxn scramble shRNA, biological rep2

source_name: MM231_scramble shRNA

value: scramble shRNA


title: MM231 cells tfxn scramble shRNA (LSD1), biological repB

description: MDA-MB-231 cells, scramble shRNA transfection, biological replicate B

source_name: breast cancer cell line


title: MM231 cells tfxn LSD1 shRNA, biological rep2

description: MDA-MB-231 cells, LSD1 shRNA transfection, biological replicate 2

value: LSD1 shRNA


title: MM231 cells tfxn HDAC5 shRNA, biological rep2


title: MM231 cells tfxn scramble shRNA, biological rep1


title: MM231 cells tfxn LSD1 shRNA, biological rep3

description: MDA-MB-231 cells, LSD1 shRNA transfection, biological replicate 3


title: P7358_1593


title: P7358_1594


title: MM231 cells tfxn HDAC5 shRNA, biological rep3


title: P7358_1592


title: genomic DNA from cord blood 19

description: cord blood sample

source_name: cord blood 19

tag: tissue


title: P7358_1589


title: genomic DNA from cord blood 18

description: cord blood sample

source_name: cord blood 18

value: male


title: genomic DNA from cord blood 20

description: cord blood sample

source_name: cord blood 20


title: RNA-seq_siTOE1

city: Cheonan-si, Chungcheongnam-do

first: Ahyeon

last: Son

address: 25 Bongjeong-ro, Dongnam-gu

country: South Korea

institute: Soonchunhyang Institute of Medi-bio Science

description: rRNA-depleted RNA-seq

data_processing:
The base calling was done by CASAVA v1.8.2
Using cutadapt 1.11 (Martin, 2011), adapter sequences were removed with the following command: cutadapt -a NNNNTGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 20.
The processed reads were collapsed by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit; version 0.0.13.2) and aligned using STAR 2.5.1b (Dobin et al., 2013) with the following command: STAR --alignIntronMin 9999999 --outFilterMultipleNmax 1000.
The alignments were annotated by using reduced RefSeq transcript set (Chang et al., 2014) and BEDtools 2.26.0 (Quinlan and Hall, 2010) with minimum 50% overlapping: bedtools intersect -f 0.50.
For each read 2 alignment, the 5′ most nucleotide and 5′ soft-clipped sequences were regarded as the 3′ end and untemplated addition, respectively. If a read was mapped to multiple loci, the alignment with the shortest modification and nearest annotation was selected.
Genome_build: hg38
Supplementary_files_format_and_content: a comma-delimited file including read counts, separated by processing status and tailing information

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM (Welgene) supplemented with 9% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted from cells by using TRIzol reagent (Thermo Fisher Scientific) and treated with DNase I (Takara).
Conventional RNA-seq library protocol after 3′ adapter ligation and size fractionation (100-500 nt) without fragmentation step

treatment_protocol: HeLa cells were transfected with 20 nM of siRNAs for four days using Lipofectamine 3000 (Thermo Fisher Scientific). Equal amounts of four different siRNAs were used for each knockdown. In the combinatorial knockdown, we mixed two sets to have a final concentration of 20 nM per siRNA set.

value: HeLa

value: human cervical cancer cell line

tag: sirna

value: TOE1 siRNA treated


title: MM231 cells tfxn scramble shRNA (LSD1), biological repA

description: MDA-MB-231 cells, scramble shRNA transfection, biological replicate A


title: RNA-seq_siNC

description: rRNA-depleted RNA-seq

value: Negative control siRNA treated


title: RNA-seq_siPARN

description: rRNA-depleted RNA-seq

value: PARN siRNA treated


title: RNA-seq_siPARN-TOE1

description: rRNA-depleted RNA-seq

value: PARN/TOE1 siRNA treated


title: genomic DNA from cord blood 17

description: cord blood sample

source_name: cord blood 17


title: genomic DNA from cord blood 16

description: cord blood sample

source_name: cord blood 16


title: P7358_1586

source_name: CD3+ T cells

value: CD3+ T cells


title: genomic DNA from cord blood 15

description: cord blood sample

source_name: cord blood 15


title: MM231 cells tfxn scramble shRNA, biological rep3


title: P7358_1579

value: Type 1 diabetes


title: RH30 SR, replicate 2

city: Columbus

first: Peter

state: OH

address: 460 W 12th Ave

institute: Ohio State University

description: Gene expression data from RH30 SR cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: Gene expression levels were estimated from Expression console software from affymetrix (RMA-Gene-Core)

source_name: RH30 cells, SR

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

growth_protocol: Cells were grown in DMEM 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Cells were infected with SR or vector.

value: Rhabdomyosarcoma


title: genomic DNA from cord blood 14

description: cord blood sample

source_name: cord blood 14

value: female

value: cord blood


title: MM231 cells tfxn scramble shRNA (LSD1), biological repC

description: MDA-MB-231 cells, scramble shRNA transfection, biological replicate C


title: RH30 SR, replicate 1

description: Gene expression data from RH30 SR cells


title: P7358_1578


title: genomic DNA from cord blood 13

description: cord blood sample

source_name: cord blood 13


title: genomic DNA from cord blood 12

description: cord blood sample

source_name: cord blood 12


title: P7358_1577


title: RH30 vector, replicate 1

description: Gene expression data from RH30 vector cells

source_name: RH30 cells, vector


title: RH30 vector, replicate 2


title: genomic DNA from cord blood 11

description: cord blood sample

source_name: cord blood 11


title: genomic DNA from cord blood 9

description: cord blood sample

source_name: cord blood 9


title: genomic DNA from cord blood 8

description: cord blood sample

source_name: cord blood 8


title: genomic DNA from cord blood 7

description: cord blood sample

source_name: cord blood 7


title: RH30 SR, replicate 3

description: Gene expression data from RH30 SR cells


title: genomic DNA from cord blood 10

description: cord blood sample

source_name: cord blood 10


title: genomic DNA from cord blood 6

description: cord blood sample

source_name: cord blood 6


title: P7358_1573


title: genomic DNA from cord blood 5

description: cord blood sample

source_name: cord blood 5


title: genomic DNA from cord blood 3

description: cord blood sample

source_name: cord blood 3


title: genomic DNA from cord blood 4

description: cord blood sample

source_name: cord blood 4


title: RH30 vector, replicate 3


title: P7358_1614

value: Nondiabetic


title: P7358_1609


title: P7358_1605


title: P7358_1601


title: P7358_1610


title: P7358_1569


title: P7358_1597


title: P7358_1611


title: P7358_1571


title: P7358_1619


title: P7358_1602


title: P7358_1570


title: P7358_1617


title: Granulocytes before ET 4 (Day 7)

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description: US22502550_251896410021_S01_GE1-v5_95_Feb07_1_1.txt

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: ET F842 P D7

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from granulocytes using TRIzol (Invitrogen) according to the manufacturer's instructions.

tag: study

value: In vivo

tag: group

value: before ET

value: Granulocytes


title: Granulocytes on Day 21 pregnant by ET 3

description: US22502550_251896410044_S01_GE1-v5_95_Feb07_2_3.txt

source_name: ET F835 P D21

value: Day 21 pregnant


title: Keratinocyte_replicate 2

city: Toronto

first: Philip

middle: A

last: Marsden

address: 209 Victoria Street, Room 522

department: Medicine

country: Canada

institute: University of Toronto

description: Basal gene expression

hyb_protocol: Cy3-Labeled cDNA was hybridized to Custom Arraystar Human LncRNA Array version 1 (12x 135K, Arraystar) using the NimbleGen Hybridization system.

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Axon GenePix 400B scanner.

data_processing: NimbleScan v2.5 Software was used to extract raw data, quantile normalization, and background correction. Subsequent data processing, including detection of differentially expressed non-coding RNA and protein coding genes, was performed using the Agilent GeneSpring GX (version 10.0) software package (Agilent Technologies).

source_name: Keratinocyte

label_protocol: RNA samples were used to synthesize double-stranded cDNA using Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s instructions. The double-stranded cDNA was subsequenty labeled with Cy3 using the NimbleGen One-Color DNA Labeling Kit (Nimblegen) according to the manufacturer's instructions.

growth_protocol: HUVEC were isolated from umbilical cords of male and female births. HUVEC were cultured in supplemented M199 medium for 2 passages and all biological replicates were used at passage 3-4. HMVEC, fibroblasts, hepatocytes, and keratinocytes were purchased from Lonza, while HASMC were purchased from Sciencell. All purchased cells were cultured according to the manufacturer’s instructions for 2 passages and all biological replicates were used at passage 3-4.

extract_protocol: RNA was extracted from the different cell types using guanidinium-acid-phenol reagents that are based on the research of Chomczynski and Sacchi, 1987. A known amount of exogenous luciferase RNA was introduced at the beginning of the extraction to assess for RNA extraction and first strand cDNA synthesis efficiency.

treatment_protocol: Cells were extracted without any treatment.

value: keratinocyte


title: Hepatocyte_replicate 3

description: Basal gene expression

source_name: Hepatocyte

value: hepatocyte


title: MM231 cells tfxn LSD1 shRNA, biological rep1

description: MDA-MB-231 cells, LSD1 shRNA transfection, biological replicate 1

source_name: breast cancer cell line

value: breast cancer cell line

value: LSD1 shRNA


title: Hepatocyte_replicate 2

description: Basal gene expression


title: Keratinocyte_replicate 1

description: Basal gene expression


title: Keratinocyte_replicate 3

description: Basal gene expression


title: Fibroblast_replicate 2

description: Basal gene expression

source_name: Fibroblast

value: fibroblast


title: Hepatocyte_replicate 1

description: Basal gene expression


title: genomic DNA from cord blood 1

description: cord blood sample

source_name: cord blood 1

value: male


title: genomic DNA from cord blood 2

description: cord blood sample

source_name: cord blood 2


title: Fibroblast_replicate 1

description: Basal gene expression


title: Fibroblast_replicate 3

description: Basal gene expression


title: P7358_1572

source_name: CD3+ T cells


title: Granulocytes before ET 3 (Day 7)

description: US22502550_251896410044_S01_GE1-v5_95_Feb07_2_2.txt

source_name: ET F835 P D7


title: Granulocytes on Day 21 pregnant by ET 4

description: US22502550_251896410021_S01_GE1-v5_95_Feb07_1_2.txt

source_name: ET F842 P D21


title: P7358_1587


title: P7358_1595


title: P7358_1575


title: P7358_1583


title: P7358_1588


title: P7358_1591


title: P7358_1590


title: P7358_1582


title: Granulocytes on Day 21 pregnant by ET 1

description: US22502550_251896410027_S01_GE1-v5_95_Feb07_1_2.txt

source_name: ET F840 P D21


title: Granulocytes before ET 1 (Day 7)

description: US22502550_251896410027_S01_GE1-v5_95_Feb07_1_1.txt

source_name: ET F840 P D7


title: Granulocytes before ET 2 (Day 7)

description: US22502550_251896410027_S01_GE1-v5_95_Feb07_1_3.txt

source_name: ET F785 P D7


title: HMVEC_replicate 3

description: Basal gene expression

source_name: HMVEC

value: human dermal microvascular endothelial cells


title: INOC_2

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

description: This is the culture used to inoculate different nitrogen treatments of the same biological replicate

data_processing:
Quality control, filtering, and trimming were performed using FastQC and the FAST-X toolkit and resulted in an average loss of 3% of reads
Reads from each sample were mapped to the previously de novo assembled reference transcriptome of Dunaliella viridis strain dumsii (Srirangan et al., 2015) using the RNA-Seq Analysis module of the CLC Genomics Workbench version 10.0 (https://www.qiagenbioinformatics.com/). The RNA-Seq Analysis module, which uses an expectation -maximization (EM) algorithm like RSEM (B. Li and Dewey, 2011), was run with default parameters (mismatch cost = 2; insertion cost = 3, deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8), but strand specificity was ignored. Since putative alternate splice transcripts are represented individually in the reference transcriptome, the “maximum number of hits for a read” was increased to 30 so that reads that matched the multiple transcripts were not discarded.
As putative transcripts are only predicted and not verified for D. viridis, gene counts are preferable to transcript differences.  To obtain gene specific data, raw counts and TPM (transcripts per million) values for each transcript were exported from the CLC Genomics Workbench, and the counts and TPM values for each putative transcript of each gene were summed to give a total raw read count per gene and a separate summed TPM value per gene.
Differential expression analysis was used to determine transcriptional differences between the four nitrogen sources (NO3, STAR, GLU, GLN) at each of the three time points (0 h, 24 h, and 48 h).  Comparisons were also made between the time points within each nitrogen source to determine transcriptional differences over time for a single nitrogen source.  All samples were also compared to the inoculum culture (PAR) to provide a common comparison point (Figure 3.1).  Differential expression was performed using the “Empirical analysis of DGE” tool in CLC, which utilizes the edgeR version 3.4.0 implementation of Fisher’s Exact Test for two-group comparisons (Robinson et al., 2010).  Only genes that had a total number of read counts >5 within each comparison group were used to estimate tagwise dispersions, and counts from biological replicates were averaged together.  Initial analysis showed all comparisons between the GLU and STAR conditions were not statistically different, and thus all comparisons were regenerated without GLU data.  Differential expression was considered significant based on the following parameters: False Discovery Rate (FDR) corrected p-value ≤ 0.05, Log2 fold change ≥ |2|, and the total read count for the gene within the comparison was > 75.
Genome_build: Dunaliella_viridis_annotated_transcripts.fasta
Supplementary_files_format_and_content: Raw_Read_Counts.txt:  The matrix file contains the raw read counts for each sample (sample title) for each gene.  The read count for each transcript of each gene have already been summed to give the gene read count.  This is the data that was analyzed with the “Empirical analysis of DGE” tool in CLC, which utilizes the edgeR version 3.4.0 implementation of Fisher’s Exact Test for two-group comparisons (Robinson et al., 2010) for differential expression analysis.   Dunaliella_viridis_annotated_transcripts.fasta:  The file contains the annotated fasta sequences of the reference transcriptome used for mapping of reads.  The original transcriptome annotations for D. viridis strain dumsii were derived from a 2012 Blast2GO annotation run (Srirangan et al., 2015).  Since the Dunaliella salina CCAP 19/18 genome is available through Phytozome (Polle et al., 2017), a decision was made to re-annotate based upon similarity of D. viridis transcripts to D. salina proteins.  The D. salina proteome was obtained from Phytozome on June 11, 2017 and converted to a Blast database within the CLC Genomics Workbench version 10.0 (https://www.qiagenbioinformatics.com/).  Blastx was used to extract the best protein hit for each D. viridis transcript using the following parameters: maximum number of blast hits = 1; e-value cutoff = 10-1; low complexity filter = off.  D. salina annotations were then ascribed to the D. viridis transcripts.  Previous manual annotations were kept as they had already been confirmed.  This rough annotation increased the number of annotated genes in D. viridis strain dumsii from 9400 to 13273.  The annotation of each sequence is a combination of the original Blast2GO annotation, the name of the Arabidopsis hit and then the Chlamydomonas hit from the Dunaliella salina proteome.  Names are separated by **.
Supplementary_files_format_and_content: TPM_values.txt

organism: Dunaliella viridis

source_name: whole cells

growth_protocol: Dunaliella viridis strain dumsii was grown in a modified Ben-Amotz medium as reported (Murphree et al., 2017).  Experiments were performed in a Percival E-36L growth chamber under continuous cool white fluorescent light (~125 µmol photons m2/s) at a temperature of 23.5 °C.

extract_protocol:
Total RNA was extracted from the 30 ml frozen pellets of the 39 samples using the RNeasy Plant Mini Kit (Qiagen) following standard procedures for use with a QIAcube.  DNA was removed from total RNA using RNase-Free DNase (Qiagen), and rRNA was depleted from the samples using the Ribo-Zero™ Magnetic Kit (Plant Leaf) (Epicentre Cat. No. MRZPL1224).  After each processing step, RNA quality was confirmed using a Bioanalyzer RNA Pico Chip (Agilent)
Strand specific cDNA libraries with 300–450 bp inserts were generated with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England BioLabs).  Sample libraries were barcoded using the TruSeq DNA LT Sample Prep Kit, Indexed Adapter Sequences (Illumina).  Final quality of the libraries was confirmed using a Bioanalyzer DNA high sensitivity chip (Agilent).  Libraries were split into 2 groups and submitted for single end 125 bp Illumina HiSeq 2500 sequencing runs in 2 flow cells at the North Carolina State University Genome Sciences Laboratory (GSL).

treatment_protocol: Four experimental media were created with nitrogen sources of 5 mM KNO3, 5 mM L-glutamine (Sigma-Aldrich), 5 mM L-glutamate (Sigma-Aldrich), or no addition of KNO3 (Figure 3.1).  The L-glutamate condition was used to control for nitrogen starvation in the presence of an unused and stable amino acid (Murphree et al., 2017).  Cultures for inoculation were grown for a week in experimental conditions and were harvested by centrifugation (3500 g, 6 min.) in mid-logarithmic phase for use as inoculum.  Cells were suspended in 450 ml of the proper experimental media in 1 liter narrow-necked Erlenmeyer flasks to a concentration of 1 million cells/ml.  Each of the 4 experimental cultures was duplicated to give 2 technical replicates and the entire experiment was repeated 3 times to provide 3 biological replicates.  The first set of samples (T0) were taken three hours after inoculation in an attempt to decrease effects seen from transfer shock and to detect quicker transcriptional changes.  Two more collections were taken at 24 hours (T24) and 48 hours (T48) after the first collection.  In addition to the samples taken from the experimental cultures, half volume samples were taken in duplicate from the inoculum at the point of inoculation (T-3).  Sample collection consisted of aliquots taken for cell density/diameter/pH measurements (1 ml), RNA extraction (30 ml), neutral lipid fluorescence assay (5 ml), carbohydrate/starch detection (100 ml), soluble protein assay (5 ml), and chlorophyll content measurement (1 ml).  The aliquots for RNA, carbohydrate/starch, and protein were pelleted and flash frozen in liquid nitrogen for bulk processing.

value: dumsii

tag: biological replicate

tag: nitrogen source

value: Nitrate

tag: hours after inoculation

tag: run


title: INOC_1


title: HASMC_replicate 2

description: Basal gene expression

source_name: HASMC

value: human aortic vascular smooth muscle cells


title: HMVEC_replicate 1

description: Basal gene expression


title: HUVEC_replicate 3

description: Basal gene expression

source_name: HUVEC

value: human umbilical vein endothelial cells


title: HASMC_replicate 3

description: Basal gene expression


title: INOC_3


title: HUVEC_replicate 1

description: Basal gene expression


title: HUVEC_replicate 2

description: Basal gene expression


title: HASMC_replicate 1

description: Basal gene expression


title: Granulocytes on Day 21 pregnant by ET 2

description: US22502550_251896410009_S01_GE1-v5_95_Feb07_2_4.txt

source_name: ET F785 P D21


title: 04379_18_14415_Mouse430A_2

city: New York

first: Brian

middle: Roy

last: Untch

state: NY

address: 1275 York Ave

department: Surgery

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Affymetrix protocol, Mouse 430A 2.0

scan_protocol: Affymetrix protocol

data_processing: Partek Genomics Suite, RMA, Quantile normalization, Log base 2

source_name: Tpo-Cre, HrasG12V(Hom)

label_protocol: Affymetrix protocol

extract_protocol: RNA extraction with PrepEase RNA Spin Kit, USB corp

value: Thyroid gland

value: Tpo-cre;HrasG12V (Homozygous)


title: 04379_12_23621_Mouse430A_2

source_name: TPO-Cre, HrasG12V(Hom), p53f/f (ATC)

value: Thyroid tumor (ATC)

value: Tpo-cre;HrasG12V,p53f/f (ATC)


title: 04379_17_14903_Mouse430A_2


title: 04379_10_29145_Mouse430A_2


title: 04379_25_Cre_Pool 2_Mouse430A_2

source_name: Cre Negative Pool 2

value: Pool of normal thyroid glands

value: Cre-negative


title: 04379_19_14422_Mouse430A_2


title: 04379_13_26647_Mouse430A_2

source_name: TPO-Cre, HrasG12V(Hom), p53f/f (PDTC)

value: Thyroid tumor (PDTC)

value: Tpo-cre;HrasG12V,p53f/f (PDTC)


title: 04379_14_26868_Mouse430A_2


title: HMVEC_replicate 2

description: Basal gene expression


title: 04379_16_21688_Mouse430A_2


title: ND+_3

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

hyb_protocol: Labeled material was hybridized to mouse GeneChip HT MG-430 PM Plates as described in the Affymetrix GeneChip 3' IVT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA)

scan_protocol: Scanning was performed using an Affymetrix GeneTitan system

data_processing: Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the variance stabilization normalization followed by a quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach

source_name: NKG2D+ antigen-induced memory CD8 - VV NP68 infected C57BL/6

label_protocol: Total RNA from each sample was labeled as described in the Affymetrix GeneChip 3' IVT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from dry cell pellets according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany)

treatment_protocol: Spleens from three to eight mice were pooled and CD8 T cells were enriched by negative selection using a MACS CD8a+ T Cell Isolation Kit II for mouse (Miltenyi Biotec). Then, memory CD8 T cell (CD8+CD44+) were sorted by FACS based on the expression of  NKG2D. Purity was > 98%

tag: strain/genotype

value: CD8 T cells


title: ND+_2


title: F5-VV_1

source_name: memory F5 TCR Tg CD8 - VV NP68 infection

value: CD45.1 F5 TCR (B6/J-Tg(CD2-TcraF5,CD2-TcrbF5)1Kio/Jmar)


title: 04379_11_26864_Mouse430A_2


title: ND-_1

source_name: NKG2D- innate memory CD8 - VV NP68 infected C57BL/6


title: ND-_5


title: F5N_4

source_name: Naive F5 Tcr Tg CD8


title: Na ND+_1

source_name: NKG2D+ antigen-induced memory CD8 - naive C57BL/6


title: 04379_24_Cre_Pool 1_Mouse430A_2

source_name: Cre Negative Pool 1


title: ND-_4


title: F5N_5


title: Control siRNA treated HUVEC 4

description: HUVEC, control siRNA, 48h, biological replicate 4

hyb_protocol: Cy3-Labeled cRNA was hybridized to Custom Arraystar Human LncRNA Array v2.0 (8x 60K, Arraystar) using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 7 out of 14 samples have flags in Present or Marginal (All Targets Value) were chosen for further data analysis.

source_name: HUVEC, control siRNA, 48h

label_protocol: The Agilent Quick Amp Labeling Kit (Agilent Technologoies) was used to simultaneously amplify and label RNA with Cy3 according to manufacturer's instructions.

growth_protocol: HUVECs were isolated from umbilical cords of male and female births. HUVECs were cultured in supplemented M199 medium for 2 passages and all biological replicates were used at passage 3-4. HMVECs were purchased from Lonza and cultured according to the manufacturer’s instructions for 2 passages and all biological replicates were used at passage 3-4.

extract_protocol: RNA was extracted from siRNA-treated HUVECs using guanidinium-acid-phenol reagents that are based on the research of Chomczynski and Sacchi, 1987. A known amount of exogenous luciferase RNA was introduced at the beginning of the extraction to assess for RNA extraction and first strand cDNA synthesis efficiency.

treatment_protocol: Each biological replicate was subjected to either control siRNA or STEEL siRNA (40 nM) for 48 hrs before extraction.

value: Human umbilical vein endothelial cells

tag: treatment

value: Control siRNA


title: STEEL siRNA treated HUVEC 4

description: HUVEC, STEEL siRNA, 48h, biological replicate 4

source_name: HUVEC, STEEL siRNA, 48h

value: STEEL siRNA


title: ND+_4


title: Na ND+_4


title: Na_4

source_name: Naive C57BL/6 CD8


title: F5N_3


title: FACS sorted E17.5 lung ciliated cells biological replicate 4

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Bioconductor

label: Biotin

source_name: Differentiating ciliated cells from E17.5 mouse lungs

label_protocol: Standard Affymetrix protocol using Ovation RNA Amplification Kit V2 and FL-Ovation Biotin V2 (NuGEN)

growth_protocol: Timed matings of FOXJ1-GFP mice with out-bred ICR strain. Noon on day of plug = embryonic day 0.5.

extract_protocol: Total RNA using Qaigen RNEasy Mini Kit as per manufacturer's instructions

treatment_protocol: E17.5 embryos were dissected and GFP+ lungs selected under GFP-dissecting microscope. Lungs were dissociated to single cells using trypsin/EDTA and GFP+ cells isolated by flow cytometry.

value: embryonic lung

value: Differentiating ciliated cells

tag: age


title: F5-VV_5


title: STEEL siRNA treated HUVEC 3

description: HUVEC, STEEL siRNA, 48h, biological replicate 3


title: Na_5


title: ND+_1


title: Na ND+_3


title: Na_1


title: FACS sorted E17.5 lung ciliated cells biological replicate 3


title: Control siRNA treated HUVEC 2

description: HUVEC, control siRNA, 48h, biological replicate 2


title: STEEL siRNA treated HUVEC 2

description: HUVEC, STEEL siRNA, 48h, biological replicate 2


title: Control siRNA treated HUVEC 3

description: HUVEC, control siRNA, 48h, biological replicate 3


title: STEEL siRNA treated HUVEC 1

description: HUVEC, STEEL siRNA, 48h, biological replicate 1


title: ND+_5


title: Control siRNA treated HUVEC 1

description: HUVEC, control siRNA, 48h, biological replicate 1


title: STEEL siRNA treated HMVEC 3

description: HMVEC, STEEL siRNA, 48h, biological replicate 3

source_name: HMVEC, STEEL siRNA, 48h

value: Human dermal microvascular endothelial cells


title: FACS sorted E17.5 lung ciliated cells biological replicate 2


title: STEEL siRNA treated HMVEC 1

description: HMVEC, STEEL siRNA, 48h, biological replicate 1


title: ND-_3


title: STEEL siRNA treated HMVEC 2

description: HMVEC, STEEL siRNA, 48h, biological replicate 2


title: F5N_1


title: FACS sorted E17.5 lung ciliated cells biological replicate 1


title: Na_2


title: Control siRNA treated HMVEC 3

description: HMVEC, control siRNA, 48h, biological replicate 3

source_name: HMVEC, control siRNA, 48h


title: Na_3


title: Control siRNA treated HMVEC 2

description: HMVEC, control siRNA, 48h, biological replicate 2


title: L2x_3

city: Tianjin

first: Yiheng

last: Wang

address: 17km Jinjing Road

institute: Tianjin Academy of Agricultural Sciences

description: FPKM.xls

data_processing:
Illumina software used for base-calling.
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Clean reads were mapped to the reference genome. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq R package (1.18.0).
Genome_build: http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/
Supplementary_files_format_and_content: processed data file include FPKM values for genes in each sample.

source_name: doubled haploid leaves

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The integrity of the RNA samples was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
3 μg RNA per sample were used to generate the sequencing libraries using the NEBNext® Ultra™ RNA library prep kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: leaf

tag: ploidy

value: doubled haploid

tag: sampling

value: mature leaves from the main stem below the first branch were collected at the stage of bolting


title: L4x_3

description: FPKM.xls

source_name: autotetraploid leaves

value: autotetraploid


title: F5-VV_4

tag: cell type


title: L4x

description: TPM.xls

data_processing:
Illumina software used for base-calling.
Raw data of fastq format were firstly processed through custom perl and python scripts. In this step, clean data were obtained by removing reads containing ploy-N, with 5' adapter containing ploy A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
miRNA expression levels were estimated by transcript per million (TPM)..
Differential expression analysis of two samples was performed using the DEGseq R package.
Genome_build: http://brassicadb.org/brad/datasets/pub/Genomes/Brassica_rapa/V2.0/
Supplementary_files_format_and_content: processed data file include TPM values for genes in each sample.


title: ND-_2


title: L4x_1

description: FPKM.xls


title: L2x_1

description: FPKM.xls


title: L2x_2

description: FPKM.xls


title: L4x_2

description: FPKM.xls


title: F5-VV_2


title: Control siRNA treated HMVEC 1

description: HMVEC, control siRNA, 48h, biological replicate 1


title: F5N_2


title: Na ND+_2


title: L2x

description: TPM.xls


title: SPHK1-I (2)

city: Bethesda

first: Ana

last: Olivera

address: 10 Center Dr, Bldg 10

institute: NIAID (National Institutes of Health)

data_processing: Analyzed using Qiagen data analysis software

label: SYBR

source_name: Cells treated with an inhibitor of SPHK1, 24h, duplicate 2

label_protocol: SYBR

growth_protocol: A million HMC1.2 cells were plated in 6 well plates and cultured with the SPHK inhibitors for 24 h in full media

extract_protocol: RNA was extracted from cell lysates with a Qiagen RNA extraction kit. RNA was converted into cDNA using the RT2 First-Strand Kit (Qiagen), and then used as a template to perform a quantitative RT2 Profiler PCR Array for Human Cell Cycle (Qiagen PAHS-020Z)

treatment_protocol: HMC-1.2 cells treated with SPHK1-I (5 µM), SPHK2-I (50 µM) or vehicle (0.1% DMSO) for 24 h

value: Human mast cells

tag: genotype/variation

value: Cells have oncogenic KIT mutations (D816V and V560G)


title: SPHK2-I (1)

source_name: Cells treated with an inhibitor of SPHK2, 24h, duplicate 1

tag: cell line


title: SPHK2-I (2)

source_name: Cells treated with an inhibitor of SPHK2, 24h, duplicate 2


title: F5-VV_3


title: Vehicle 2

source_name: Control cells treated with vehicle ,24h , duplicate 2


title: SPHK1-I (1)

source_name: Cells treated with an inhibitor of SPHK1, 24h, duplicate 1


title: PaBt-Surf-C_rep_2

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Following fragmentation, 2.4 ug of cRNA were hybridized on the Custom KpSmPaBc Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed via RMA using Affymetrix's Expression Console and default settings. Statistical analysis and further data assessment was then performed using Affymetrix's transcriptome analysis console version 3.0. Genes exhibiting at least a 2.5 fold change in transcript abundance between conditions with an ANOVA p value <0.05  were considered significantly altered by surfactant. To obtain the data reflected in the associated manuscpript, the affymetrix gene cluster ID column was filtered  to obtain the  klebsiella-specific probe intensities by restricting the displayed IDs to those beginning with the Kp MGH 78578 genebank chromosome and plasmid accession numbers (CP000647,CP000648, CP000649, CP000650, CP000651, and CP000652) . Probe values specific to non-coding regions of the genome were also removed by filtering the description column to those not containing the word intergenic region.     This methodology can also be used to obtain Pseudomonas aeruginosa UCBS PA14 (CP000468), Burkholderia thailandensis E264 (CP000845 & CP000846), and Stenotrophomonas maltophilia K279A (AM743169)-specific probe data.

organism:
Burkholderia thailandensis E264
Pseudomonas aeruginosa PA14

source_name: Pa & Bt cultured in MOPS surfactant for 4 h (experimental condition), biological replicate 2

label_protocol: Biotinylated cDNA was prepared from 50 ng of total RNA using the NuGen Ovation Pico system and the Encore Biotin Module according to manufacturer's instructions. For each cDNA sample prepared, the input consisted of 1:1 mixtures of either P.aeruginosa and B. thailandensis, or K. pneumoniae and S. maltophilia total RNA.

growth_protocol: Strains were first  grown overnight in MOPS minimal supplemented with lactate as a carbon source. The following day, cells from these cultures were adjusted to the same optical density, and then cultured for 4 h in both MOPS lactate media and MOPS lactate media supplemented with purified pulmonary surfactant (Survanta).

extract_protocol: Total RNA was first extracted using RNAzol and Zymo's RNA mini prep kit. Small RNAs were then removed through a second extraction via Qiagen's RNEasy kit & provided protocol. RNA quality was assessed  via Agilent BioAnalyzer and quantified through Qubit fluorometer.

treatment_protocol: Following completion of the gene induction period, the cells from each culture were gathered via centrifiguation, resuspended in 800µL of ~70˚C RNAzol, and  frozen at -80˚C until extraction.

tag: condition

value: MOPS Surfactant

tag: replicate

value: C


title: KpSm-Surf-C_rep_2

organism:
Stenotrophomonas maltophilia K279a
Klebsiella pneumoniae MGH 78578

source_name: Kp & Sm cultured in MOPS surfactant for 4 h (experimental condition), biological replicate 2


title: PA-BT_Lact_rep_1

source_name: Pa & Bt cultured in MOPS lactate for 4 h (control condition), biological replicate 1

value: MOPS Lactate

value: B


title: KP-SM-Surf_rep_1

source_name: Kp & Sm cultured in MOPS surfactant for 4 h (experimental condition), biological replicate 1


title: KP-SM-Lact_rep_1

source_name: Kp & Sm cultured in MOPS lactate for 4 h (control condition), biological replicate 1


title: KpSm-Lact-C_rep_2

source_name: Kp & Sm cultured in MOPS lactate for 4 h (control condition), biological replicate 2


title: PaBt-Lact-C_rep_2

source_name: Pa & Bt cultured in MOPS lactate for 4 h (control condition), biological replicate 2


title: Pa-BT-Surf_rep_1

source_name: Pa & Bt cultured in MOPS surfactant for 4 h (experimental condition), biological replicate 1


title: Vehicle 1

source_name: Control cells treated with vehicle ,24h , duplicate 1


title: Ishikawa_ctrl_Erα+_rep1

status: Public on Mar 29 2018

city: Shenyang

first: Wensu

last: Liu

state: Liaoning

address: 77 Puhe Road, Shenyang North New Area

institute: China Medical University

hyb_protocol: Microarray hybridization, washing and staining were performed based on the manufacturer’s standard protocols

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000

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.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

label_protocol: Biotin labeling was performed based on the manufacturer’s standard protocols

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

value: Ishikawa

value: endometrial adenocarcinoma cell line

value: control

value: ERα(+)


title: E058ΔrstAB in vivo, biological rep2

city: Yangzhou

first: Qingqing

last: Gao

state: Jiangsu

address: Yangzhou wenhui Road 12

department: Colledge of Veterianry medicine

institute: Yangzhou university

description: Gene expression profile of rstAB mutant in vivo

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

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

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Escherichia coli APEC O2

source_name: bacteria harvested from blood of chickens

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

growth_protocol: To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection.

extract_protocol: Total RNA from in vivo samples of APEC E058 and E058ΔrstAB was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions.

treatment_protocol: The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum.

tag: strain

tag: genotype/varation

value: mutant

value: in vivo


title: E058 in vivo, biological rep3

description: Gene expression profile of APEC O2 strain E058 in vivo

value: wild-type


title: E058 in vivo, biological rep2


title: LRP1B-expressed MCF-7 cells

city: Gifu

first: Tamotsu

last: Takeuchi

address: Yanagido

department: Pathology and Translational Research

institute: Gifu University School of Medcine

hyb_protocol: 109 μL Hybridization Master Mix and 3.5 μg Fragmented and Labeled cDNA, 45C for 16hr.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G

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

source_name: MCF-7 wit Doxycyline

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

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco Life Technologies, Grand Island, NY, USA) containing 10% heat-inactivated fetal bovine serum (FBS).

extract_protocol: RNA was extracted by using Qiagen RNA Easy kits.

treatment_protocol: MCF-7 cell clones, in which intracellular domain of LRP1B was tightly regulated by doxycycline (Dox) at 100ng/ml.

tag: tissue

value: Human breast cancer cells


title: Ishikawa_sh_Erα+_rep2

value: shMOF


title: E058ΔrstAB in vivo, biological rep1


title: Ishikawa_sh_Erα-_rep2

value: ERα(-)


title: E058 in vivo, biological rep1


title: Ishikawa_ctrl_Erα+_rep2


title: Ishikawa_sh_Erα-_rep3


title: E058ΔrstAB in vivo, biological rep3


title: Ishikawa_sh_Erα+_rep1


title: Ishikawa_sh_Erα-_rep1


title: Ishikawa_sh_Erα+_rep3


title: Ishikawa_ctrl_Erα-_rep2


title: Ishikawa_ctrl_Erα+_rep3


title: non-LRP1B expression MCF-7 cells

source_name: MCF-7 witout Doxycyline


title: FACS sorted E17.5 lung ciliated cells biological replicate 5

source_name: Differentiating ciliated cells from E17.5 mouse lungs

value: embryonic lung

value: Differentiating ciliated cells

tag: genotype


title: Ishikawa_ctrl_Erα-_rep3


title: Ishikawa_ctrl_Erα-_rep1


title: Fraction 2-2

city: Suita

first: Eri

last: Nishiyama

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

institute: Riken

description: rep1-3: independent library preparations;

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using TopHat2
Mapped reads seperated by genes, and the reads mapped for each gene were clustered by molecular barcode
The number of clusters for each was counted, which provides the number of molecules detected for each gene
The copy number of RNA moelcules per cell for each gene is calculated based on spike-in RNA detection efficiency
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene is listed.

source_name: lymph node GC B cells_Fraction 2 (Bcl6hi CD69hi LZ)

growth_protocol: B cells from B1-8hi Bcl6-YFP reporter mice (CD45.1+) or from B1-8hi S1pr2-ERT2cre Ai14 mice (CD45.1+) were transferred to C57BL6 mice, followed by immunization with NP-CGG/CFA. The mice transferred with B1-8hi S1pr2-ERT2cre Ai14 B cells were treated with tamoxifen on day 6, 7, 8. On day 12, 100 GC B cell subsets or 100 tomato+ plasmablasts in the draining lymph nodes were sorted for RNA preparation.

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

value: GC B cells

value: lymph node

tag: background strain

value: B1-8hi (KI/+) Bcl6-YFP (KI/+)

tag: marker


title: Fraction 2-3


title: Fraction 1-3

source_name: lymph node GC B cells_Fraction 1 (Bcl6lo CD69hi LZ)


title: Fraction 1-2


title: GC-PB 2

source_name: Lymph node plasmablasts_GC-derived plasmablast

value: plasmablasts

value: B1-8hi (KI/+) S1pr2-ERT2cre Tg ROSA-Ai14 (KI/+)

value: CD45.1+CD138hiCD44hi tdTomato+


title: GC-PB 1


title: GC-PB 3


title: Fraction 1-1


title: Fraction 3-3

source_name: lymph node GC B cells_Fraction 3 (Bcl6hi CD69lo LZ)


title: Fraction 3-1


title: Fraction 3-2


title: DZ 2

source_name: lymph node GC B cells_DZ

value: B220+CD45.1+CD38loGL7hi CXCR4hiCD86lo


title: DZ 1


title: Fraction 2-1


title: DZ 3


title: THP1_Vector_1

city: Badalona

first: Maria Rosa

last: Sarrias

address: Ctra Can Ruti camí de les escoles, s/n

department: Innate Immunity Group

country: Spain

institute: Health Sciences Research Institute Germans Trias i Pujol (IGTP)

hyb_protocol: cRNA samples were hybridized to the human whole genome microarray” (Applied microarrays, CodeLink) at 37ºC for 16 h by using the TrayMix hybridizer (BioTray, France).

scan_protocol: Arrays were scanned with an InnoScan 700 scanner (Innopsys).

data_processing:
Data normalization and analysis were performed with Bioconductor R, LIMMA software by the bioinformatics platform of CIBERehd, Spain
Those controls and spots with a background lower than 2 fold their standard deviation in the 25% of samples were eliminated (resulting in a reduced data set of 25,160 rows). Microarray were background substracted using normexp algorithm and normalised by quantiles method. All processes were done using LIMMA Bioconductor v3.4.

label_protocol: Samples were labeled with Cy5 (Bionova)

growth_protocol: Cells were grown in RPMI-1640 2 mM glutamine, 100 u/mL penicillin, and 100 μg/mL streptomycin supplemented with 10% heat-inactivated FBS and 250 μg/mL geneticin. Prior to the experiments, cells were differentiated to macrophages by incubation with 10 ng/mL of phorbol 12-myristate 13-acetate (PMA) in culture medium for 24 h. They were then washed with PBS and grown in culture medium for 24 h

extract_protocol: Total RNA was isolated and purified from 106 THP1-Vector or THP1-CD5L macrophages by using TRIzol reagent (Invitrogen) and RNeasy columns (Qiagen). cRNA was generated from 10 μg of total RNA by using Superscript (Invitrogen)

treatment_protocol: Stably transfected THP1-Vector and THP1-CD5L cell lines were generated as described in Amézaga et al. (Amézaga N, Sanjurjo L, Julve J, Aran G, Perez-Cabezas B, Bastos-Amador P, Armengol C, Vilella R, Escola-Gil JC, Blanco-Vaca F, et al. Human scavenger protein AIM increases foam cell formation and CD36-mediated oxLDL uptake. J Leukoc Biol (2014) 95:509–520).

value: PMA-differentiated THP1  monocyte-like cells

tag: stably trasfected with

value: Vector (pCIneo)


title: THP1_CD5L_2

value: CD5L (pCineo-CD5L)


title: THP1_CD5L_3


title: THP1_Vector_2


title: THP1_CD5L_1


title: 3147

city: Montreal

first: Corine

last: Martineau

state: Quebec

address: 1003 Decarie Boulevard

department: Research Centre

institute: Shriners Hospital for Children - Canada

hyb_protocol: Samples were prepared and hybridized to GeneChip Mouse 430_2 Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The signal intensity data was analyzed with the Applied Biosystem Transcriptome Analysis Suite (v. 4.0.1) considering at least a 2-fold increased expression with a significance threshold set at p < 0,05 and a FDR of < 0.05.
The resulting CHP files are with the Applied Biosystem Transcriptome Analysis Suite (v. 4.0.1) considering at least a 2-fold increased expression with a significance threshold set at p < 0,05 and a FDR of < 0.05.
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

source_name: Cyp24a1 (+/-)_Bone callus tissue, D14 post-OT

extract_protocol: Total RNA was extracted using Trizol and RNAeasy (QIAGEN) as indicated in manufacturer's protocols.

treatment_protocol: 12-week-old mice were used for tibial intramedullary rod-stabilized osteotomy and left to heal for 14 days. On day 14 post-OT, mice were sacrificed, callus tissue was harvested in RNAlater until analysis.

tag: strain background

value: C57BL6J x 129SV mixed

value: 12 weeks

tag: time point

value: 14 post-OT

value: bone callus


title: 3018

label_protocol: Samples were prepared and hybridized to GeneChip Mouse 430_2 Array according to Affymetrix specifications.

tag: age

tag: treatment

value: tibial intramedullary rod-stabilized osteotomy


title: 3137

source_name: Cyp24a1 (-/-)_Bone callus tissue, D14 post-OT


title: 3016