title: FM003_DOMINANT_2

description: Bulk RNA-seq from dominant NPK clones

value: prostate


title: D-lactic acid-producing Pichia pastoris without ScFLO1 overexpression, replicate 1

status: Public on Apr 01 2023

type: SRA

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

library_source: transcriptomic

data_processing:
The raw reads were processed using FASTP software. Clean reads were obtained from removing low quality reads from raw data using default parameters (the quality score cutoff of 20).
Assembly: Komagataella phaffii GS115 (GCF_000027005.1_ASM2700v1_genomic.fna)
Supplementary files format and content: normalizedReadCount.csv

molecule: total RNA

organism: Komagataella pastoris

source_name: cell pellets

extract_protocol:
The pellets were washed with 5 mL of distilled water. Total RNA was extracted using the QIAgen RNeasy Kit following the manufacturer's protocol. Contaminating genomic DNA was removed from the RNA samples by DNaseI (NEB) digestion using the manufacturer's protocol.
The RNA quantity was analyzed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and samples were stored at -80 °C until transcriptomics analysis. RNA Integrity Numbers (RIN) for the purified RNA samples were obtained using an Agilent 2100 Bioanalyzer (Agilent Technologies). All purified RNA samples had a RIN number higher than 8.0 and were sequenced by NovogeneAIT (Tianjin, China).
Paired-end 150bp

tag: cell type

value: cell pellets

tag: treatment


title: C3_65

city: Jena

first: Axel

last: Mithöfer

state: Thuringia

address: Hans-Knöll-Straße 8

department: Plant Defense Physiology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

data_processing:
Raw reads were trimmed by in-house scripts.
Assembly: The clean reads were mapped onto Ipomoea trifida reference genome (http://sweetpotato.uga.edu/), using HISAT2 V2.0.5 with default parameter. HTSeq V0.6.1 software was used with the union mode to count read numbers mapped of genes for each sample.
Supplementary files format and content: Data matrix with read counts for further analysis with DESeq2 V1.22.2

organism: Ipomoea batatas

source_name: I. batatas 3rd leaves, 1 h water treatment

growth_protocol: Sweet potato scions (Ipomoea batatas Lam.; cultivar Tainong 57) were grown in phytochambers under long day conditions (16 h light : 8 h dark) at 28 °C (day) and 25°C (night) in 70% relative humidity for 3 weeks

extract_protocol:
RNA was extracted according to 1 using TRIzol Reagent (Invitrogen, USA). 1 Meents, A. K. et al. Volatile DMNT systemically induces jasmonate-independent direct anti-herbivore defense in leaves of sweet potato (Ipomoea batatas) plants. Scientific Reports 9, doi:10.1038/s41598-019-53946-0 (2019).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendationsies for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Sweet potatoe leaves were treated for 1 h with IbHypSysIV, IbPep1 or water (control)

tag: tissue

value: 3rd leave

tag: genotype

value: Control


title: C2_64

value: Ipomoea batatas Lam.; cultivar Tainong 57


title: non-slick rep5

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
The genome of Bos taurus from JGI  was used as the reference sequences for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the read mapper of the STAR package were done to visualize differential gene expression for each treatment with in-house R scripts. In addition, we also conducted a multi-factor analysis (e.g., control, treatment, and age) for differences between the samples while estimating the effect of the treatment on an individual animal.
Pathway enrichment analysis were done with GSEA , which is an essential computational method for determining the statistical and concordant differences of the defined set of genes between two phenotypes. The log2 fold-change between the genotypes were ranked and run through the GSEA using the clusterProfiler (v3.16.1) package in R (v.4.1.3) against the information of Bos taurus in the MSigDB , the ‘org.Bt.eg.db’ in Bioconductor, and the ‘Bos_taurus.gmt’ in WikiPathways. The GO and KEGG enrichment analysis of differentially expressed genes (DEGs) (p-value <0.05, log2 fold change > |1.5|) between phenotypes were also conducted based on the MSigDB search.
Assembly: Bos_taurus.ARS-UCD1.2.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include the gene names and the mapped read counts for each Sample

organism: Bos taurus

source_name: skin

extract_protocol:
RNA extraction was performed with the Qiagen RNeasy Mini kit (Germantown MD, USA) according to the user’s guide. Quantity of RNA was determined using the QUBIT fluorescent method (Invitrogen, Carlsbad, CA, USA) and Agilent Bioanalyzer (Santa Clara, CA, USA).
An amount of 100 ng of high quality of total RNA with RIN of 7 or higher was used for library construction using the reagents provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer's instructions. Briefly, 100 ng total RNA was used for mRNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Then the poly A enriched RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. Synthesis of ds cDNA was done using the 2nd strand master mix provided in the kit, followed by end-repair and dA-tailing.  At this point, Illumina adaptors were ligated to the sample. Finally, library was amplified and then purified with AMPure beads (Beckman Coulter, Brea, CA, USA).  Library size and mass were assessed by analysis in the Agilent TapeStation using a DNA5000 Screen Tape.  Quantitative PCR was used to validate the library's functionality using the KAPA library quantification kit (Kapa Biosystems, Wilmington, MA, USA) and monitoring on the BioRad CFX 96 real-time PCR system (Richmond, CA, USA). Twelve barcoded libraries were pooled equimolarly for sequencing simultaneously for 0.23 lanes using the Illumina NovaSeq6000. Normalized libraries were submitted to the Illumina  Free Adapter Blocking Reagent protocol to minimize presence of adaptor-dimers and index hopping rates.  The library pool was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2x150 cycles) of the Illumina NovaSeq6000. The instrument’s computer utilized the NovaSeq Control Software v1.6. Cluster and SBS consumables were v1.5. The final loading concentration of the library was 120 pM with 1% PhiX spike-in control. One lane generated 2.5-3 billion paired-end reads (~950Gb) with an average Q30%>= 92.5% and Cluster PF= 85.4%.

treatment_protocol: Heifers were genotyped for the SLICK1 mutation in PRLR using either the CLARIFIDEÒ Plus platform from Zoetis (Parsippany, NJ, USA) or ta KASP-PCR procedure. All heifers were sired by one of two SL+/- Holstein bulls [Slick-Gator Blanco 551HO03574) or Slick-Gator Lone Ranger (047HO01029)] .Skin biopsy from the shoulder area was performed while the animal was restrained in a head chute. The skin sample was collected by rotating a 5 mm skin punch (Integra™ Miltex™ Standard Biopsy Punch, Fisher Scientific, Pittsburgh, PA, USA) while pressing downwards with mild force, and then the skin sample was taken from the skin punch using a tweezer and placed into a cassette between sponges. A sterile gauze was placed on the biopsy site to remove excess blood or stop bleeding, and subsequently the wound site was closed with super glue. A tick spray consisting of 0.5% (w/v) permethrin (Neogen, Lansing, MI, USA) was applied around the biopsy site.

value: skin

tag: geographic location

value: USA:Basinger, FL

tag: age

value: 49 weeks

value: WT


title: FM002_MINOR1

city: stony brook

first: Fu

last: Luo

state: New York

address: 100 Nicholls Road

institute: Stony Brook University

description: Bulk RNA-seq from minor NPK clones

data_processing:
For single cell RNA-seq samples, FASTQ files were processed using the entire Cell Ranger (v3.0.2) single-cell analysis pipeline (10x Genomics). This pipeline includes both a ‘count’ and ‘aggregate’ step. Briefly, data were aligned with the 10x Genomics pre-built mouse genome for filtering, barcode counting, and UMI counting using default parameters.
For bulk RNA-seq samples, RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.17) for conversion of BCL to fastq format, coupled with adaptor trimming. Reads were mapped to the mouse genome (UCSC/mm10) using STAR (2.5.2b) and FeatureCounts (v1.5.0-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample or every cell

organism: Mus musculus

source_name: Prostate luminal cancer cells

extract_protocol:
Library preparation was done using a Clontech’s SMART-seq v4 Ultra Low Input RNA Kit to create amplified cDNA, followed by library preparation using Illumina’s Nextera XT kit.
Briefly, mouse prostate tissue from AP lobes was dissected in cold phosphate buffered saline (PBS) and minced with scissors, followed by incubation in DMEM/F12 (Gibco) supplemented with 5% FBS and 0.1% collagenase/hyaluronidase (STEMCELL Technologies) at 37°C for 2 hours. Dissociated tissues were spun at 350 g for 5 min and resuspended in TrypLE (Gibco), followed by incubation at 37°C for 20 minutes. After centrifugation at 350 g, pelleted cells were resuspended with pre-warmed 5 mg/ml dispase (STEMCELL Technologies) and, if necessary, incubated for an additional 20 minutes at 37°C. The cell suspension was then supplemented with 1:10 dilution of 1 mg/ml DNase I (STEMCELL Technologies) and triturated vigorously for 2 min. Enzymes were deactivated and diluted by addition of HBSS/2% FBS. Finally, the resulting cell suspension was passed through a 40 μm cell strainer (Falcon) to remove any large clumps of cells remaining. Filtered single cells were resuspended in Opti-MEM (Gibco) and flow sorted based on RFP, CFP or YFP expression on a BD FACS Aria II instrument. The Confetti+ FACS sorted cells were processed for single cell RNAseq on a 10x Genomics platform. Similarly collected cells were also flash-frozen in liquid nitrogen and stored at −80 °C for subsequent RNA processing.
Protocols applicable to each sample are included in the SAMPLES section

tag: strain

value: Nkx3.1CreERT2/+; Ptenflox/flox; K-RasLSLG12D/+; R26r-Confetti

value: 3 month


title: slick rep6

value: 51 weeks

value: slick mutation


title: D-lactic acid-producing Pichia pastoris with ScFLO1 overexpression, replicate 3


title: C1_63


title: slick rep5

value: 60 weeks


title: FM001_DOMINANT_1

description: Bulk RNA-seq from dominant NPK clones


title: FM004_MINOR_2

description: Bulk RNA-seq from minor NPK clones


title: non-slick rep4

value: 52 weeks


title: RNA_seq_WT_non-pregnant_biliary epitheial cells_ex2

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STATR  (version STAR-2.7.9a) with the GENCODE  vM23 annotation gtf file after trimming the adaptor sequences and low-quality bases using cutadapt-3.4.
The uniquely mapped reads were counted at the gene level (protein coding) using HTSeq-count v0.13.5 and the GENCODE vM25 annotation file. The expression levels were caluculated as FPKM usign DEseq2 (v. 1.30.1) and GenomicFeatures packages.
Genome_build: mm10
Supplementary_files_format_and_content: A tsv file includes FPKM values for each sample.

source_name: BECs in liver from non-pregnant mice

extract_protocol:
Mice were laparotomized under isoflurane inhalation anesthesia, and the portal vein was cannulated and perfused with liver perfusion medium. Then, the liver was perfused with liver digestion medium. To isolate BECs, remaining undigested liver pieces were further treated with collagenase, DNase I, and Dispase. The cell suspension was filtered with 70 micrometer cell strainer, then the filtrates were centrifugation at 50g to remove the parenchymal fraction. The non-parenchymal fraction in the supernatant was stained with anti-FcR antibody (rat, 1:100, Bio Legend, 101302), followed by staining with the fluorescence-conjugated antibodies for 1 h. After wash with PBS plus 1 % BSA, the cells were sorted by FACS. RNA was extracted from the FACS-sorted BECs by using an RNeasy Micro Kit (Qiagen).
50 ng Total RNA was used to generate RNA-seq libraries using KAPA RNA HyperPrep Kit with RiboErase (Roche).

tag: Sex

value: female

value: liver

tag: condition

value: non-pregnant

value: biliary epithelial cells


title: D-lactic acid-producing Pichia pastoris with ScFLO1 overexpression, replicate 1

value: cell pellets


title: FM006_DOMINANT_3

description: Bulk RNA-seq from dominant NPK clones

value: prostate


title: MIG-Snai1, rep3

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

description: HPC7 cells transduced with a retroviral vector for ectopic expression of wildtype Snai1

library_source: genomic

data_processing:
Reads were filtered with FASTP (Chen et. al., 2018) using the parameters - fastp -l 35 -W 3 -5 -3
Singleton reads were discarded (fastq-pair)
Paired-end reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) to the reference genome (mm10)
Aligned reads were filtered for optical and PCR duplicates (Picard Tools)
Reads aligning to ENCODE blacklisted regions (Amemiya et. al., 2019), mitochondrial genome, improper pairs, and mapping quality <20 were discarded
Analysis of differential enrichment at promoter regions (-1kb to 100bp around the TSS) was performed using DiffBind (Stark et al 2011)
Genome_build: Illumina iGenomes UCSC reference genome (mm10) & gene annotation
Supplementary_files_format_and_content: CSV file was generated from DiffBind (Bioconductor R) and contains results of differential enrichment analysis at gene promoters

molecule: genomic DNA

source_name: Hematopoietic progenitor cells

growth_protocol: HPC7 cells were maintained in IMDM supplemented with 10% fetal bovine serum (Sigma), penicillin (100 U/ml), streptomycin (100 µg/ml), 2 mM L-glutamine (Gibco), 0.05 mM 2-mercaptoethanol and 100 µg/ml mSCF (Peprotech).

extract_protocol:
100,000 cells were collected and washed with PBS and pelleted by centrifugation (300 g). Cells were then washed with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) following a 3 min incubation on ice.
The tagmentation reaction was performed in a thermocycler for 30 mins at 37°C with 1x TD buffer, 0.3x PBS, 0.1% Tween 20, 2.5 µl Tn5 (Illumina) in a 50 µl volume as previously described (Corces et al. 2017).

tag: parental cell line

tag: cell line

value: MIG-Snai1, rep3-HPC7


title: slick rep4

value: skin

value: 61 weeks


title: Adult murine lung cells

city: San Francisco

first: Tien

last: Peng

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description: single cell RNA sequencing of adult murine lung cells

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: lung

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 °C and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 °C and washed with FACS buffer. The following antibodies were used at 1:200 for staining: anti-CD45-PE-Cy7, anti-CD31-Percp, and anti-Epcam-BV421. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument, using Single cell 3' v2 chemistry kit.
droplet-based single cell RNA-Seq

value: Lung mesenchyme

value: adult

value: lung


title: 2y3_muscle

city: Chengdu

first: Yi

state: Sichuan

address: gongpin road #211

country: China

institute: Sichuan Agricultural University

description:
quant_lnc.tpm_0.1.txt
quant_mRNA.tpm_0.5.txt

data_processing: Clean data were aligned to the pigeon (Columba livia) genome (Cliv_1.0) using STAR. Transcripts were ab initio assembled using the Cufflinks software. For long non-coding RNA identification, transcripts that were clipped (first or last exons <15 bp), with short lengths or in a lowly abundance were discarded as poorly assembled ones for each sample. Secondly, transcripts were merged and compared to the reference genome by TACO software and those transcripts un-annotated by protein-coding genes (PCGs) were kept as putatively lncRNA transcripts. Thirdly, CPC2 was used to perform coding potential analysis, and PfamScan was applied to check the domain hits of the nucleic acid sequences against the Pfam database after open reading frames were obtained utilizing EMBOSS. A domain hit by PCGs and putative lncRNAs were checked by Fisher's exact test, and those domains with an odds ratio of less than 10.0 or P value greater than 0.05 were considered as likely artifacts. After removing transcripts in all likely domains and with coding potential, the remains were identified to be lncRNAs.

organism: Columba livia

source_name: breast muscle

growth_protocol: The pigeons were grouped into four developmental stages: 1 day (1D), 14 days (14D), 28 days (28D), and 2 years old (2Y).

extract_protocol:
Total RNA was extracted from frozen breast muscle samples using Trizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The breast muscle of pigeon was collected and then frozen in liquid nitrogen rapidly.

value: White-King pigeon

value: breast muscle

value: 2 years old


title: MIG-Snai1, rep2

value: MIG-Snai1, rep2-HPC7


title: 2y2_muscle


title: non-slick rep3

value: USA:Basinger, FL

value: 73 weeks

value: WT


title: slick rep3

value: slick mutation


title: 2y1_muscle


title: DED2 KO cross1 small RNAs @10 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Sequence reads were filtered as described (Schoeberl et al. 2012; Noto et al. 2015). Briefly, following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed, and reads that perfectly match the MIC genome were used.
Genome_build: Tetrahymena thermophila MIC genome assembly released in 2016 was used for mapping. The positions of the predicted IESs were described in (Noto et al. 2015).
Supplementary_files_format_and_content: Sequenced 26 to 32 nt RNAs that map uniquely to 4,691 Type-A IESs, 3,295 Type-B IESs and 10,235 10 kb fragments of MDSs (described in Noto et al. 2015  are counted, and normalized numbers (reads per kb per million reads [RPKM]) are shown.
The sequences of MDSs were downloaded from Tetrahymena Genome database (below). The sequences were fragmented to 10 kb pieces and used as fragments 1, 2, 3 and so on.    http://www.ciliate.org/system/downloads/1-upd-Genome-assembly.fasta        List of the sequences of Type-A IESs and Type-B IESs are attached as text files but these are described in Noto et al. (2015) Mol Cell 59, 229-42, as mentioned in "processed data files format and content".    Sequences are ordered as 1, 2, 3.. in each file.

organism: Tetrahymena thermophila

source_name: DED2 KO cross#1 10h

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight.

extract_protocol:
Total RNA was extracted with TRIzol reagent . 1 mL of Trizol reagent was used to lyse1x10e6 cells.
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

treatment_protocol: To induce conjugation, exponentially growing cells (~3-5x 10e5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for overnight and mixed for conjugation (5x 10e5/ml) at 30°C.

tag: strains

value: mating cells of DED2 KO strains 15-6 and 2-12-4, which lack the DED2 gene in the MAC.


title: DED2 KO cross2 small RNAs @10 hpm

source_name: DED2 KO cross#2 10h

value: mating cells of DED2 KO strains 22-3 and 2-2-2, which lack the DED2 gene in the MAC.


title: slick rep2

value: 74 weeks


title: D-lactic acid-producing Pichia pastoris with ScFLO1 overexpression, replicate 2

value: cell pellets


title: DED2 KO cross1 small RNAs @6 hpm

source_name: DED2 KO cross#1 6h


title: 28d2_muscle

value: 28 days old


title: 28d3_muscle


title: non-slick rep1

value: skin

value: 75 weeks


title: DED2 KO cross2 small RNAs @6 hpm

source_name: DED2 KO cross#2 6h


title: DED2 KO cross2 small RNAs @3 hpm

source_name: DED2 KO cross#2 3h


title: slick rep1

value: 79 weeks


title: 14d3_muscle

data_processing:
Clean data were aligned to the pigeon (Columba livia) genome (Cliv_1.0) using STAR (v.2.6.0c) with suggested parameters in GENCODE to identify mRNA transcripts.
For long non-coding RNA identification, the mapped reads were assembled and filtered using the Cufflinks (v.2.1.1) and TACO software.
CPC2 (http://cpc2.cbi.pku.edu.cn/) was used to perform coding potential analysis, and PfamScan (v.1.6) was applied to check the domain hits of the nucleic acid sequences against the Pfam (release31) database.
After removing all the likely domains, the remaining transcripts were identified to be long non-coding RNAs based on the results of coding potential analysis.
Genome_build: Cliv_1.0
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

value: 14 days old


title: DED2 KO cross1 small RNAs @3 hpm

source_name: DED2 KO cross#1 3h


title: WIR-13706

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

data_processing:
Illumina platform used for base calling
TASSEL5 GBSv2 pipeline was used for identification of tags at cut sites and SNPs located across reference genome.
The fastq files were aligned against the tomato reference genome using the Bowtie2 tool version 2.2.9. The .sam file created from the Bowtie2 aligner program was used through SAMToGBSdbPlugin()
DiscoverySNPCallerPluginV2 took a GBSv2 database file as input and identified SNPs from the aligned tags.
Assembly: mm9
Supplementary files format and content: The VCF file generated from tassel pipeline was generated.
Supplementary files format and content: After filtration SNPs were retained provided in hapmap (hmp) format.

organism: Solanum lycopersicum var. cerasiforme

source_name: Leaf

extract_protocol:
gDNA was isolated from leaf samples by using Xcelgen Plant gDNA Isolation Kit (XG2611-01) as per the protocol described. The DNA was eluted in 50µl Nuclease-Free Water. The samples were quantified using Qubit Fluorometer. For determining A260/280 ratio, 1µl of sample was loaded in Nanodrop8000 spectrophotometer. The quality of samples was checked in 0.8% Agarose gel electrophoresis along with Hind III marker for the presence of intact bands.
To 100ng of gDNA, barcoded adapters (~0.1pM) were added and digested with Apek1 enzyme for 12h at 75oC. The barcoded and common adapters were ligated to the sticky ends of the digested DNA with T4 DNA Ligase enzyme at 22oC for 180 mins, followed by heat inactivation. The ligated products were pooled into 12 groups of 12 samples each group. The pool was PCR amplified to generate the final library pool.
High Sensitivity (HS) DNA chip and library pool was sequenced on Illumina platform to generate ~ 3 million reads/sample.

tag: domestication

value: Cultivated

value: Leaf


title: Neutrophils_BD_treated_rep1

type: RNA

city: Paris

first: Paul

last: Régnier

address: 83 boulevard de l'hôpital

institute: AP-HP

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Subsequent CEL files were processed and RMA-normalized using affy and oligo R packages and concatenated into a single text file summarizing all samples and genes. Differential gene analysis was performed using DESeq2 and limma R packages, while Gene Set Enrichment Analysis was performed using gsva R package. In both cases, the p-values obtained after the moderated t tests were corrected using Benjamini-Hochberg method.

label: biotin

organism: Homo sapiens

source_name: Neutrophils, BD, treated

label_protocol: Affymetrix protocol

extract_protocol: Blood samples from heathy donors (HD) or Behçet’s patients (BD) were collected by venipuncture into acid citrate dextrose (ACD-A) blood collection tubes. Neutrophils were then isolated by a two-step centrifugation of whole blood onto Ficoll less than 3 hours after venipuncture. Sample purities were assessed afterwards and were all > 95%. Total RNA from neutrophils was then extracted using the NucleoSpin RNA kit (Macherey-Nagel) and quantified by a NanoDrop 1000 spectrophotometer. The mean RNA concentration ± SEM in the processed samples was 94.54ng/µL ± 20.45. For quality control, RNA dilution was performed using Agilent RNA 6000 Nano Kit and 1µL of the sample was run on the Nano chip using an Agilent 2100 electrophoresis bioanalyzer. The quality of total RNA was assessed using the profile of the electropherogram and the RNA integrity number (RIN) was calculated. The mean RIN ± SEM number for the processed samples was 6.46 ± 0.43. 100ng of RNA for each sample were then hybridized to Affymetrix Clariom S Human microarray.

treatment_protocol: Blood from patients with BD was collected before or after Apremilast treatment (30mg twice a day during 12 weeks).

tag: disease state

value: Behçet's disease

value: Neutrophils

value: PDE4 inhibitor Apremilast


title: Neutrophils_BD_treated_rep3


title: Neutrophils_BD_treated_rep4


title: non-slick rep2

value: USA:Basinger, FL


title: 14d2_muscle

value: White-King pigeon

value: breast muscle


title: Neutrophils_BD_untreated_rep4

source_name: Neutrophils, BD, untreated

value: untreated


title: Neutrophils_BD_treated_rep2


title: Neutrophils_BD_untreated_rep1


title: EC-528372


title: EC-165690


title: ifh1 KO

city: HERSHEY

first: Yen Teng

last: Tai

state: PA

address: 700 HMC Cres Rd

department: Biochemistry and Molecular Biology

institute: Penn State College of Medicine

data_processing:
Miseq Control Software v2.6  for MiSeqTM II System
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BaseSpace Onsite v2.1 (default parameters)
Trimmed sequence reads were mapped to S.pombe genome using Tophat2 (v2.0.9)
Read count extaction and normalization were performed using Cufflinks (v2.1.1)
Assembly: Reference genome sequence and annotations from PomBase (ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz ver. 2017/11/01 9:00:00; ftp://ftp.pombase.org/pombe/genome_sequence_and_features/gff3/schizosaccharomyces_pombe.genome.gff3.gz ver. 2017/10/31 9:00:00)
Supplementary files format and content: excel files include FPKM values for each Sample

organism: Schizosaccharomyces pombe

source_name: ifh1 knockout

growth_protocol: S. pombe cells were grown to exponential phase and a total of 20 OD units of cells were harvested through filtration onto 0.45 μm mixed cellulose ester membrane

extract_protocol:
The cell pellets were resuspended in a preheated (65°C) solution composed of 25 µL of 10 % SDS and 300 µL of acid phenol: chloroform. Acid washed glass beads and bead buffer (75 mM NH4OAc and 10 mM EDTA, pH 8) were then added to the cell resuspension. The samples were vortexed for 1 minute, incubated at 65°C for 1 minute and this process was repeated for 3 times. After cell disruption, the samples were incubated at 65°C for 10 minutes and vortexed for 1 minute. The aqueous phase was recovered through centrifugation at 16000 ×g for 15 minutes and mixed with 250 µL of preheated (65°C) bead buffer. The samples were further subjected to centrifugation (16000 ×g, 4 °C, 15 minutes) and the supernatant was transferred to prechilled bead buffers with isopropanol (Wako). After centrifuged at 22000 ×g, 4°C for 30 minutes, the pellets were washed with RNase-free 70% ethanol. The RNA pellets were dried and dissolved in 30 µL of DEPC water.
RNA libraries for RNA-seq were prepared using NEBNext ultra directional RNA library prep kit for Illumina following manufacturer's protocols.

treatment_protocol: No treatment

value: ifh1 knockout

value: Untreated


title: fhl1 KO

source_name: fhl1 knockout

value: fhl1 knockout


title: 1d3_muscle

data_processing: Clean data were aligned to the pigeon (Columba livia) genome (Cliv_1.0) using STAR. Transcripts were ab initio assembled using the Cufflinks software. For long non-coding RNA identification, transcripts that were clipped (first or last exons <15 bp), with short lengths or in a lowly abundance were discarded as poorly assembled ones for each sample. Secondly, transcripts were merged and compared to the reference genome by TACO software and those transcripts un-annotated by protein-coding genes (PCGs) were kept as putatively lncRNA transcripts. Thirdly, CPC2 was used to perform coding potential analysis, and PfamScan was applied to check the domain hits of the nucleic acid sequences against the Pfam  database after open reading frames were obtained utilizing EMBOSS . A domain hit by PCGs and putative lncRNAs were checked by Fisher's exact test, and those domains with an odds ratio of less than 10.0 or P value greater than 0.05 were considered as likely artifacts. After removing transcripts in all likely domains and with coding potential, the remains were identified to be lncRNAs.

value: 1 day old


title: 28d1_muscle

value: 28 days old


title: 1d2_muscle


title: sfp1 KO

source_name: sfp1 knockout

value: sfp1 knockout


title: IARI-2


title: WIR-13717


title: WT

source_name: WT

value: WT


title: 1d1_muscle


title: Neutrophils_HD_untreated_rep3

source_name: Neutrophils, HD, untreated

value: control


title: Neutrophils_BD_untreated_rep3


title: Neutrophils_HD_untreated_rep5


title: Neutrophils_BD_untreated_rep2


title: Neutrophils_HD_untreated_rep4


title: 14d1_muscle

value: 14 days old


title: Neutrophils_HD_untreated_rep1


title: Line_E_10_1

status: Public on Mar 31 2023

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

country: United Kingdom

institute: University of Stirling

description: mRNA expression data from Clariom D GeneChip

hyb_protocol: Samples were hybridised to the Clariom D GeneChip microarray (Thermofisher UK) as per directions for the GeneChip WT Plus Reagent kit (Thermofisher UK). Overnight hybridisation to the Clariom D GeneChip took place at 45oC for 16 hours.

scan_protocol: After washing and staining as per directions for the  GeneChip WT Plus Reagent kit (Thermofisher UK) images were captured and cel files generated using the GeneChip Scanner 3000 and raw data converted to .CEL files using the Affymetrix GCOS Software (Thermofisher UK).

data_processing:
The .CEL data were analysed using R/Bioconductor using an updated chip definition file (CDF) from the Brainarray resource based on Ensembl gene definitions (ENSG version 25.0.0). Raw microarray data were normalised using the SCAN method (Piccolo et al, 2012 DOI:10.1016/j.ygeno.2012.08.003). Normalised data were filtered using the UPC method (see Piccolo et al) with expression intensity and UPC filters were set at 0 and 0.5 respectively. Changes in differential expression were examined using empirical Bayes and a moderated t statistic implemented in the limma package.
The SCAN algorithm generates a log2 signal for expression. The CDF used was the updated chip definition file (CDF) from the Brainarray resource based on Ensembl gene definitions (CDF = ENSG version 25.0.0)

source_name: Primary cell line E, 10ng/ml intelectin

label_protocol: Sense strand cDNA was generated, fragmented and labelled using the GeneChip WT Plus Reagent kit (Thermofisher UK) as per kit manufacturer directions.

growth_protocol: Primary human skeletal muscle cells (SkMCs) sourced from three different healthy donors (lot 20TL182717, 20TL070666 and 18TL180368) were purchased from Lonza (CC-2580, UK) and cultured as per the manufacturer’s protocol. Briefly, the cells were incubated at 37ᵒC and 5% CO2 in growth medium (CC-3245, Lonza, UK) and passaged when a confluence of 80% was reached. The cells were washed with Dulbecco's phosphate-buffered saline (DPBS, 14040117, Thermo Fisher, UK) and the culture medium was replaced every 48 hours. After four passages, the myoblasts were harvested using Gibco’s trypsin-EDTA (25200056, Thermo Fisher, UK), counted with a Bio-Rad TC20 automated cell counter using cell counting slides (Bio-Rad, 1450016, UK) and transferred to 6-well or 96-well (polystyrene) plates. To induce differentiation, the cells were incubated in Dulbecco's Modified Eagle Medium/Ham's F-12 supplemented with 2% horse serum (DMEM, 12634010, Thermo Fisher, UK) for 3 to 5 days depending on protocol requirements.

extract_protocol: Following incubation with intelectin treatment, the RNeasy mini kit (Qiagen, 173046459, UK) was used to extract and purify total RNA.  Briefly, the myotubes were lysed and homogenised with a highly denaturing buffer that inactivates RNAses and ethanol was subsequently added to provide suitable binding conditions. The samples were then added to RNeasy spin columns, allowing total RNA to bind to the membrane. Afterwards, contaminants were washed away and RNA was eluted in 50µl RNAse-free water. Lastly, RNA concentration and quality was assessed for all samples with a Denovix DS-11 FX+ spectrophotometer (Denovix, UK).

treatment_protocol: After five days of differentiation, various concentrations of ITLN1 (i.e., 0, 10, 100 and 500ng/ml) were added to the skeletal muscle cells for six hours.

value: myotube

tag: lot number

value: Lonza lot #20TL070666


title: Line_H_10_1

source_name: Primary cell line H, 10ng/ml intelectin

value: Lonza lot #18TL180368


title: Line_B_100_1

source_name: Primary cell line B, 100ng/ml intelectin

value: Lonza lot #20TL182717


title: SAMR1_cont_2

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: Gene expression data from RAW264 cells, pre-treated with BTEE for 24 h and then LPS-induced for 17h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, mouse; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (CEL file) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7). CHP files were generated using freely available Expression Console software.
Signal intensity of all the samples derived from Transcriptome analysis console software. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL. files ).

organism: Mus

source_name: SAMR1 mice treated with saline  for 30 days  and then trained for MWM test.

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: After one week of acclimatization, SAMP8 mice were randomly divided into SAMP8 saline-administered group (n = 6~8) and a TG-administered group (n = 6~8). SAMR1 saline-administered group (n =6~8) was housed as normal aging controls. The mice were housed individually under controlled temperature (21−23°C), photoperiod, (12-h light/dark) and provided food and water freely.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Trigonelline(3-carboxy-1-methyl-pyridinium);TG was purchesed from Cayman chemical (CAS Number 6138-41-6). TG (5 mg/ml) was dissolved in Mill-Q water and orally administered to SMAP8 mice at 5 mg/kg for 30 days. This concentration was determined following our previous study. SAMP8 controls and SAMR1 mice were administered an equal volume of Saline to that of the extract. After completion of the 30 days administration, the mice were tested in the behavioral test for eight days,  TG administration was continued during this period.

value: Hippocampus


title: SAMR1_cont_3


title: Daoy_shDDX3X_3

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

data_processing:
Illumina bcl2fastq2 was used for base calling
The fastq data was aligned to the Human genome GRCh37-hg19 assembly using HISAT2 aligner
HTseq algorithm was used to derive the raw count of the number of reads per transcript from the aligned sequence file in the BAM format
DESeq2 algorithm was used for normalization of the HTSeq count data using the variance stabilized transformation as well as for identifying genes differentially expressed upon miR-592 expression.
Assembly: GRCh37-hg19
Supplementary files format and content: tab-delimited text files containing counts per gene normalized using the variance stabilized transformation

source_name: Medulloblastoma cell line

growth_protocol: Daoy and its polyclonal populations expressing DDX3X shRNA in a doxycycline-inducible manner were grown in Dulbecco's Modified Eagle's Medium/F12  medium at 37 °C in a CO2 incubator.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit as per manufacturer's protocol.
Librarieswere prepared from Poly-A enriched fraction of total RNA using the Ilumina TruSeq RNA library preparation kit version 2.0
The libraries were sequenced in a 100 nucleotide single-end read run on the Illumina Hiseq 2500 platform

treatment_protocol: The cells were treated with 1 µg/ml doxycycline for 72 h for the induction of shRNA expression and exogenous wild type or mutant DDX3X expression

value: Daoy

value: Medulloblastoma cell line

value: shRNA targeting 3'-UTR of DDX3X expressing Daoy cells


title: Daoy_shDDX3X_wtDDX3X

value: exogenous wild type DDX3X expressing shDDX3X_UTR Daoy cells


title: Daoy_shDDX3X_DDX3XR534H

value: exogenous mutant DDX3XR534H expressing shDDX3X_UTR Daoy cells


title: Daoy_shDDX3X_DDX3XP568L

value: exogenous mutant DDX3XP568L exogenous expressing shDDX3X_UTR Daoy cells


title: Daoy_vector control_WT2

value: vector control Daoy cells


title: Daoy_shDDX3X_DDX3XG302V

value: exogenous mutant DDX3XG302V expressing shDDX3X_UTR Daoy cells


title: Line_H_500_1

source_name: Primary cell line H, 500ng/ml intelectin


title: Neutrophils_HD_untreated_rep2

value: Neutrophils

value: untreated


title: SAMR1_cont_1

description: Gene expression data from RAW264 cells, maintained in culture medium for 24 h and then LPS-induced for 6h


title: Line_B_500_1

source_name: Primary cell line B, 500ng/ml intelectin


title: Line_B_10_1

source_name: Primary cell line B, 10ng/ml intelectin


title: SAMP8_cont_3

source_name: SAMP8 mice treated with saline  for 30 days  and then trained for MWM test.


title: Line_H_0_1

source_name: Primary cell line H, 0ng/ml intelectin


title: SAMP8_TG Treated_1

description: Gene expression data from RAW264 cells, maintained in culture medium for 24 h and then LPS-induced for 17h

source_name: SAMP8 mice treated with TG (5mg/ml) for 30 days  and then trained for MWM test.


title: Line_B_0_1

source_name: Primary cell line B, 0ng/ml intelectin


title: SAMP8_TG Treated _3


title: Line_E_0_1

source_name: Primary cell line E, 0ng/ml intelectin


title: Line_E_500_1

source_name: Primary cell line E, 500ng/ml intelectin


title: Line_E_100_1

source_name: Primary cell line E, 100ng/ml intelectin


title: Line_H_100_1

source_name: Primary cell line H, 100ng/ml intelectin


title: SAMP8_cont_1

description: Gene expression data from RAW264 cells, pre-treated with BTEE for 24 h and then LPS-induced for 6h


title: SAMP8_TG Treated _2


title: W1118 Control-2

city: Beirut

first: Margret

last: Shirinian

address: Bliss street

country: Lebanon

institute: American University of Beirut

data_processing:
Quality check for raw sequencing reads was performed using FastQC v0.11.8
RNA-seq reads were aligned to dm6 genome assembly using hisat2 v2.1.0 with parameters --rna-strandness RF --dta --max-intronlen 300000
RNA-seq bigwig files were generated using deeptools v3.5.0 and normalized using CPM.
RNA-seq featurecounts matrix was generated using FeatureCounts v2.0.1 from SubRead package
Assembly: dm6
Supplementary files format and content: featureCounts file and bigwig files

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were maintained on standard cornmeal-agar medium at room temperature at 18˚C for maintenance and 25°C for experiments.

extract_protocol:
Total RNA from heads of 1-day old ''mTet2-R1261C, mTET2-Wt, mTET2-R43G, and W1118 Control'' adult fruit flies was extracted using the TRI Reagent (Sigma-Aldrich). Twelve RNA samples (three biological replicates for each of the mTet2-R1261C, mTET2-Wt, mTET2-R43G, and W1118 groups) were sent in ethanol to Macrogen (Seoul, South Korea) for RNA-Seq analysis.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

value: Head

value: 1-day old

value: W1118 Control;Tet-Gal4


title: W1118 Control-3


title: W1118 Control-1


title: mTet2-R43G-2


title: mTet2-R43G-3


title: mTet2-Wt-2


title: mTet2-R1261C-3


title: mTet2-R1261C-1


title: Terp-wt-AUG_4_16

city: Moscow

first: Leonid

middle: M

last: Kats

address: Leninskye gory, 1, building 40

country: Russia

institute: Lomonosov Moscow State University

data_processing:
Reads were trimmed using cutadapt v. 2.10. for 3’ adapter sequences: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Read counting and mapping against the GRCm39 assembly and vM28 annotation (GENCODE) were obtained with STAR v. 2.7.9a.
Assembly: GRCm39
Supplementary files format and content: Tab-separated text files containing read counts per gene as estimated by STAR.

source_name: Liver samples, mouse, mTERC wild type, rep8

growth_protocol: Individually ventilated cage, 12:12 light cycle, food ad libitum

extract_protocol:
Liver samples were sliced and frozen in liquid N2 and stored at −80 °C. For subsequent analyses liver samples were mechanically disrupted in liquid N2. 10 mg of each sample was taken, thawed and mechanically disrupted in 400 µL of Direct-Zol Tri Reagent. Total RNA was isolated from 350 µL of obtained solution using Direct-zol RNA Miniprep Kit (#R2050) (treated with RNase-Free DNase for 30 min at 37 °C) and precipitated with ethanol (with the addition of 1/100 volume of glycogen RNA grade).
Five hundred and fifty nanograms of DNase I-treated total RNA was depleted of ribosomal RNA with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (#E6310) and used for transcriptome library preparation with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760).

value: Liver

value: WT


title: mTet2-Wt-1


title: Terp-wt-AUG_3_15

source_name: Liver samples, mouse, mTERC wild type, rep7


title: mTet2-Wt-3


title: Terp-del7_1_9

source_name: Liver samples, mouse, mTERC-d7 (deletion of 7 nucleotides in positions 29-35) mutant, rep1

value: mTERC 29_35del


title: Terp-AUG_3_3

source_name: Liver samples, mouse, mTERC-AUG mutant, rep3

value: mTERC CUG/AUG


title: Terp-AUG_4_4

source_name: Liver samples, mouse, mTERC-AUG mutant, rep4


title: Terp-wt-AUG_2_14

source_name: Liver samples, mouse, mTERC wild type, rep6


title: Terp-del7_4_12

source_name: Liver samples, mouse, mTERC-d7 (deletion of 7 nucleotides in positions 29-35) mutant, rep4


title: Terp-wt-AUG_1_13

source_name: Liver samples, mouse, mTERC wild type, rep5


title: Terp-del7_2_10

source_name: Liver samples, mouse, mTERC-d7 (deletion of 7 nucleotides in positions 29-35) mutant, rep2


title: Terp-del7-wt_4_8

source_name: Liver samples, mouse, mTERC wild type, rep4


title: Terp-AUG_1_1

source_name: Liver samples, mouse, mTERC-AUG mutant, rep1


title: Terp-del7_3_11

source_name: Liver samples, mouse, mTERC-d7 (deletion of 7 nucleotides in positions 29-35) mutant, rep3


title: Terp-AUG_2_2

source_name: Liver samples, mouse, mTERC-AUG mutant, rep2


title: SAMP8_cont_2

source_name: SAMP8 mice treated with saline  for 30 days  and then trained for MWM test.

value: Hippocampus


title: mTet2-R43G-1


title: Terp-del7-wt_3_7

source_name: Liver samples, mouse, mTERC wild type, rep3


title: Sample 10_mouse dentate gyrus, Stimx10+2wks 2

city: Toyoake

first: Tomoyuki

last: Murano

address: 1-98 Dengakugakubo, Kutsukake-cho

institute: Fujita Health University

data_processing:
We first aligned reads using the BWA algorithm (mem mode; default settings).
Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome.
The resulting histograms (genomic "signal maps") were stored in bigWig files.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig

source_name: dentate gyrus

growth_protocol: Three or four wild-type B6J mouse  were housed in one cage and switched to individual breeding 1–2 weeks before the experiment.

extract_protocol: DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). The resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems) and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: Optic fiber was implanted above the dentate gyrus, and blue light was illuminated for 5 min per day, repeatedly.

value: dentate gyrus

value: dentate gyrus neurons

value: Stimx10, sampled 2wks later

value: Day 14


title: Sample 7_mouse dentate gyrus, Stimx3+2wks 3

value: Stimx3, sampled 2wks later


title: mTet2-R1261C-2

source_name: Head


title: Terp-del7-wt_2_6

source_name: Liver samples, mouse, mTERC wild type, rep2


title: Sample 8_mouse dentate gyrus, Stimx3+2wks 4


title: Sample 12_mouse dentate gyrus, Stimx10+2wks 4


title: Sample 11_mouse dentate gyrus, Stimx10+2wks 3


title: Sample 5_mouse dentate gyrus, Stimx3+2wks 1


title: Sample 9_mouse dentate gyrus, Stimx10+2wks 1


title: Terp-del7-wt_1_5

source_name: Liver samples, mouse, mTERC wild type, rep1


title: Sample 3_mouse dentate gyrus, No Stimulation 3

value: No stimulation control

value: Day 0


title: Sample 6_mouse dentate gyrus, Stimx3+2wks 2


title: 1_week_control

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1. R package Seurat was used to extract expressions and comparisons of genes. Both Seurat and Loupe Browser were used for data visualization.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Adult epidermis

extract_protocol:
DNp63fl/fl (control) and DNp63fl/fl;K14-CreT2 (experimental) mice, age 2-17 months, 50:50 males/females ratio, were treated with 200mg/kg Tamoxifen to genetically ablate DNp63 in the basal epidermal cells (basal keratiocytes). Primary mouse keratinocytes were isolated after 1 day or 1 week post-ablation as previously described (Jensen KB, Driskell RR, Watt FM. Nat Protoc. 2010;5(5):898-911) with slight modifications. Mice were euthanized by CO2 asphyxiation and the back hair removed using hair clippers and Nair hair remover lotion. The skin was washed with 70% ethanol, dissected, and placed the dermal side up on a 10 cm plate on ice, the muscle and adipose tissue was carefully removed with a cell scraper and forceps. The skin was then floated epidermal side up in 10 ml 0.25% trypsin without EDTA (Gibco) either overnight at 4°C or for two hours at 37°C, transferred to a new 10 cm plate, and the epidermal layer was carefully scraped off the dermis using a cell scraper. The epidermis was then minced with a razor blade and clumps were disaggregated by pipetting in trypsin. Ice-cold PBS/10% FBS was added to the cell suspension and passed through a 40 mm mesh. Isolated KCs were gently pelleted and washed twice with ice-cold PBS/10% FBS. Cell number and viability was determined using Trypan blue (Sigma) and the Beckman Coulter Z1 Counter (Beckman Coulter).
At 1 day post-ablation, Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1, PN-1000121 was used. At 1 week post-ablation, Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v1.1, PN-1000165 was used.

treatment_protocol: Mice were treated with 200 mg/kg Tamoxifen daily for five days via oral gavage

value: Adult epidermis

value: Keratinocytes and other


title: Sample 4_mouse dentate gyrus, No Stimulation 4


title: 1_week_experimental

description: 10x Genomics

value: 200 mg/kg Tamoxifen daily for five days via oral gavage


title: 1_day_control

description: 10x Genomics


title: mouse dentate gyrus, Stimx10+2wks [PR0714_30]

data_processing:
Sequenced data were mapped onto the Mus musculus genome (GRCm38/mm10) using the TopHat (v2.0.14).
Fragments per kilobase per million (FPKM) values were computed by the Genedata Profiler Genome (v10.1.12).
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA from tissue samples were extracted using the NucleoSpin RNA (Macherey-Nagel) according to the manufacturer’s instruction. The quality of RNA were assessed with an Agilent 2200 TapeStation (Agilent Technologies).
Sequenceing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina), and sequenced as 100-bp paired-end reads in the Illumina HiSeq 2500.


title: mouse dentate gyrus, Stimx10+2wks [PR0714_29]


title: Sample 2_mouse dentate gyrus, No Stimulation 2


title: Mouse testes, RAD51 ChIP-SSDS, Fignl1 cKO, rep3

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

institute: Osaka University

data_processing:
A published bioinformatic pipeline (https://nf-co.re/ssds/dev) was run for the resulting reads for the identification of single-stranded sequences.
The bigWig files were generated from the BAM files using bamCoverage in Deeptools.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: testes

extract_protocol:
One testis from the control and a pair of testes from Fignl1 cKO mice (14-18 weeks) were dissected, the tunica albuginea was removed, and seminiferous tubules were transferred into 10 ml of 1% formaldehyde (Pierce, 28908) in PBS (Nakarai, 14249-24) and immediately homogenized in a Dounce homogenizer with 20 strokes of the tight-fit pestle. The homogenate was passed through a 70 m cell strainer (Falcon, 352350), and after a total of 10 min of incubation at room temperature, crosslinking was quenched by adding 2.5 M glycine to a final concentration of 125 mM. After 5 min of incubation at room temperature, cells were pelleted by centrifugation at 900 x g for 5 min at 4℃, washed once with 10 ml of cold PBS, and suspended in 1 ml of cold PBS. The cell suspension was transferred to a 1.5 ml tube, centrifuged at 900 x g for 5 min at 4℃, and after removal of the supernatant, the cell pellet was snap-frozen on liquid nitrogen and stored at -80℃. The frozen cell pellet was suspended in 500 μl of cell lysis buffer (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0) supplemented with protease inhibitor (Roche, 04693159001), incubated for 10 min on ice, centrifuged at 300 x g for 3 min at 4℃, and the nuclei pellet was resuspended in 500 l of lysis wash buffer (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0) supplemented with protease inhibitor. After centrifugation at 300 x g for 3 min at 4℃, the nuclei pellet was resuspended in 200 l of RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 140 mM NaCl) supplemented with protease inhibitor and split into two ~130 μl aliquots and sonicated on the Covaris M220 for 5 min 30 sec at 5-9oC with a setting of Peak Power 50.0, Duty Factor 20.0, and Cycles/Burst 200. Sheared nuclei were combined, and after adding 700 l of RIPA buffer, centrifuged at 15,000 rpm for 15 min at 4℃ to remove insoluble debris. 800 l of the chromatin-containing supernatant was mixed with 50 l of Dynabeads protein G bound to 9.7 g of RAD51 antibody (Novus, NB100-148) and incubated overnight on a rotating wheel at 4℃ for immunoprecipitation. Beads were washed once with 1 ml of cold ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), 1 ml of cold ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), 1 ml of cold ChIP wash buffer 3 (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and twice with 1 ml of cold TE (1 mM EDTA and 10 mM Tris-HCl pH 8.0), followed by elution with 100 l of elution buffer (0.1 M NaHCO3 and 1% SDS) for 30 min at 65℃ with vortexing every 10 min. The elutes were incubated overnight at 65℃ for de-crosslinking, neutralized by adding 4 l of 1M Tris-HCl (pH 6.5) and 2 μl of 0.5 M EDTA, and RNA was digested by adding 2 l of 10 mg/ml RNase-A and incubation for 15 min 37oC. After adding 5 l of 10 mg/ml Proteinase-K (Wako, 165-21043) and incubation for 1 h at 55℃, DNA was purified using QIAquick PCR Purification Kit (QIAGEN).
7-10 ng of ChIP DNA was further sonicated on the Covaris M220 for 8 min 30 sec at room temperature with a setting of Peak Power 75.0, Duty Factor 10.0, and Cycles/Burst 200, followed by end-repair and dA-tailing using ChIP-Seq Library Prep Reagent Set for Illumina (NEB, E6200L). DNA was incubated for 3 min at 95℃ and returned to room temperature for kinetic enrichment for single-stranded DNA. After adapter ligation using IDT for Illumina TruSeq DNA UD Indexes (Illumina, 20022370), SSDS libraries were amplified during 15 cycles of PCR using TruSeq DNA Nano LP (Illumina, 20016328) and purified with AMPureXP beads (Beckman Coulter, A63880).

tag: strain background

value: testes

value: adult (14-18 weeks)

value: Stra8-Cre +; Fignl1 flox/-

tag: antibody lot


title: 1_day_experimental

description: 10x Genomics

tag: cell type


title: Mouse testes, RAD51 ChIP-SSDS, control, rep1

value: Stra8-Cre +; Fignl1 +/+


title: Mouse testes, RAD51 ChIP-SSDS, control, rep2


title: mouse dentate gyrus, Stimx10+2wks [PR0714_28]

value: WT

tag: treatment


title: mouse dentate gyrus, Stimx10+2wks [PR0714_27]

tag: tissue


title: mouse dentate gyrus, Stimx10+2wks [PR0714_26]

tag: genotype


title: Mouse testes, RAD51 ChIP-SSDS, Fignl1 cKO, rep1


title: Sample 1_mouse dentate gyrus, No Stimulation 1


title: mouse dentate gyrus, Stimx10+2wks [PR0714_25]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_24]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_23]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_20]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_22]


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_17]

value: Stimx10, sampled 24hrs later

value: Day 1


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_16]

value: dentate gyrus


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_15]

value: dentate gyrus neurons


title: Mouse testes, RAD51 ChIP-SSDS, control, rep3


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_18]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_19]


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_10]

value: Stimx3, sampled 24hrs later


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_09]


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_12]


title: mouse dentate gyrus, Stimx3+2wks [PR0714_21]

value: Day 14


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_08]


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_11]


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_14]


title: mouse dentate gyrus, No Stimulation [PR0714_04]


title: mouse dentate gyrus, No Stimulation [PR0714_03]


title: mouse dentate gyrus, No Stimulation [PR0714_02]


title: mouse dentate gyrus, No Stimulation [PR0714_05]


title: mouse dentate gyrus, No Stimulation [PR0714_01]


title: Mouse testes, RAD51 ChIP-SSDS, Fignl1 cKO, rep2


title: mouse dentate gyrus, Stimx3+24hrs [PR0714_07]


title: mouse dentate gyrus, Stimx10+24hrs [PR0714_13]


title: WT2 [Bisulfite-Seq]

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

data_processing:
Raw sequence reads were trimmed with TrimGalore! (version 0.4.1) and Cutadapt (version 1.15)
Aligned to TAIR10 reference genome using Bismark (version 0.19.0) with bowtie2 (version 2.3.3.1).
Genome_build: TAIR10.38
Supplementary_files_format_and_content: tab-delimited, <chromosome> <position> <strand> <count methylated> <count unmethylated > <C-context> <trinucleotide context>

organism: Arabidopsis thaliana

growth_protocol: Seeds were stratified at 4°C in distilled water for 2d, sown on soil, and placed in a growth chamber at 22°C/20°C and 12-h photoperiod

extract_protocol:
ground tissue was used for DNA extraction, using DNeasy Plant Kit (Qiagen, Germany).
DNA was sonicated to 100-300bp fragments and purified with the MiniElute PCR Purification Kit (Qiagen, Germany), End Repair Mix was added, and samples were incubated at 20°C. After DNA purification, a single “A” nucleotide was added to 3’ blunt ends, DNA was repurified, and methylated adapters were added on 5’ and 3’ ends. Fragments of 300-400bp were purified with QIAquick Gel Extraction Kit (Qiagen, Germany), treated with Methylation-Gold Kit (ZYMO), PCR-amplified and purified.
150-bp read, paired-end option, with a minimum depth of 60 million reads per sample, with DNBseqTM (BGI-Tech, China)

tag: phenotype

tag: ecotype

tag: replicate type

value: biological replicate 2

tag: developmental stage

value: bolting


title: WT1 [Bisulfite-Seq]

value: biological replicate 1


title: WT5 [Bisulfite-Seq]

value: biological replicate 5


title: WT6 [Bisulfite-Seq]

value: biological replicate 6


title: WT4 [Bisulfite-Seq]

value: biological replicate 4


title: Gen2_7 [Bisulfite-Seq]

value: PPD3-OX null Gen2

value: large


title: mouse dentate gyrus, No Stimulation [PR0714_06]

value: No stimulation control

value: Day 0


title: Gen2_4 [Bisulfite-Seq]

value: dwarf


title: Gen1_2 [Bisulfite-Seq]

value: PPD3-OX null Gen1


title: Gen1_3 [Bisulfite-Seq]

value: biological replicate 3


title: Gen2_5 [Bisulfite-Seq]


title: Gen2_6 [Bisulfite-Seq]


title: Gen1_1 [Bisulfite-Seq]


title: Gen2_1 [Bisulfite-Seq]


title: T+5 [Bisulfite-Seq]

value: PPD3-OX T+

value: normal


title: T+4 [Bisulfite-Seq]


title: EJ, shNC,rep3

city: Tianjin

first: Jingxian

address: Pingjiang Road 23#, Hexi District, Tianjin

institute: Tianjin institute of urology

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The limma was used to perform differential expression analysis.limma: Adjusted Pvalue <= 0.05
Assembly: hg38
Supplementary files format and content: tab-delimited text files include LCPM(log2(CPM+1)) values for each Sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

source_name: bladder cancer

extract_protocol:
RNA was harvested using Trizol reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA librares were prepared for sequencing using the standard BGI protocols.

value: bladder cancer

value: EJ

value: shNC


title: EJ, shSTIL,rep1

value: shSTIL


title: EJ, shSTIL,rep3


title: EJ, shNC,rep2


title: EJ, shNC,rep1


title: T+6 [Bisulfite-Seq]

value: bolting


title: EJ, shSTIL,rep2


title: T+2 [Bisulfite-Seq]

value: biological replicate 2


title: Gen2_8 [Bisulfite-Seq]


title: Gen2_2 [Bisulfite-Seq]


title: T+1 [Bisulfite-Seq]

value: biological replicate 1


title: WT3

data_processing:
RNA sequencing reads were trimmed with TrimGalore! (version 0.4.1) and aligned with STAR (version 2.7.0a, -twopassMode=Basic, -outFilterMultimapNmax=1).
The read count data were generated from the BAM files by using QoRTs software package (version v1.3.0) with –minMAPQ = 25 option.
Genome_build: TAIR10.37
Supplementary_files_format_and_content: tab-delimited, <GeneID> <read count>
Supplementary_files_format_and_content: raw counts

extract_protocol:
ground tissue was used for RNA extraction, including DNA removal, using NucleoSpin RNA Plant Kit (Macherey-Nagel, Germany).
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
100-bp read, paired-end option, with minimum depth of 4Gb per sample, with DNBseqTM (BGI-Tech, China)

value: WT


title: WT2


title: big1

value: PPD3-RNAi T+


title: big2

value: large


title: WT1


title: big3


title: WT3 [RNA-Seq]

data_processing:
RNA sequencing reads were trimmed with TrimGalore! (version 0.4.1) and aligned with STAR (version 2.7.0a, -twopassMode=Basic, -outFilterMultimapNmax=1).
The read count data were generated from the BAM files by using QoRTs software package (version v1.3.0) with –minMAPQ = 25 option.
Genome_build: TAIR10.38
Supplementary_files_format_and_content: tab-delimited, <GeneID> <read count>
Supplementary_files_format_and_content: raw counts


title: WT1 [RNA-Seq]


title: Gen2_8 [RNA-Seq]

value: PPD3-OX null Gen2


title: T+3 [Bisulfite-Seq]


title: sml1


title: sml3


title: sml2


title: Gen2_7 [RNA-Seq]


title: Gen2_5 [RNA-Seq]

value: biological replicate 5


title: Gen2_3 [RNA-Seq]

value: dwarf


title: Gen2_2 [RNA-Seq]


title: Gen2_1 [RNA-Seq]


title: Gen1_3 [RNA-Seq]

value: PPD3-OX null Gen1


title: Gen1_2 [RNA-Seq]


title: WT2 [RNA-Seq]


title: Gen1_1 [RNA-Seq]


title: T+6 [RNA-Seq]

value: biological replicate 3


title: Gen2_6 [RNA-Seq]


title: T+4 [RNA-Seq]

value: PPD3-OX T+


title: T+1 [RNA-Seq]


title: T+2 [RNA-Seq]


title: T+3 [RNA-Seq]


title: T+5 [RNA-Seq]

value: normal


title: neutrophils, Anifrolumab, donor 3

city: Birmingham

first: Camilla

last: Margaroli

address: 901 19th St S

institute: University of Alabama at Birmingham

data_processing:
lanes were merged in terminal using "cat" command
reads were aligned using hisat2 and bam files were created with samtools
bam files were sorted and indexed using samtools
raw counts were obtained using featureCounts in the terminal
Counts were normalized and analyzed using DESeq2
Assembly: human GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample and tab-delimited text files include normalized values

source_name: blood

growth_protocol: Neutrophil were isolated from blood using density grandient

extract_protocol:
RNA was extracted using the Takara Clontech Nucleospin RNA kit
Manufacturer protocol for NEB Ultra II Directional RNA-Seq kit for Illumina

treatment_protocol: Isolated neutrophils were checked for purity and transmigrated in vitro through collagen and airway epithelium into apical side for 14hrs. RNA was extracted from purified cells.

value: healthy

value: blood

value: primary cells

value: neutrophils

value: wt

value: in vitro transmigration ARDS fluid with Anifrolumab


title: neutrophils, IgG, donor 2

value: in vitro transmigration ARDS fluid with IgG


title: neutrophils, IgG, donor 1


title: neutrophils, IgG, donor 3


title: neutrophils, Anifrolumab, donor 1


title: neutrophils, ARDS fluid, donor 3

value: in vitro transmigration ARDS airway fluid


title: neutrophils, LTB4, donor 3

value: in vitro transmigration LTB4


title: neutrophils, ARDS fluid, donor 2


title: neutrophils, LTB4, donor 2


title: Gen2_4 [RNA-Seq]

value: biological replicate 4

value: bolting


title: neutrophils, LTB4, donor 1


title: Male, HUVEC, AngII, 2

city: College Park

first: Alisa

last: Morss Clyne

state: MD

address: 8278 Paint Branch Dr.

institute: University of Maryland

data_processing:
usegalaxy.org version 22.05.rc1
Quality assessment using FASTQC (all passed)
Trimmomatic on paired-end reads to remove low-quality bases and adaptor sequences
HISAT2 on paired-end reads to align them
FeatureCounts to align HISAT2 data to human (hg38) genome
EdgeR to compare gene expression in AngII vs. No Treatment for each sex
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing FeatureCounts for each sample

source_name: HUVEC

growth_protocol: Male and female HUVEC were maintained in EGM-2 (Lonza) and used from passage 4-9.

extract_protocol:
RNA was extracted using a phenol/chloroform extraction
Library constructed by Novogene USA (Sacramento, CA)

treatment_protocol: Confluent male and female HUVEC were treated with either 1 uL/mL H2O as a vehicle control or 1 uM AngII for 24 hours in EGM-2.

value: HUVEC

tag: cell sex

value: Male

value: WT

value: 1 uM AngII


title: Male, HUVEC, AngII, 3


title: Male, HUVEC, AngII, 1


title: Female, HUVEC, No Treatment, 3

value: Female

value: No Treatment


title: Female, HUVEC, No Treatment, 2


title: Female, HUVEC, No Treatment, 1


title: Colon pre_treat_biopsy P044 [D63]

type: genomic

city: Baltimore

first: leslie

last: cope

address: 550 N. Broadway

institute: leslie cope

description: Colon Biopsy pre_treat_biopsy

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
preprocessed using the funNorm algorithm as implemented in the minfi package
Average Beta

label: Cy5 and Cy3

source_name: Colon Biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

value: Colon Biopsy

tag: subject

tag: biopsytime

tag: analyzed

tag: site

value: JHU


title: Colon pre_treat_biopsy P112 [D65]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P103 [D62]

description: Colon Biopsy post_treat_biopsy

value: USC


title: neutrophils, Anifrolumab, donor 2

tag: disease state

value: healthy

value: blood

tag: cell line

value: primary cells

value: neutrophils


title: SW480 cells, Input

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

institute: The University of Tokyo

description: 2 × 150 bp

data_processing:
ChIP-seq reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.33).
Trimmed reads were aligned to the UCSC GRCh38 genome using Bowtie2 (v2.4.1).
Peak calling was performed using MACS2 (v3.6) with the significance cut-off q-value <=0.05.
The bigWig files were generated using the deepTools (v1.5.12). The narrowPeak files were generated using MACS2 with default settings.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Colon

growth_protocol: HCT116 and SW480 cells were maintained in McCoy's 5A Modified Medium and Leibovitz's L-15 Medium, respectively, supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
The cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin extracts were sheared by micrococcal nuclease digestion (New England Biolabs), and protein-DNA complexes were subsequently immunoprecipitated with 2 µg of anti-BRD8 polyclonal antibody.
ChIP-seq libraries were prepared using an NEBNext Ultra II DNA Library Prep kit (New England Biolabs) according to manufacturer's instructions. 1 ng of DNA was used for the construction of sequencing libraries.

value: Colon

value: Colorectal cancer

tag: chip antibody


title: HCT116 cells, BRD8

description: 2 × 150 bp

value: BRD8 (Merck, HPA001841)


title: Colon post_treat_biopsy P044 [D64]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P103 [D61]

description: Colon Biopsy pre_treat_biopsy


title: SW480 cells, BRD8

description: 2 × 150 bp


title: neutrophils, ARDS fluid, donor 1

value: wt

value: in vitro transmigration ARDS airway fluid


title: Colon post_treat_biopsy P057 [D60]

description: Colon Biopsy post_treat_biopsy

value: VU


title: Colon pre_treat_biopsy P031 [D43]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P066 [D45]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P057 [D59]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P031 [D44]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P025 [D42]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P033 [D40]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P033 [D39]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P025 [D41]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P003 [D38]

description: Colon Biopsy post_treat_biopsy

value: MSK


title: Colon post_treat_biopsy P091 [D24]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P015 [D22]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P091 [D23]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P117 [D19]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P103 [D18]

description: Colon Biopsy post_treat_biopsy


title: HCT116 cells, Input

description: 2 × 150 bp


title: Colon pre_treat_biopsy P117 [D1]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P115 [D77]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P115 [D78]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P003 [D76]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P055 [D73]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P103 [D17]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P055 [D74]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P003 [D75]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P033 [D69]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P028 [D58]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P033 [D70]

description: Colon Biopsy post_treat_biopsy


title: Colon _treat_biopsy P038 [D72]

description: Colon Biopsy _treat_biopsy


title: Colon post_treat_biopsy P049 [D56]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P070 [D54]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P049 [D55]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P070 [D53]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P115 [D51]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P015 [D21]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P003 [D37]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P093 [D49]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P117 [D20]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P008 [D36]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P008 [D35]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P074 [D34]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P074 [D33]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P069 [D32]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P016 [D28]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P069 [D31]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P008 [D16]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P091 [D14]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P006 [D30]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P074 [D10]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P066 [D11]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P028 [D57]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P015 [D8]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P091 [D13]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P015 [D7]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P112 [D66]

description: Colon Biopsy post_treat_biopsy


title: Colon _treat_biopsy P038 [D71]

description: Colon Biopsy _treat_biopsy


title: Colon post_treat_biopsy P115 [D52]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P009 [D67]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P093 [D50]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P047 [D47]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P066 [D46]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P047 [D48]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P006 [D29]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P009 [D26]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P016 [D27]

description: Colon Biopsy pre_treat_biopsy


title: Colon pre_treat_biopsy P009 [D25]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P069 [D4]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P031 [D6]

description: Colon Biopsy post_treat_biopsy


title: Colon post_treat_biopsy P117 [D2]

description: Colon Biopsy post_treat_biopsy


title: Colon pre_treat_biopsy P031 [D5]

description: Colon Biopsy pre_treat_biopsy


title: Colon post_treat_biopsy P009 [D68]

description: Colon Biopsy post_treat_biopsy


title: 200652310035_R06C01

first: Smita

last: Bhatia

state: AL

address: 1600 7th Avenue South Lowder 500

department: Pediatrics

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC_v-1-0 Beadchip using standard Illumina protocol

data_processing:
Raw IDAT files were analyzed in R (v4.0.2, https://www.r-project.org/), using the Bioconductor packages minfi (v.1.34.0) and ChAMP (Chip Analysis Methylation Pipeline, v.2.18.3) for EPIC arrays. Data were normalized using Noob for within-array normalization, correcting for background fluorescence and dye bias . To account for DNA methylation differences due to cell-type composition in whole blood, we performed reference based deconvolution using FlowSorted.Blood.EPIC (v.1.6.1)  and corrected the beta matrix in ChAMP.
Normalized β using Noob
Set12345_matrixSignalIntensities.csv: The methylation score for each CpG was represented as a ‘β’ value according to the fluorescent intensity ratio (range: 0 [non-methylated] to 1 [completely methylated]).

source_name: Peripheral Blood

extract_protocol: Genomic DNA was isolated using Gentra Puregene Blood Kit (Qiagen Inc., Valencia, CA). DNA concentration was measured on Nanodrop ND-1000 Spectrophotometer (ThermoFisher Scientific Inc., Waltham, MA). DNA integrity was analyzed by Quant-iT™ PicoGreen™ dsDNA Assay Kit (ThermoFisher Scientific Inc., Waltham, MA).

tag: Sex

value: Male

tag: group

value: Control


title: 200652310029_R04C01


title: 200652310035_R07C01

value: Female

value: Case


title: 200652310035_R08C01


title: 200652310029_R01C01


title: 200652310029_R03C01


title: 200652310029_R02C01


title: Colon pre_treat_biopsy P074 [D9]

description: Colon Biopsy pre_treat_biopsy

value: Colon Biopsy


title: 200652310035_R01C01


title: 200969820153_R08C01


title: Gen2_3 [Bisulfite-Seq]

value: PPD3-OX null Gen2

value: dwarf

value: biological replicate 3

value: bolting


title: 200652310035_R03C01


title: 200652310035_R04C01


title: 200969820153_R07C01


title: 200969820153_R04C01


title: 200969820153_R05C01


title: 200969820153_R03C01


title: 200969820153_R01C01


title: 200969820153_R02C01


title: 200652310017_R08C01


title: Colon pre_treat_biopsy P069 [D3]

description: Colon Biopsy pre_treat_biopsy

value: USC


title: 200652310017_R07C01


title: 200652310017_R06C01


title: 200652310017_R05C01


title: 200652310035_R05C01


title: 200652310035_R02C01


title: WT3 [Bisulfite-Seq]

value: WT


title: 200969820153_R06C01


title: 200652310017_R04C01


title: 200652310017_R02C01


title: 200652310037_R05C01


title: 200652310037_R02C01


title: 200652310037_R07C01


title: 200652310017_R03C01


title: 200652310037_R08C01


title: 200652310037_R06C01


title: 200652310017_R01C01


title: 200652310024_R07C01


title: 200652310024_R06C01


title: 200652310024_R08C01


title: 200652310024_R05C01


title: 200652310037_R01C01


title: 200652310024_R04C01


title: 200652310024_R03C01


title: 200652310038_R07C01


title: 200652310038_R08C01


title: 200652310024_R01C01


title: 200652310024_R02C01


title: 200652310038_R05C01


title: 200652310038_R02C01


title: 200652310038_R01C01


title: 200652310038_R04C01


title: 200652310038_R03C01


title: 200661820012_R08C01


title: 200661820012_R07C01


title: 200661820012_R06C01


title: 200661820012_R05C01


title: 200661820012_R01C01


title: 200661940032_R06C01


title: 200661820012_R03C01


title: 200661940032_R07C01


title: 200661820012_R02C01


title: 200661820012_R04C01


title: 200661940032_R03C01


title: 200661940032_R08C01


title: 200661940032_R02C01


title: 200661940030_R07C01


title: 200661940030_R06C01


title: 200661940030_R08C01


title: 200661940032_R04C01


title: 200661940030_R04C01


title: 200661940030_R05C01


title: 200661940046_R02C01


title: 200661940046_R07C01


title: 200661940046_R03C01


title: 200661940046_R01C01


title: 200934330101_R08C01


title: 200934330101_R06C01


title: 200934330101_R05C01


title: 200934330101_R04C01


title: 200934330101_R03C01


title: 200661940032_R01C01


title: 200661940030_R03C01


title: 200661940046_R08C01


title: 200934330101_R01C01


title: 200934330101_R02C01


title: 200934330088_R06C01


title: 200934330091_R03C01


title: 200934330091_R04C01


title: 200969820031_R06C01


title: 200934330091_R01C01


title: 200969820031_R08C01


title: 200934330091_R07C01


title: 200934330088_R05C01


title: 200934330091_R08C01


title: 200934330101_R07C01


title: 200934330091_R02C01


title: 200969820031_R03C01


title: 200934330088_R02C01


title: 200934330088_R08C01


title: 200934330088_R01C01


title: 200969820031_R07C01


title: 200969820031_R02C01


title: 200934330091_R05C01


title: 200969820031_R04C01


title: lung.NET.77.tumor [methylation]

city: Madrid

first: GarciaCarbonero

last: Lab

state: Comunidad de Madrid

address: Av/ Córdoba s/n

department: Centro de Oncología Experimental

country: Spain

institute: Instituto de Investigación Hospital 12 de Octubre

description:
204676960004_R08C01
FFPE tumor tissue

hyb_protocol: Samples were hybridized using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed scanned using an Illumina iScan System (Illumina).

data_processing:
IDAT files were open and processed using minfi R package. Beta values were normalized using the SWAN method.
unmethylated_methylated_signal_intensities.txt: Umethylated values, methylated values, and detection p-values.
Matrix_Processed.txt: Normalized SWAN Average Beta values and detection p-values.

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was extracted from paired FFPE tumor (N=30) and non-tumor (N=10) tissues using QIAamp DNA FFPE Tissue Kit (QIAGEN, Valencia, CA) according to manufacturer’s recommendations. DNA purity and concentration were assessed with the Qubit® Fluorimeter (Life Technologies).

value: lung

value: tumor

tag: gender

tag: grade

tag: death


title: lung.NEC.85.tumor [methylation]

description:
204676960005_R04C01
FFPE tumor tissue


title: lung.NET.86.tumor [methylation]

description:
204674440015_R04C01
FFPE tumor tissue


title: lung.NET.86.normal [methylation]

description:
204674440015_R03C01
normal tissue

value: normal


title: 200934330088_R04C01


title: lung.NET.64.tumor [methylation]

description:
204674440015_R01C01
FFPE tumor tissue


title: lung.NEC.61.tumor [methylation]

description:
204676960004_R05C01
FFPE tumor tissue


title: lung.NET.60.tumor [methylation]

description:
204676960004_R04C01
FFPE tumor tissue


title: lung.NET.59.tumor [methylation]

description:
204676960004_R03C01
FFPE tumor tissue


title: lung.NEC.58.tumor [methylation]

description:
204676960004_R06C01
FFPE tumor tissue


title: 200969820031_R01C01


title: lung.NET.56.tumor [methylation]

description:
204676960031_R06C01
FFPE tumor tissue


title: lung.NEC.57.tumor [methylation]

description:
204676960031_R08C01
FFPE tumor tissue


title: lung.NEC.52.tumor [methylation]

description:
204676960005_R07C01
FFPE tumor tissue


title: lung.NET.50.tumor [methylation]

description:
204676960004_R01C01
FFPE tumor tissue


title: lung.NET.55.tumor [methylation]

description:
204676960031_R05C01
FFPE tumor tissue


title: lung.NET.54.tumor [methylation]

description:
204676960031_R03C01
FFPE tumor tissue


title: lung.NEC.57.normal [methylation]

description:
204676960031_R07C01
normal tissue


title: lung.NET.53.normal [methylation]

description:
204676960005_R08C01
normal tissue


title: lung.NEC.45.tumor [methylation]

description:
204676960005_R03C01
FFPE tumor tissue


title: lung.NET.49.normal [methylation]

description:
204676960005_R05C01
normal tissue


title: lung.NET.53.tumor [methylation]

description:
204676960031_R01C01
FFPE tumor tissue


title: lung.NET.49.tumor [methylation]

description:
204676960005_R06C01
FFPE tumor tissue


title: lung.NEC.55.normal [methylation]

description:
204676960031_R04C01
normal tissue


title: lung.NET.44.tumor [methylation]

description:
204676960005_R02C01
FFPE tumor tissue


title: lung.NEC.43.tumor [methylation]

description:
204676960005_R01C01
FFPE tumor tissue


title: lung.NET.42.tumor [methylation]

description:
204676960013_R08C01
FFPE tumor tissue


title: lung.NEC.39.tumor [methylation]

description:
204676960013_R06C01
FFPE tumor tissue


title: lung.NEC.39.normal [methylation]

description:
204676960013_R05C01
normal tissue


title: lung.NET.38.tumor [methylation]

description:
204676960004_R07C01
FFPE tumor tissue


title: lung.NET.40.tumor [methylation]

description:
204676960013_R07C01
FFPE tumor tissue


title: lung.NET.36.tumor [methylation]

description:
204676960013_R04C01
FFPE tumor tissue


title: lung.NET.36.normal [methylation]

description:
204676960013_R03C01
normal tissue


title: lung.NET.51.tumor [methylation]

description:
204676960004_R02C01
FFPE tumor tissue


title: gastroenteropancreatic.NET.35.tumor [methylation]

description:
204676960013_R02C01
FFPE tumor tissue

value: stomach


title: lung.NET.54.normal [methylation]

description:
204676960031_R02C01
normal tissue


title: 200934330088_R07C01


title: gastroenteropancreatic.NET.34.tumor [methylation]

description:
204674440043_R08C01
FFPE tumor tissue

value: small intestine


title: gastroenteropancreatic.NET.27.normal [methylation]

description:
204674440043_R03C01
normal tissue

value: pancreas


title: gastroenteropancreatic.NET.35.normal [methylation]

description:
204676960013_R01C01
normal tissue


title: gastroenteropancreatic.NET.29.tumor [methylation]

description:
204674440043_R05C01
FFPE tumor tissue

value: Male


title: gastroenteropancreatic.NET.27.tumor [methylation]

description:
204674440043_R04C01
FFPE tumor tissue


title: Blood_Patient_V_V9

city: Ankara

first: Ali

middle: Kemal

last: Oguz

address: Baskent Universitesi Ankara Hastanesi, Maresal Fevzi Cakmak Caddesi No: 45

department: Internal Medicine

country: Turkey

institute: Baskent University School of Medicine

hyb_protocol: For microarray hybridization, “GeneChip® Human Genome U133 Plus 2.0” (Applied Biosystems®, Catalog no: 900466, U.S.A.) microarrays were used. Each microarray was loaded with a target RNA sample of 15 µg added to a hybridization cocktail prepared using the “GeneChip® Hybridization, Wash, and Stain Kit” (Applied Biosystems®, Catalog no: 900720, U.S.A.). The preparation of the hybridization cocktail and the loading procedure of the microarrays were carried out in complete adherence to the manufacturer’s protocol (GeneChip® Expression Analysis Technical Manual). Loaded microarrays were then allowed to hybridize in “GeneChip® Hybridization Oven” (Applied Biosystems®, Catalog no: 00-0331, U.S.A.) at a temperature of 45C and 60 rpm rotation speed for 16 hours. Microarrays, upon completion of the hybridization step, were subjected to washing and staining processes in the “GeneChip® Fluidics Station 450” (Applied Biosystems®, Catalog no: 00-0079, U.S.A.), using the relevant components in the “GeneChip® Hybridization, Wash, and Stain Kit” (Applied Biosystems®, Catalog no: 900720, U.S.A.). Again, the protocol defined by the manufacturer was precisely followed for this step (GeneChip® Expression Analysis Technical Manual).

scan_protocol: Consequent to the washing & staining steps, the microarrays were transferred to and scanned on the “GeneChip® Scanner 3000” (Applied Biosystems®, Catalog no: 00-0186, U.S.A.)  by using the “Affymetrix®, GeneChip® Command Console® 4.0” (AGCC) software. Upon completion of the scanning process, the AGCC software generated .dat and .cel files along with .exp, .chp and .rpt files. Among these files, the .dat file contained the scanned microarray image, and the .cel file contained the light intensity (brightness) values of each probe set defined by a grid. For the downstream bioinformatic analyses, these raw .cel files were used.

data_processing: The collation and all of the pre-processing steps of the microarray data were conducted using the “BRB-ArrayTools v4.4.1 Stable release” developed by Dr. Richard Simon and the “BRB-ArrayTools” development team (https://brb.nci.nih.gov/BRB-ArrayTools/). Initially, the raw microarray data existing as individual .cel files were collated using the data import function of the “BRB-ArrayTools” software. Normalization of the imported microarray data was performed using the “Robust Multiarray Average” (RMA) algorithm, which includes (1) background correction, (2) binary logarithmic transformation, and (3) quantile normalization. Following this normalization step, the replicate probe sets were averaged. Finally, gene filters were implemented, which helped to exclude genes that are not likely to be informative. For this purpose, a “minimum fold-change filter” in addition to a “percent missing filter” were used, which were ready-to-use functions of the “BRB-ArrayTools” software.

source_name: Peripheral blood

label_protocol: Before the microarray hybridization step, the target RNA was amplified, labeled with biotin, and then fragmented to increase the hybridization efficiency and obtain optimal results.  Starting with an RNA sample of 500 ng, this step was carried out using the GeneChip® 3' IVT Express Kit (Affymetrix®, Catalog no: 901229, U.S.A.) and the protocol described by the manufacturer (GeneChip® 3' IVT Express Kit User Manual). Biotin-labeled amplified RNA was evaluated for quantity and purity by nano-spectrophotometer (NanoDrop® 2000/2000c Spectrophotometer, Thermo Scientific®, U.S.A.) and then fragmented and visualized on a 1% agarose gel.

extract_protocol: RNA isolation & purification from blood samples collected for the study were performed using the PAXgene® Blood RNA Kit (PreAnalytiX®, Catalog no: 762174, Switzerland). Following the manufacturer's protocol, the tubes removed from the freezer just before the RNA isolation process were first equilibrated to room temperature and then kept at room temperature for an additional 2 hours. All steps of the RNA isolation & purification process were performed in complete adherence to the protocol recommended by the manufacturer, as described in the PAXgene® Blood RNA Kit Handbook. For every purified RNA sample, a 500 ng amount required for the downstream analysis was stored at -80C, in addition to aliquots for RNA quantity/quality analyses and stocking purposes.

tag: age

value: Behcet syndrome

tag: clinical phenotype

value: Vascular

tag: clinical phenotype details


title: Blood_Patient_V_V1


title: Blood_Patient_V_V2


title: Blood_Patient_O_O4

value: Female

value: Ocular


title: Blood_Patient_V_V7


title: Blood_Patient_V_V6


title: Blood_Patient_V_V8


title: gastroenteropancreatic.NET.23.tumor [methylation]

description:
204674440015_R06C01
FFPE tumor tissue

value: apendix


title: Patient sample16:N

city: GuangZhou

first: Jianrong

last: Guo

address: Dongfengdong Road NO.651

institute: SYSUCC

description:
Patient sample16:N
A6791

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: Normal tissue

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

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

value: Normal tissue


title: Blood_Patient_V_V4


title: Patient sample10:N

description:
Patient sample10:N
A6814


title: Patient sample5:N

description:
Patient sample5:N
A6428


title: Blood_Patient_V_V5


title: Blood_Patient_V_V3


title: Blood_Patient_O_O3


title: Blood_Patient_M_M8

value: Mucocutaneous


title: Patient sample2:N

description:
Patient sample2:N
A6431


title: Blood_Patient_O_O5


title: Blood_Patient_O_O2


title: Patient sample4:N

description:
Patient sample4:N
A6436


title: Blood_Patient_M_M6


title: Patient sample12:N

description:
Patient sample12:N
A6435


title: Patient sample17:N

description:
Patient sample17:N
A6804


title: Patient sample18:N

description:
Patient sample18:N
A6806


title: Patient sample9:N

description:
Patient sample9:N
A6802


title: Blood_Patient_M_M7


title: Blood_Patient_M_M4


title: Patient sample6:N

description:
Patient sample6:N
A6427


title: Patient sample14:N

description:
Patient sample14:N
A6430


title: Blood_Patient_M_M1


title: Blood_Patient_O_O1


title: Patient sample19:N

description:
Patient sample19:N
A6808


title: Blood_Patient_M_M3


title: Patient sample8:N

description:
Patient sample8:N
A6426


title: Blood_Patient_M_M2


title: Patient sample11:N

description:
Patient sample11:N
A6423


title: Blood_HealthyControl_C_C7

value: Healthy control


title: Blood_HealthyControl_C_C8


title: Patient sample20:N

description:
Patient sample20:N
A6810


title: Blood_Patient_M_M5


title: Blood_HealthyControl_C_C9


title: Patient sample7:N

description:
Patient sample7:N
A6798


title: Patient sample13:N

description:
Patient sample13:N
A6425


title: Blood_HealthyControl_C_C4


title: Blood_HealthyControl_C_C2


title: Blood_HealthyControl_C_C6


title: Patient sample3:N

description:
Patient sample3:N
A6789


title: Patient sample15:N

description:
Patient sample15:N
A6421


title: Blood_HealthyControl_C_C14


title: Patient sample1:N

description:
Patient sample1:N
A6795


title: Blood_HealthyControl_C_C5


title: Patient sample5:GIST

description:
Patient sample5:GIST
A6408

source_name: GIST with liver metastasis

value: GIST


title: Blood_HealthyControl_C_C15


title: Blood_HealthyControl_C_C3


title: Patient sample3:GIST

description:
Patient sample3:GIST
A6417


title: Blood_HealthyControl_C_C11


title: Patient sample18:GIST

description:
Patient sample18:GIST
A6805


title: Blood_HealthyControl_C_C10


title: Blood_Patient_D_D7

value: Complex

value: Ocular, vascular, musculoskeletal


title: Patient sample10:GIST

description:
Patient sample10:GIST
A6813


title: Blood_HealthyControl_C_C13


title: Blood_HealthyControl_C_C12


title: Patient sample11:GIST

description:
Patient sample11:GIST
A6403


title: Patient sample20:GIST

description:
Patient sample20:GIST
A6809


title: Blood_Patient_D_D6

value: Central nervous system


title: Blood_HealthyControl_C_C1


title: Blood_Patient_D_D5

value: Ocular, vascular


title: Patient sample4:GIST

description:
Patient sample4:GIST
A6416


title: Patient sample1:GIST

description:
Patient sample1:GIST
A6404


title: Patient sample14:GIST

description:
Patient sample14:GIST
A6410


title: Patient sample19:GIST

description:
Patient sample19:GIST
A6807


title: Blood_Patient_D_D3

value: Vascular, musculoskeletal


title: Patient sample12:GIST

description:
Patient sample12:GIST
A6415


title: Blood_Patient_D_D2

value: Gastrointestinal


title: Blood_Patient_D_D4


title: Patient sample13:GIST

description:
Patient sample13:GIST
A6405


title: Blood_Patient_D_D1


title: Patient sample15:GIST

description:
Patient sample15:GIST
A6401


title: C2C12 scramble (control) 3

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: Gene expression data from myoblastoma cell line

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Mouse Gene 2.1 ST ArrayStrip (20 h, 292 48 °C)

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cells were grown in standard media as per ATCC protocols

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: Cells were transfected with siRNA pools as per manufacturer's instruction (Dharmacon).

tag: transfection

value: control