title: Sample_198: genomic DNA from PDB case 198

description: Blood Sample

source_name: White blood cells_198


title: 28C10

status: Public on May 18 2022

type: SRA

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

country: USA

institute: Pacific Northwest National Laboratory

library_source: transcriptomic

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the mouse genome using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Assembly: Genome Reference Consortium Mouse Build 39 (https://www.ncbi.nlm.nih.gov/genome/?term=txid10090)
Supplementary files format and content: .txt files represent number of raw read counts mapping to each gene

molecule: total RNA

organism: Mus musculus

source_name: C10 alveolar type II epithelial cells

growth_protocol: standard culture protocols

extract_protocol:
Full length cDNA was generated from single cell using SMART-Seq v4 Plus according to the manufacture protocol. The cDNA quality is determined by 5200 Agilent Fragment analyzer.
For RNA‐Seq, SMART-Seq v4 Plus(c at#R400753) was used to generate template library for sequencing on illumina NextSeq550 platform according to the manufacture protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2.5 kit 150 cycles (cat#20024907).

tag: cell line


title: Sample_196: genomic DNA from PDB case 196

type: genomic

city: Doha

first: Omar

middle: M E

last: Albagha

address: Qatar Foundation

department: College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

description: Blood Sample

hyb_protocol: Bisulfite conversion was performed on 500µg of DNA. DNA methylation profiling was performed using the Illumina Infinium HumanMethylation 450K array (Illumina, USA) by following the manufacturerís protocol

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

data_processing: The R package RnBeads version 1.10.8

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: White blood cells_196

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood using standard protocols.

tag: gender

value: Male

tag: sample type

value: Blood

tag: disease state

value: Paget’s disease of bone (PDB)

tag: cell type

value: White blood cells

tag: age

tag: array


title: 26C10


title: 25C10


title: Sample_195: genomic DNA from PDB case 195

description: Blood Sample

source_name: White blood cells_195

value: Female

value: Date _5


title: Sample_203: genomic DNA from PDB case 203

description: Blood Sample

source_name: White blood cells_203

value: Date _1


title: 23C10


title: Sample_192: genomic DNA from PDB case 192

description: Blood Sample

source_name: White blood cells_192


title: Sample_194: genomic DNA from PDB case 194

description: Blood Sample

source_name: White blood cells_194


title: Sample_193: genomic DNA from PDB case 193

description: Blood Sample

source_name: White blood cells_193


title: 22C10


title: Sample_191: genomic DNA from PDB case 191

description: Blood Sample

source_name: White blood cells_191


title: Sample_190: genomic DNA from PDB case 190

description: Blood Sample

source_name: White blood cells_190


title: 20C10


title: 19C10


title: Sample_187: genomic DNA from PDB case 187

description: Blood Sample

source_name: White blood cells_187


title: Sample_186: genomic DNA from PDB case 186

description: Blood Sample

source_name: White blood cells_186


title: 16C10


title: Sample_189: genomic DNA from PDB case 189

description: Blood Sample

source_name: White blood cells_189


title: Sample_188: genomic DNA from PDB case 188

description: Blood Sample

source_name: White blood cells_188


title: 13C10


title: 17C10


title: 18C10


title: Sample_184: genomic DNA from PDB case 184

description: Blood Sample

source_name: White blood cells_184


title: 15C10


title: 9C10


title: 14C10


title: Sample_183: genomic DNA from PDB case 183

description: Blood Sample

source_name: White blood cells_183


title: Sample_180: genomic DNA from PDB case 180

description: Blood Sample

source_name: White blood cells_180


title: 21C10


title: Sample_185: genomic DNA from PDB case 185

description: Blood Sample

source_name: White blood cells_185

value: Date _3


title: 10C10

source_name: C10 alveolar type II epithelial cells


title: Sample_181: genomic DNA from PDB case 181

description: Blood Sample

source_name: White blood cells_181


title: 5C10


title: 12C10


title: Sample_174: genomic DNA from PDB case 174

description: Blood Sample

source_name: White blood cells_174


title: Sample_179: genomic DNA from PDB case 179

description: Blood Sample

source_name: White blood cells_179


title: 3C10


title: Sample_173: genomic DNA from PDB case 173

description: Blood Sample

source_name: White blood cells_173


title: 2C10


title: 8C10


title: Sample_172: genomic DNA from PDB case 172

description: Blood Sample

source_name: White blood cells_172


title: Sample_178: genomic DNA from PDB case 178

description: Blood Sample

source_name: White blood cells_178


title: 7C10


title: Sample_177: genomic DNA from PDB case 177

description: Blood Sample

source_name: White blood cells_177


title: Sample_176: genomic DNA from PDB case 176

description: Blood Sample

source_name: White blood cells_176


title: Sample_175: genomic DNA from PDB case 175

description: Blood Sample

source_name: White blood cells_175


title: Sample_169: genomic DNA from PDB case 169

description: Blood Sample

source_name: White blood cells_169


title: 4C10


title: Sample_182: genomic DNA from PDB case 182

description: Blood Sample

source_name: White blood cells_182


title: 1C10


title: Sample_171: genomic DNA from PDB case 171

description: Blood Sample

source_name: White blood cells_171


title: 10cells10


title: 10cells9


title: 10cells2


title: Sample_170: genomic DNA from PDB case 170

description: Blood Sample

source_name: White blood cells_170


title: 11C10


title: Sample_166: genomic DNA from PDB case 166

description: Blood Sample

source_name: White blood cells_166


title: 3cells10


title: 6C10


title: 3cells9


title: 10cells6


title: 3cells6


title: Sample_168: genomic DNA from PDB case 168

description: Blood Sample

source_name: White blood cells_168


title: 10cells5


title: Sample_167: genomic DNA from PDB case 167

description: Blood Sample

source_name: White blood cells_167


title: 10cells1

source_name: C10 alveolar type II epithelial cells


title: Sample_160: genomic DNA from PDB case 160

description: Blood Sample

source_name: White blood cells_160


title: Sample_165: genomic DNA from PDB case 165

description: Blood Sample

source_name: White blood cells_165


title: Sample_164: genomic DNA from PDB case 164

description: Blood Sample

source_name: White blood cells_164


title: Sample_159: genomic DNA from PDB case 159

description: Blood Sample

source_name: White blood cells_159


title: 1cell14


title: 3cells5


title: Sample_162: genomic DNA from PDB case 162

description: Blood Sample

source_name: White blood cells_162


title: 3cells2


title: Sample_163: genomic DNA from PDB case 163

description: Blood Sample

source_name: White blood cells_163


title: Sample_157: genomic DNA from PDB case 157

description: Blood Sample

source_name: White blood cells_157


title: 1cell10


title: 3cells1


title: 1cell13


title: Sample_153: genomic DNA from PDB case 153

description: Blood Sample

source_name: White blood cells_153


title: Sample_161: genomic DNA from PDB case 161

description: Blood Sample

source_name: White blood cells_161


title: 1cell9


title: 1cell2


title: 1cell5


title: Sample_156: genomic DNA from PDB case 156

description: Blood Sample

source_name: White blood cells_156


title: 1cell1


title: 1cell6


title: Sample_154: genomic DNA from PDB case 154

description: Blood Sample

source_name: White blood cells_154


title: Sample_152: genomic DNA from PDB case 152

description: Blood Sample

source_name: White blood cells_152


title: Sample_151: genomic DNA from PDB case 151

description: Blood Sample

source_name: White blood cells_151


title: Sample_158: genomic DNA from PDB case 158

description: Blood Sample

source_name: White blood cells_158


title: Sample_150: genomic DNA from PDB case 150

description: Blood Sample

source_name: White blood cells_150


title: Sample_148: genomic DNA from PDB case 148

description: Blood Sample

source_name: White blood cells_148


title: Sample_149: genomic DNA from PDB case 149

description: Blood Sample

source_name: White blood cells_149


title: Sample_147: genomic DNA from PDB case 147

description: Blood Sample

source_name: White blood cells_147


title: WM9Kidney

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

source_name: Kidney

growth_protocol: Wild caught

extract_protocol:
Tissues were extracted from recently (<12hr) deceased or euthanized animals and flash frozen in liquid nitrogen. Animals not euthanized in lab were kept at 4°C and processed within 12hr of death. Frozen tissues were pulverized using a Cell Crusher piston chilled with liquid nitrogen to produce uniform powdered tissue. Approximately 30mg of frozen tissue powder was used for Trizol RNA extraction. Contaminating DNA was removed from RNA samples using Purelink DNase kit along with Purelink RNA columns. Purified RNA quality was checked using agarose gel examination for rRNA integrity and Qubit analysis
For RNAseq, the RNA samples were processed with the Illumina TruSeq stranded total RNA RiboZero Gold kit and then subjected to Illumina HiSeq 4000 paired-end 150bp sequencing; For MeDIP, genomic DNA samples were processed using the NEBNext UltraII DNA Library Prep kit.
Ribo-depletion for RNAseq

treatment_protocol: No treatment

tag: tissue

value: Kidney


title: WM8Liver

source_name: Liver

value: Liver


title: WM8Kidney


title: WM9Heart

source_name: Heart

value: Heart


title: WM14Liver


title: WM8Heart


title: Sample_155: genomic DNA from PDB case 155

description: Blood Sample

source_name: White blood cells_155


title: Sample_144: genomic DNA from PDB case 144

description: Blood Sample

source_name: White blood cells_144


title: WM14Kidney


title: Sample_145: genomic DNA from PDB case 145

description: Blood Sample

source_name: White blood cells_145


title: Sample_142: genomic DNA from PDB case 142

description: Blood Sample

source_name: White blood cells_142


title: WM13Liver


title: Sample_143: genomic DNA from PDB case 143

description: Blood Sample

source_name: White blood cells_143


title: Sample_141: genomic DNA from PDB case 141

description: Blood Sample

source_name: White blood cells_141


title: WM12Heart


title: Sample_140: genomic DNA from PDB case 140

description: Blood Sample

source_name: White blood cells_140


title: WM11Heart


title: WM13Kidney


title: Sample_138: genomic DNA from PDB case 138

description: Blood Sample

source_name: White blood cells_138


title: WM10Kidney


title: WM9Liver


title: Sample_137: genomic DNA from PDB case 137

description: Blood Sample

source_name: White blood cells_137


title: WM10Liver


title: Sample_139: genomic DNA from PDB case 139

description: Blood Sample

source_name: White blood cells_139


title: Sample_146: genomic DNA from PDB case 146

description: Blood Sample

source_name: White blood cells_146


title: Sample_136: genomic DNA from PDB case 136

description: Blood Sample

source_name: White blood cells_136


title: WM10Heart


title: Sample_134: genomic DNA from PDB case 134

description: Blood Sample

source_name: White blood cells_134


title: Sample_135: genomic DNA from PDB case 135

description: Blood Sample

source_name: White blood cells_135


title: Sample_133: genomic DNA from PDB case 133

description: Blood Sample

source_name: White blood cells_133


title: Sample_131: genomic DNA from PDB case 131

description: Blood Sample

source_name: White blood cells_131


title: Sample_129: genomic DNA from PDB case 129

description: Blood Sample

source_name: White blood cells_129


title: Sample_127: genomic DNA from PDB case 127

description: Blood Sample

source_name: White blood cells_127


title: Sample_128: genomic DNA from PDB case 128

description: Blood Sample

source_name: White blood cells_128


title: tap3_4DAF biological rep3 [SK328]

type: RNA

city: Yokohama

first: Atsushi

last: Fukushima

address: 1-7-22 Suehiro, Tsurumi

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: After that 80 μl of fragmented and labeled cRNA and hybridization cocktail mixture was injected into the GeneChip Tomato Genome Array and incubated at 45°C at 60 rpm for 16 h according to the protocol. The chips of the microarray were set into the GeneChipR Fluidics Station 450 (Affymetrix) and the chips were washed and stained according to the accompanying manual.

scan_protocol: The Gene Chip scanner 3000 (Affymetrix) was used to scan the Chip and quantify the gene expression level.

data_processing: The data were analyzed with Bioconductor 'simpleaffy' package using RMA as normalization method.

label: biotin

organism: Solanum lycopersicum

source_name: Ovary of tomato tap3 mutant harvested 4 days after flowering

label_protocol: Labeled cRNA was then purified for the same concentration of RNA using the Gene ChipR 3' IVT Express Kit (Affymetrix) according to the kit protocol. The concentration was measured with Nano Drop and sufficient concentration was obtained. Labeled cRNA was prepared to 15 μg / 32 μl and fragmented according to the kit protocol.

growth_protocol: The seeds were absorbed overnight in deionized water and stored at 25°C for 4 to 6 days on deionized water-moistened filter paper under a photoperiod of 16 h/ 8 h with a light intensity of PPF100. Tomato seedlings were transplanted into Rockwool cubes (75 × 75 × 65 mm) and grown in a nutrient solution with an electrical conductivity (EC) of 1.6 dSm^-1 (Otsuka A, Otsuka Chemical Co., Ltd., Japan) under fluorescent light with a photoperiod of 16 h/8 h and a light intensity of PPF 300 under light conditions of 25°C in bright conditions and 20°C in dark conditions.

extract_protocol: Total RNA isolation was performed using RNeasy Plant Mini Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instruction.

treatment_protocol: MicroTom-J plants were divided into groups to be pollinated and emasculated on the flowering day: one that was manually pollinated on the day of flowering and the other that was manually emasculated. Day After Flowering (DAF) was used as a reference for the sampling of pistils from each line at 2 days before flowering (-2 DAF), flowering day (0 DAF), 2 days after flowering (2 DAF), 4 days after flowering (4 DAF), and 8 days after flowering (8 DAF). Sampled stamens were weighed raw and then frozen at -80°C in liquid nitrogen.

value: ovary

tag: genotype

tag: treatment

tag: day

value: 4 DAF


title: tap3_8DAF biological rep1 [SK329]

source_name: Ovary of tomato tap3 mutant harvested 8 days after flowering

value: 8 DAF


title: Sample_126: genomic DNA from PDB case 126

description: Blood Sample

source_name: White blood cells_126


title: Sample_125: genomic DNA from PDB case 125

description: Blood Sample

source_name: White blood cells_125


title: tap3_8DAF biological rep3 [SK331]


title: tap3_4DAF biological rep2 [SK327]


title: tap3_2DAF biological rep3 [SK325]

source_name: Ovary of tomato tap3 mutant harvested 2 days after flowering

value: 2 DAF


title: tap3_4DAF biological rep1 [SK326]


title: tap3_2DAF biological rep2 [SK324]


title: Sample_122: genomic DNA from PDB case 122

description: Blood Sample

source_name: White blood cells_122


title: Sample_121: genomic DNA from PDB case 121

description: Blood Sample

source_name: White blood cells_121


title: Sample_120: genomic DNA from PDB case 120

description: Blood Sample

source_name: White blood cells_120


title: tap3_-2DAF biological rep2 [SK318]

source_name: Ovary of tomato tap3 mutant harvested two days before flowering

value: -2 DAF


title: tap3_0DAF biological rep3 [SK322]

source_name: Ovary of tomato tap3 mutant harvested on flowering day

value: 0 DAF


title: tap3_2DAF biological rep1 [SK323]


title: Sample_132: genomic DNA from PDB case 132

description: Blood Sample

source_name: White blood cells_132


title: tap3_-2DAF biological rep1 [SK317]


title: Sample_124: genomic DNA from PDB case 124

description: Blood Sample

source_name: White blood cells_124

value: Male


title: Sample_123: genomic DNA from PDB case 123

description: Blood Sample

source_name: White blood cells_123

value: Blood


title: tap3_-2DAF biological rep3 [SK319]


title: Sample_119: genomic DNA from PDB case 119

description: Blood Sample

source_name: White blood cells_119

value: Paget’s disease of bone (PDB)


title: tap3_0DAF biological rep1 [SK320]


title: MicroTom-J_8DAF_Emas biological rep3 [SK316]

source_name: Ovary of tomato MicroTom-J harvested 8 days after flowering

value: MicroTom-J

value: Emasculated


title: tap3_0DAF biological rep2 [SK321]


title: 2_supernatant_rep1

city: Bethesda

first: Anupama

last: Khare

state: MD

address: 37 Convent Drive

institute: National Cancer Institute

data_processing:
Reads were cut with Cutadapt. Sequence AGATCGGAAGAGC was removed.
Reads were trimmed with Trimmomatic for single end using leading (3), trailing (3), sliding window (4-15), and minimum length of 10.
Rockhopper was run to match reads to P. aeruginosa UCBPP-PA14 genome and compare expression levels.
Genome_build: RefSeq NC_008463.1
Supplementary_files_format_and_content: txt files were generated using Rockhopper

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: P. aeruginosa was grown in a modified M63 medium shaking at 300 rpm at 37C to OD600 = 0.5 before treatment.

extract_protocol:
RNA Purification Plus Kit (Norgen)
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)

treatment_protocol: Either 25% (v/v) of media or S. aureus supernatant was added to the sample.

tag: strain

tag: time point

value: 120 min

value: S. aureus supernatant


title: Sample_130: genomic DNA from PDB case 130

description: Blood Sample

source_name: White blood cells_130

value: Female

value: White blood cells


title: tap3_8DAF biological rep2 [SK330]


title: MicroTom-J_8DAF_Emas biological rep2 [SK315]


title: 2_supernatant_rep2


title: Sample_116: genomic DNA from PDB case 116

description: Blood Sample

source_name: White blood cells_116

value: Date _1


title: 1_supernatant_rep2

value: 60 min


title: Sample_118: genomic DNA from PDB case 118

description: Blood Sample

source_name: White blood cells_118


title: MutatedAO_resupply_rep3

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

institute: The University of Tokyo

description: Gene expression after 24 hours of nitrate resupply

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction mixture (55 ul) that contained 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent, following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis (v4) Gene Expression Microarray (G2519F-21169) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one-color scan setting for 4x44k array slides with eXtended Dynamic range setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters (Protocol: GE1_1200_Jun14 and Grid: 021169_D_F_201902010) to obtain background subtracted and spatially detrended Processed Signal intensities. Values are normalized with the 75 percentile values of Control type=0 probes. The values of Features flagged by Feature Extraction as gIsPosAndSignif=0 were set to 0.

organism: Arabidopsis thaliana

source_name: Nitrate-non-inducible AO line_nitrate resupply 24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the Ultrospec 6300 pro Spectrophotometer (Amersham Biosciences).

growth_protocol: Arabidopsis seeds on a urethane sponge wetted with 1/10MS solution were incubated under continuous illumination for 1 day and subsequently in the dark for 2 days. Etiolated seedlings were then hydroponically grown under constant illumination with 1/10MS solution for 17 days.

extract_protocol: RNA was prepared using the Isospin plant RNA kit (NIPPON GENE, Tokyo, Japan), following the manufacturer’s recommendations.

treatment_protocol: For N-starvation treatment, the hydroponic solution was changed with nitrogen-free 1/10MS solution supplemented with 0.5 mM K2SO4, and plants were grown for an additional 3 days. These nitrogen-starved plants were then resupplied with 10 mM KNO3 and incubated for 24 hours before collection.

tag: genotype/variation

value: Nitrate-non-inducible AO line

value: nitrate resupply 24h

value: shoot


title: MicroTom-J_8DAF_Emas biological rep1 [SK314]

value: ovary

value: 8 DAF


title: MicroTom-J_4DAF_Emas biological rep3 [SK313]

source_name: Ovary of tomato MicroTom-J harvested 4 days after flowering

value: 4 DAF


title: Sample_117: genomic DNA from PDB case 117

description: Blood Sample

source_name: White blood cells_117


title: 2_media_rep2

value: media


title: 2_media_rep1


title: 1_media_rep2


title: Sample_113: genomic DNA from PDB case 113

description: Blood Sample

source_name: White blood cells_113

value: Blood


title: Sample_112: genomic DNA from PDB case 112

description: Blood Sample

source_name: White blood cells_112

value: Male

value: Paget’s disease of bone (PDB)


title: Sample_114: genomic DNA from PDB case 114

description: Blood Sample

source_name: White blood cells_114


title: MicroTom-J_2DAF_Emas biological rep3 [SK310]

source_name: Ovary of tomato MicroTom-J harvested 2 days after flowering

value: MicroTom-J

value: Emasculated

value: 2 DAF


title: 1_supernatant_rep1

value: S. aureus supernatant


title: MicroTom-J_4DAF_Emas biological rep1 [SK311]


title: MicroTom-J_4DAF_Emas biological rep2 [SK312]


title: WTAO_resupply_rep3

source_name: Wild-type AO line_nitrate resupply 24h

value: Wild-type AO line


title: WTAO_resupply_rep2


title: Sample_115: genomic DNA from PDB case 115

description: Blood Sample

source_name: White blood cells_115

value: Female

value: White blood cells

value: Date _1


title: WTAO_resupply_rep1

value: nitrate resupply 24h


title: 1_media_rep1

value: 60 min


title: MutatedAO_resupply_rep2

value: Nitrate-non-inducible AO line

value: shoot


title: 20_supernatant_rep2

value: 20 min


title: 20_supernatant_rep1


title: Sample_111: genomic DNA from PDB case 111

description: Blood Sample

source_name: White blood cells_111


title: Sample_110: genomic DNA from PDB case 110

description: Blood Sample

source_name: White blood cells_110


title: Sample_109: genomic DNA from PDB case 109

description: Blood Sample

source_name: White blood cells_109


title: MutatedAO_resupply_rep1


title: MicroTom-J_2DAF_Emas biological rep1 [SK308]

value: ovary


title: 20_media_rep2

value: media


title: Sample_108: genomic DNA from PDB case 108

description: Blood Sample

source_name: White blood cells_108

value: Male

value: Blood


title: MicroTom-J_8DAF_Pol biological rep13 [SK307]

source_name: Ovary of tomato MicroTom-J harvested 8 days after flowering

value: MicroTom-J

value: Pollinated

value: 8 DAF


title: MutatedAO_Nstarvation3d_rep3

description: Gene expression after 3 days of N starvation

source_name: Nitrate-non-inducible AO line_N starvation 3d

value: N starvation 3d


title: 20_media_rep1

source_name: bacterial cells


title: MicroTom-J_2DAF_Emas biological rep2 [SK309]

value: Emasculated

value: 2 DAF


title: MutatedAO_Nstarvation3d_rep2


title: Sample_106: genomic DNA from PDB case 106

description: Blood Sample

source_name: White blood cells_106

value: Paget’s disease of bone (PDB)

value: White blood cells


title: Sample_107: genomic DNA from PDB case 107

description: Blood Sample

source_name: White blood cells_107

value: Female

value: Date _1


title: MicroTom-J_8DAF_Pol biological rep1 [SK305]


title: Sample_105: genomic DNA from PDB case 105

description: Blood Sample

source_name: White blood cells_105


title: 0_rep2

value: 0 min


title: MutatedAO_Nstarvation3d_rep1

value: Nitrate-non-inducible AO line

value: shoot


title: MicroTom-J_4DAF_Pol biological rep3 [SK304]

source_name: Ovary of tomato MicroTom-J harvested 4 days after flowering

value: ovary

value: 4 DAF


title: MicroTom-J_8DAF_Pol biological rep2 [SK306]


title: Sample_104: genomic DNA from PDB case 104

description: Blood Sample

source_name: White blood cells_104


title: 0_rep1


title: MicroTom-J_4DAF_Pol biological rep2 [SK303]


title: WTAO_Nstarvation3d_rep2

source_name: Wild-type AO line_N starvation 3d

value: Wild-type AO line


title: WTAO_Nstarvation3d_rep3


title: WTAO_Nstarvation3d_rep1


title: MutatedAO_0d_rep3

description: Gene expression before treatments

source_name: Nitrate-non-inducible AO line_0d

value: none; 0d


title: MutatedAO_0d_rep2

description: Gene expression before treatments


title: MicroTom-J_4DAF_Pol biological rep1 [SK302]

value: MicroTom-J


title: MicroTom-J_2DAF_Pol biological rep3 [SK301]

source_name: Ovary of tomato MicroTom-J harvested 2 days after flowering

value: Pollinated


title: MicroTom-J_2DAF_Pol biological rep2 [SK300]


title: Sample_102: genomic DNA from PDB case 102

description: Blood Sample

source_name: White blood cells_102

value: Male

value: Blood


title: Sample_103: genomic DNA from PDB case 103

description: Blood Sample

source_name: White blood cells_103

value: Date _3


title: MicroTom-J_2DAF_Pol biological rep1 [SK299]

value: 2 DAF


title: DMR7Skin

organism: Fukomys damarensis

source_name: Skin

value: Skin


title: DMR7Lung

source_name: Lung

value: Lung


title: DMR7Heart

source_name: Heart

value: Heart


title: MutatedAO_0d_rep1

description: Gene expression before treatments


title: Sample_101: genomic DNA from PDB case 101

description: Blood Sample

source_name: White blood cells_101

value: Female

value: Paget’s disease of bone (PDB)

value: White blood cells


title: WTAO_0d_rep3

description: Gene expression before treatments

source_name: Wild-type AO line_0d

value: shoot


title: DMR7Brain

source_name: Brain

value: Brain


title: Sample_100: genomic DNA from PDB case 100

description: Blood Sample

source_name: White blood cells_100


title: WTAO_0d_rep1

description: Gene expression before treatments


title: WTAO_0d_rep2

description: Gene expression before treatments


title: Sample_99: genomic DNA from PDB case 99

description: Blood Sample

source_name: White blood cells_99

value: Date _1


title: DMR6Lung


title: T1b Tumor

city: Omaha

first: Vimla

last: Band

state: Nebraska

address: 601 Saddle Creek road

department: Department of Genetics, Cell Biology & Anatomy,

institute: University of Nebraska Medical Center

description: ECD transgenic mammary tumor

data_processing:
The reads were mapped to mouse genome GRCm38 using Star 2.5 and the transcripts were quantified using strand specific protocol in RSEM 1.3.
For differentially expressed gene (DEG) analysis, the expected read counts from control mammary gland samples and tumor samples were used. DEGs between the experimental conditions were statistically obtained with R Bioconductor package, limma with voom after batch normalization.
Genes with p-value <0.05, and fold change >1.5 were considered as DEGs. Heatmaps and enrichment score plots were generated using R. Signaling pathways were analyzed using Gene Set Enrichment Analysis (GSEA).
The gene set enrichment score for each sample was calculated using the single sample GSEA (ssGSEA) method in the Bioconductor GSVA package and the plots were generated using R.
Heatmaps for the squamous, EMT and papillary type tumors were generated using the DEG values of the signature genes in R package, complexHeatmap.
Assembly: GRCm38
Supplementary files format and content: *.txt: Tab-delimited text files include TPM values for each Sample.

source_name: Mouse mammary tumor

extract_protocol:
Total RNA was isolated using the Trizol reagents from control mammary glands or a central piece of the tumor tissue. The total RNA was treated with DNase I and further cleaned using the Qiagen RNeasy clean up kit and RNeasy micro kit, as per the manufacturer’s protocols. Illumina TruSeq RNA Sample Prep Kit v2 (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries following the manufacturer's protocols and sequenced using the 2 x 75 bases paired-end protocol on a HiSeq 2000 instrument (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Adenosquamous carcinoma


title: DMR7Kidney

source_name: Kidney

value: Kidney


title: T4 Tumor

description: ECD transgenic mammary tumor

value: Papillary Carcinoma


title: Sample_98: genomic DNA from PDB case 98

description: Blood Sample

source_name: White blood cells_98


title: DMR6Kidney


title: T1a Tumor

description: ECD transgenic mammary tumor


title: Sample_97: genomic DNA from PDB case 97

description: Blood Sample

source_name: White blood cells_97

value: Date _5


title: MicroTom-J_0DAF biological rep3 [SK298]

source_name: Ovary of tomato MicroTom-J harvested on flowering day

value: ovary

value: MicroTom-J

value: 0 DAF


title: DMR6Heart


title: DMR6Brain


title: MicroTom-J_0DAF biological rep2 [SK297]


title: DMR6Skin


title: T3 Tumor

description: ECD transgenic mammary tumor

value: Spindle Cell Carcinoma


title: MicroTom-J_-2DAF biological rep2 [SK294]

source_name: Ovary of tomato MicroTom-J harvested two days before flowering

value: -2 DAF


title: Sample_96: genomic DNA from PDB case 96

description: Blood Sample

source_name: White blood cells_96

value: Male

value: Blood


title: Ctrl MG-2

description: Control

source_name: Mouse mammary gland

value: Mammary gland


title: MicroTom-J_0DAF biological rep1 [SK296]


title: della_4DAF_Emas biological rep3 [SK205]

source_name: Ovary of tomato della mutant harvested four days after flowering with emasculation

treatment_protocol: MicroTom-B and della mutants were divided into groups to be pollinated and emasculated on the flowering day: one that was manually pollinated on the day of flowering and the other that was manually emasculated. Day After Flowering (DAF) was used as a reference for the sampling of pistils from each line at 2 days before flowering (-2 DAF), flowering day (0 DAF), 2 days after flowering (2 DAF), and 4 days after flowering (4 DAF). Sampled stamens were weighed raw and then frozen at -80°C in liquid nitrogen.

value: della

value: Emasculated

value: 4 DAF


title: DMR5Skin

source_name: Skin

value: Skin


title: Sample_94: genomic DNA from PDB case 94

description: Blood Sample

source_name: White blood cells_94

value: Paget’s disease of bone (PDB)

value: White blood cells

value: Date _3


title: DMR5Lung

source_name: Lung

value: Lung


title: MicroTom-J_-2DAF biological rep3 [SK295]


title: TGFBR1-CA-5

city: College Station

last: Ni

state: Texas

address: 400 Bizzell St

institute: Texas A&M University

data_processing:
RNA sequencing (RNA-seq) was performed using Illumina NextSeq 500
RNA quality was assessed by Agilent Bioanalyzer, Quality check of the raw RNA-seq data was performed using FastQC
STAR  was used to map the reads to the mouse genome (GRCm38.94). HTSeq-count was used to quantify of the number of reads mapped to specific genes.
Pairwise comparison was performed to determine differential gene expression. The false discovery rate (FDR) was calculated with the Benjamini–Hochberg FDR correction

source_name: Ovary

extract_protocol:
Ovarian tissues were homogenized in lysis buffer on ice. Total RNA was prepared using Qiagen RNA isolation kit (Catalog no. 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: post natal day 30


title: Ctrl MG-1

description: Control


title: DMR5Kidney

value: Kidney


title: Ctrl MG-3

description: Control


title: Sample_92: genomic DNA from PDB case 92

description: Blood Sample

source_name: White blood cells_92


title: MicroTom-J_-2DAF biological rep1 [SK293]

value: ovary

value: MicroTom-J


title: della_4DAF_Emas biological rep1 [SK203]


title: Sample_93: genomic DNA from PDB case 93

description: Blood Sample

source_name: White blood cells_93


title: DMR5Heart

source_name: Heart

value: Heart


title: TGFBR1-CA-3


title: della_4DAF_Emas biological rep2 [SK204]


title: della_2DAF_Emas biological rep3 [SK202]

source_name: Ovary of tomato della mutant harvested two days after flowering with emasculation

value: 2 DAF


title: TGFBR1-CA-2


title: DMR5Brain

source_name: Brain

value: Brain


title: Sample_95: genomic DNA from PDB case 95

description: Blood Sample

source_name: White blood cells_95

value: Female

value: Blood


title: Sample_91: genomic DNA from PDB case 91

description: Blood Sample

source_name: White blood cells_91


title: Sample_90: genomic DNA from PDB case 90

description: Blood Sample

source_name: White blood cells_90

value: Male


title: DMR4SKin

source_name: SKin

value: SKin


title: della_2DAF_Emas biological rep2 [SK201]

value: della

value: Emasculated


title: TGFBR1-CA-4


title: Ctrl-5

value: Ctrl


title: Sample_89: genomic DNA from PDB case 89

description: Blood Sample

source_name: White blood cells_89

value: Paget’s disease of bone (PDB)

value: White blood cells


title: Sample_88: genomic DNA from PDB case 88

description: Blood Sample

source_name: White blood cells_88


title: della_4DAF_Pol biological rep3 [SK199]

source_name: Ovary of tomato della mutant harvested four days after flowering with pollination

value: Pollinated

value: 4 DAF


title: Ctrl-4

value: post natal day 30


title: Sample_87: genomic DNA from PDB case 87

description: Blood Sample

source_name: White blood cells_87

value: Date _5


title: DMR4Kidney

source_name: Kidney

value: Kidney


title: DMR4Lung

value: Lung


title: DMR4Heart

value: Heart


title: della_2DAF_Emas biological rep1 [SK200]

value: ovary

value: 2 DAF


title: della_4DAF_Pol biological rep1 [SK197]


title: Ctrl-3


title: DMR4Brian

value: Brain


title: della_4DAF_Pol biological rep2 [SK198]


title: Sample_86: genomic DNA from PDB case 86

description: Blood Sample

source_name: White blood cells_86

value: Female

value: Blood


title: Ctrl-2


title: TGFBR1-CA-1


title: della_2DAF_Pol biological rep3 [SK196]

source_name: Ovary of tomato della mutant harvested two days after flowering with pollination

value: della


title: Ctrl-1

source_name: Ovary


title: della_2DAF_Pol biological rep2 [SK195]


title: Sample_84: genomic DNA from PDB case 84

description: Blood Sample

source_name: White blood cells_84


title: DMR3Lung

source_name: Lung


title: MNKPL2 germline WES

city: Tokyo

first: Akira

last: Nishimura

address: 1-5-45 Yushima, Bunkyo-ku

department: Department of Pediatrics and Developmental Biology

institute: Tokyo Medical and Dental University

description: MNKPL2 germline WES

library_source: genomic

data_processing:
Library strategy: Whole exome sequence
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

source_name: Peripheral blood

extract_protocol:
Genomic DNA was extracted from cells or tissues using QIAGEN AllPrep kit or QIAGEN DNA FFPE kit. Exome capture was carried out using SureSelect QXT Reagents or SureSelect low input XT for the construction of sequencing libraries.
DNA libraries were prepared for sequencing using standard Agilent protocols.

tag: Sex

value: Male

value: Peripheral blood

tag: subgroup


title: Sample_83: genomic DNA from PDB case 83

description: Blood Sample

source_name: White blood cells_83

value: Paget’s disease of bone (PDB)


title: della_2DAF_Pol biological rep1 [SK194]


title: DMR3Kidny


title: MNKPL2 tumor WES

description: MNKPL2 tumor WES

source_name: Bone marrow

value: Bone marrow


title: della_0DAF biological rep3 [SK193]

source_name: Ovary of tomato della mutant harvested on flowering day

value: 0 DAF


title: Sample_80: genomic DNA from PDB case 80

description: Blood Sample

source_name: White blood cells_80

value: White blood cells


title: della_0DAF biological rep2 [SK192]


title: Sample_81: genomic DNA from PDB case 81

description: Blood Sample

source_name: White blood cells_81


title: Sample_82: genomic DNA from PDB case 82

description: Blood Sample

source_name: White blood cells_82


title: Sample_85: genomic DNA from PDB case 85

description: Blood Sample

source_name: White blood cells_85


title: DM8Lung

organism: Peromyscus maniculatus


title: DM8Skin

source_name: Skin

value: Skin


title: Sample_79: genomic DNA from PDB case 79

description: Blood Sample

source_name: White blood cells_79


title: DMR3Brain

source_name: Brain


title: Sample_78: genomic DNA from PDB case 78

description: Blood Sample

source_name: White blood cells_78


title: della_0DAF biological rep1 [SK191]


title: Sample_77: genomic DNA from PDB case 77

description: Blood Sample

source_name: White blood cells_77


title: della_-2DAF biological rep3 [SK190]

source_name: Ovary of tomato della mutant harvested two days before flowering

value: -2 DAF


title: DM8Heart

source_name: Heart


title: DM8Kidney

source_name: Kidney

value: Kidney


title: della_-2DAF biological rep2 [SK189]


title: Sample_76: genomic DNA from PDB case 76

description: Blood Sample

source_name: White blood cells_76

value: Date _1


title: Sample_75: genomic DNA from PDB case 75

description: Blood Sample

source_name: White blood cells_75


title: della_-2DAF biological rep1 [SK188]


title: MicroTom-B_4DAF_Emas biological rep3 [SK187]

source_name: Ovary of tomato MicroTom-B harvested four days after flowering with emasculation

value: MicroTom-B

value: Emasculated

value: 4 DAF


title: DM7SKin

source_name: SKin

value: SKin


title: MicroTom-B_4DAF_Emas biological rep2 [SK186]

value: ovary


title: MicroTom-B_4DAF_Emas biological rep1 [SK185]


title: DM7Lung

source_name: Lung

value: Lung


title: DMR3Heart

value: Heart


title: Sample_74: genomic DNA from PDB case 74

description: Blood Sample

source_name: White blood cells_74

value: Female

value: Blood


title: DM8Liver

source_name: Liver

value: Liver


title: MicroTom-B_2DAF_Emas biological rep3 [SK184]

source_name: Ovary of tomato MicroTom-B harvested two days after flowering with emasculation

value: 2 DAF


title: Sample_72: genomic DNA from PDB case 72

description: Blood Sample

source_name: White blood cells_72

value: Male

value: Paget’s disease of bone (PDB)


title: DM7Kidney


title: DM7Liver


title: Sample_71: genomic DNA from PDB case 71

description: Blood Sample

source_name: White blood cells_71

value: White blood cells


title: DM7Heart


title: Sample_73: genomic DNA from PDB case 73

description: Blood Sample

source_name: White blood cells_73

value: Date _5


title: Sample_70: genomic DNA from PDB case 70

description: Blood Sample

source_name: White blood cells_70


title: MNKPL13 tumor WES

description: MNKPL13 tumor WES

source_name: Bone marrow

value: Bone marrow


title: MNKPL12 tumor WES

description: MNKPL12 tumor WES

source_name: Skin

value: Skin


title: MicroTom-B_2DAF_Emas biological rep2 [SK183]

value: MicroTom-B


title: Sample_69: genomic DNA from PDB case 69

description: Blood Sample

source_name: White blood cells_69


title: MicroTom-B_2DAF_Emas biological rep1 [SK182]

value: Emasculated


title: DM6Liver


title: DM6Lung


title: MicroTom-B_4DAF_Pol biological rep3 [SK181]

source_name: Ovary of tomato MicroTom-B harvested four days after flowering with pollination

value: Pollinated

value: 4 DAF


title: Sample_67: genomic DNA from PDB case 67

description: Blood Sample

source_name: White blood cells_67


title: DM6Kidney

source_name: Kidney

value: Kidney


title: MNKPL10 tumor RNA-seq

description: MNKPL10 tumor RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.7.8a.
Trimmed mean of M values (TMM) normalized counts were calculated using edgeR protocol.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text files include values of raw counts for each Sample.
Supplementary_files_format_and_content: Normalized_counts.txt: Tab-delimited text files include values of TMM normalized counts for each Sample.

molecule: polyA RNA

extract_protocol:
RNA was extracted from cells using QIAGEN RNeasy Mini Kit or AllPrep Kit. The construction of sequencing libraries was carried out using NEBNext Ultra RNA Library Prep Kit or SMARTer Stranded RNA-Seq Kit.
RNA libraries were prepared for sequencing using standard NEB or Takara protocols.


title: Sample_68: genomic DNA from PDB case 68

description: Blood Sample

source_name: White blood cells_68


title: Sample_66: genomic DNA from PDB case 66

description: Blood Sample

source_name: White blood cells_66


title: MicroTom-B_4DAF_Pol biological rep2 [SK180]

value: ovary


title: MicroTom-B_4DAF_Pol biological rep1 [SK179]


title: DM6Heart

source_name: Heart

value: Heart


title: MicroTom-B_2DAF_Pol biological rep2 [SK177]

source_name: Ovary of tomato MicroTom-B harvested two days after flowering with pollination


title: MicroTom-B_2DAF_Pol biological rep3 [SK178]


title: MicroTom-B_2DAF_Pol biological rep1 [SK176]


title: MNKPL10 tumor WES

description: MNKPL10 tumor WES


title: Sample_65: genomic DNA from PDB case 65

description: Blood Sample

source_name: White blood cells_65

value: Female


title: DM6Skin


title: MNKPL9 tumor RNA-seq

description: MNKPL9 tumor RNA-seq


title: DM20SKin

source_name: SKin

value: SKin


title: MNKPL11 tumor WES

description: MNKPL11 tumor WES


title: Sample_64: genomic DNA from PDB case 64

description: Blood Sample

source_name: White blood cells_64

value: Blood


title: MNKPL9 germline WES

description: MNKPL9 germline WES

source_name: Peripheral blood

value: Peripheral blood


title: DM20Lung

source_name: Lung

value: Lung


title: DMR3Skin


title: Sample_63: genomic DNA from PDB case 63

description: Blood Sample

source_name: White blood cells_63

value: Paget’s disease of bone (PDB)

value: Date _1


title: DM20Liver

source_name: Liver

value: Liver


title: MNKPL9 tumor WES

description: MNKPL9 tumor WES

source_name: Bone marrow

value: Bone marrow


title: MNKPL8 tumor WES

description: MNKPL8 tumor WES

value: Male


title: MicroTom-B_0DAF biological rep1 [SK173]

source_name: Ovary of tomato MicroTom-B harvested on flowering day

value: MicroTom-B

value: 0 DAF


title: Sample_61: genomic DNA from PDB case 61

description: Blood Sample

source_name: White blood cells_61

value: White blood cells


title: MicroTom-B_-2DAF biological rep3 [SK172]

source_name: Ovary of tomato MicroTom-B harvested two days before flowering

value: -2 DAF


title: DM20Heart


title: MicroTom-B_0DAF biological rep3 [SK175]


title: MicroTom-B_-2DAF biological rep2 [SK171]


title: DM1Skin

source_name: Skin

value: Skin


title: Sample_60: genomic DNA from PDB case 60

description: Blood Sample

source_name: White blood cells_60


title: MNKPL5 tumor RNA-seq

description: MNKPL5 tumor RNA-seq


title: MicroTom-B_0DAF biological rep2 [SK174]

value: ovary


title: DM1Lung


title: Sample_59: genomic DNA from PDB case 59

description: Blood Sample

source_name: White blood cells_59


title: MicroTom-B_-2DAF biological rep1 [SK170]


title: MNKPL5 germline WES

description: MNKPL5 germline WES


title: iaa9_4DAF_Emas biological rep3 [SK169]

source_name: Ovary of tomato iaa9 mutant harvested 4 days after flowering

treatment_protocol: MicroTom-J and iaa9 mutants were divided into groups to be pollinated and emasculated on the flowering day: one that was manually pollinated on the day of flowering and the other that was manually emasculated. Day After Flowering (DAF) was used as a reference for the sampling of pistils from each line at 2 days before flowering (-2 DAF), flowering day (0 DAF), 2 days after flowering (2 DAF), and 4 days after flowering (4 DAF). Sampled stamens were weighed raw and then frozen at -80°C in liquid nitrogen.

value: Emasculated

value: 4 DAF

tag: batch


title: iaa9_4DAF_Emas biological rep2 [SK168]


title: Sample_57: genomic DNA from PDB case 57

description: Blood Sample

source_name: White blood cells_57

tag: gender


title: MNKPL5 tumor WES

description: MNKPL5 tumor WES


title: Sample_58: genomic DNA from PDB case 58

description: Blood Sample

source_name: White blood cells_58

tag: sample type


title: DM1Liver


title: MNKPL4 germline WES

description: MNKPL4 germline WES

value: Female


title: Sample_56: genomic DNA from PDB case 56

description: Blood Sample

source_name: White blood cells_56

value: Blood

tag: disease state


title: DM1Kidney

source_name: Kidney

value: Kidney


title: MNKPL7 RNA-seq

description: MNKPL7 RNA-seq


title: Sample_62: genomic DNA from PDB case 62

description: Blood Sample

source_name: White blood cells_62

tag: cell type


title: iaa9_4DAF_Emas biological rep1 [SK167]


title: iaa9_2DAF_Emas biological rep3 [SK166]

source_name: Ovary of tomato iaa9 mutant harvested 2 days after flowering

value: 2 DAF


title: DM1Heart

source_name: Heart

value: Heart


title: DGLUNG

organism: Octodon degus

source_name: Lung

value: Lung


title: MNKPL4 tumor WES

description: MNKPL4 tumor WES


title: Sample_55: genomic DNA from PDB case 55

description: Blood Sample

source_name: White blood cells_55

value: Paget’s disease of bone (PDB)

tag: age


title: iaa9_2DAF_Emas biological rep2 [SK165]


title: MNKPL3 tumor WES

description: MNKPL3 tumor WES

source_name: Bone marrow

value: Bone marrow


title: DG7Brain

source_name: Brain

value: Brain


title: MNKPL1 germline WES

description: MNKPL1 germline WES

source_name: Peripheral blood

value: Male

value: Peripheral blood


title: MNKPL1 tumor RNA-seq

description: MNKPL1 tumor RNA-seq

source_name: Lymph node

value: Lymph node


title: DG6Liver

source_name: Liver

value: Liver


title: Sample_53: genomic DNA from PDB case 53

description: Blood Sample

source_name: White blood cells_53

value: White blood cells

tag: array


title: iaa9_2DAF_Emas biological rep1 [SK164]

tag: tissue

value: ovary


title: Sample_51: genomic DNA from PDB case 51

description: Blood Sample

source_name: White blood cells_51

value: Date _1


title: iaa9_-2DAF biological rep3 [SK163]

source_name: Ovary of tomato iaa9 mutant harvested two days before flowering

tag: genotype

value: -2 DAF


title: Sample_50: genomic DNA from PDB case 50

description: Blood Sample

source_name: White blood cells_50

value: Female


title: DG6Kidney


title: iaa9_-2DAF biological rep1 [SK161]

tag: treatment


title: DG5Skin

source_name: Skin

value: Skin


title: iaa9_-2DAF biological rep2 [SK162]

tag: day


title: MicroTom-J_4DAF_Emas biological rep3 [SK160]

source_name: Ovary of tomato MicroTom-J harvested 4 days after flowering

value: MicroTom-J

value: Emasculated

value: 4 DAF


title: Sample_54: genomic DNA from PDB case 54

description: Blood Sample

source_name: White blood cells_54

value: Blood


title: Sample_49: genomic DNA from PDB case 49

description: Blood Sample

source_name: White blood cells_49

value: Paget’s disease of bone (PDB)


title: hMSC-hTERT20_MIR181A1HGkd_Day14_R3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
The reads were aligned to hg38 with STAR (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation v37.
Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R studio.
Genome_build: hg38 (human)
Supplementary_files_format_and_content: Tables showing normalized counts from DESeq2 analysis.
Supplementary_files_format_and_content: HTSeq_normalized_count file

source_name: mesenchymal stromal cell

growth_protocol: Human immortalized MSCs (hMSC-hTERT20) were infected with pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFP to induce MIR181A1HG knockdown. Cells were grown in ascorbic acid-free alpha-MEM  supplemented with 16.5% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from Trizol with DNaseI treatment following manufacturers protocol using the Direct-zol RNA mini-prep kit (Zymo Research #R2050).
RNA libraries were prepared for sequencing with the SMARTer® Stranded Total RNA Sample  Prep Kit - HI Mammalian kit  (Takara) using standard protocols.
Barcoded libraries (SMARTer Stranded ) were loaded onto an Illumina HiSeq 1500 and single-end 75-base (SE75) sequencing was performed at the The Vermont Integrative Genomics Resource (VIGR).

treatment_protocol: Cells were seeded at 1x106 cells per 100 mm dish and grown to 90% confluence.  To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid, 10 mM beta-glycerophosphate, 10nM dexamethasone and 100ng/ BMP2. Cells were harvested at defined time points (0, 7, 14 days) and stored at -80C in TRIzol.

value: marrow stromal cell

tag: differentiation

value: dCas9-KRAB knockdown of MIR181A1HG


title: hMSC-hTERT20_MIR181A1HGkd_Day14_R2


title: MicroTom-J_4DAF_Emas biological rep2 [SK159]


title: DG6Heart

source_name: Heart

value: Heart


title: hMSC-hTERT20_MIR181A1HGkd_Day14_R1


title: DG5Liver


title: Sample_52: genomic DNA from PDB case 52

description: Blood Sample

source_name: White blood cells_52

value: Male


title: DG5Lung

source_name: Lung

value: Lung


title: Sample_48: genomic DNA from PDB case 48

description: Blood Sample

source_name: White blood cells_48


title: MNKPL1 tumor WES

description: MNKPL1 tumor WES

value: Lymph node


title: Sample_47: genomic DNA from PDB case 47

description: Blood Sample

source_name: White blood cells_47

value: White blood cells


title: DG5Kidney

source_name: Kidney

value: Kidney


title: MicroTom-J_4DAF_Emas biological rep1 [SK158]

value: ovary


title: hMSC-hTERT20_MIR181A1HGkd_Day7_R2


title: MicroTom-J_2DAF_Emas biological rep3 [SK157]

source_name: Ovary of tomato MicroTom-J harvested 2 days after flowering

value: 2 DAF


title: DG5Brain

source_name: Brain

value: Brain


title: MicroTom-J_2DAF_Emas biological rep2 [SK156]


title: hMSC-hTERT20_MIR181A1HGkd_Day0_R3


title: Sample_46: genomic DNA from PDB case 46

description: Blood Sample

source_name: White blood cells_46

value: Female

value: Date _1


title: hMSC-hTERT20_MIR181A1HGkd_Day0_R1


title: Sample_43: genomic DNA from PDB case 43

description: Blood Sample

source_name: White blood cells_43


title: Sample_44: genomic DNA from PDB case 44

description: Blood Sample

source_name: White blood cells_44


title: Sample_42: genomic DNA from PDB case 42

description: Blood Sample

source_name: White blood cells_42


title: MicroTom-J_2DAF_Emas biological rep1 [SK155]

value: MicroTom-J

value: Emasculated


title: hMSC-hTERT20_MIR181A1HGkd_Day0_R2


title: Sample_45: genomic DNA from PDB case 45

description: Blood Sample

source_name: White blood cells_45

value: Blood


title: MicroTom-J_-2DAF biological rep3 [SK154]

source_name: Ovary of tomato MicroTom-J harvested two days before flowering

value: -2 DAF


title: DG4Kidney


title: MicroTom-J_-2DAF biological rep2 [SK153]


title: hMSC-hTERT20_MIR181A1HGkd_Day7_R3

value: marrow stromal cell


title: DG4Lung


title: DG4Liver

source_name: Liver

value: Liver


title: hMSC-hTERT20_MIR181A1HGkd_Day7_R1

value: dCas9-KRAB knockdown of MIR181A1HG


title: DG5Heart

value: Heart


title: Sample_40: genomic DNA from PDB case 40

description: Blood Sample

source_name: White blood cells_40

value: Male

value: Paget’s disease of bone (PDB)


title: DG4Heart


title: hMSC-hTERT20_control_Day14_R3

source_name: mesenchymal stromal cell

value: control


title: iaa9_0DAF biological rep3 [SK151]

source_name: Ovary of tomato iaa9 mutant harvested on flowering day

value: 0 DAF


title: Sample_41: genomic DNA from PDB case 41

description: Blood Sample

source_name: White blood cells_41

value: White blood cells


title: hMSC-hTERT20_control_Day14_R2


title: Sample_39: genomic DNA from PDB case 39

description: Blood Sample

source_name: White blood cells_39


title: DG3Skin

source_name: Skin

value: Skin


title: DG4Brain

value: Brain


title: hMSC-hTERT20_control_Day14_R1


title: hMSC-hTERT20_control_Day7_R3


title: iaa9_0DAF biological rep1 [SK149-2]

value: ovary


title: iaa9_0DAF biological rep2 [SK150]


title: Sample_38: genomic DNA from PDB case 38

description: Blood Sample

source_name: White blood cells_38

value: Date _1


title: DG3Lung

source_name: Lung

value: Lung


title: hMSC-hTERT20_control_Day7_R2


title: hMSC-hTERT20_control_Day7_R1


title: Sample_37: genomic DNA from PDB case 37

description: Blood Sample

source_name: White blood cells_37


title: DG3Liver


title: Sample_36: genomic DNA from PDB case 36

description: Blood Sample

source_name: White blood cells_36


title: DG3Kidney

source_name: Kidney

value: Kidney


title: hMSC-hTERT20_control_Day0_R2


title: Sample_35: genomic DNA from PDB case 35

description: Blood Sample

source_name: White blood cells_35

value: Female

value: Blood


title: DG3Heart

source_name: Heart


title: Sample_34: genomic DNA from PDB case 34

description: Blood Sample

source_name: White blood cells_34


title: iaa9_2DAF_Pol biological rep3 [SK148-2]

source_name: Ovary of tomato iaa9 mutant harvested 2 days after flowering

value: Pollinated

value: 2 DAF


title: iaa9_2DAF_Pol biological rep1 [SK146-2]


title: DG3Brain

source_name: Brain


title: iaa9_2DAF_Pol biological rep2 [SK147-2]


title: Sample_32: genomic DNA from PDB case 32

description: Blood Sample

source_name: White blood cells_32


title: iaa9_4DAF_Pol biological rep2 [SK144]

source_name: Ovary of tomato iaa9 mutant harvested 4 days after flowering

value: 4 DAF


title: DG2Lung


title: hMSC-hTERT20_control_Day0_R3

source_name: mesenchymal stromal cell

value: marrow stromal cell


title: DG2Liver

source_name: Liver

value: Liver


title: hMSC-hTERT20_Day14_R5

data_processing:
The reads were aligned to hg38 with STAR (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation v37.
Genome_build: Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R studio.
Supplementary_files_format_and_content: Tables showing normalized counts from DESeq2 analysis.

growth_protocol: Human immortalized MSCs (hMSC-hTERT20) were grown in ascorbic acid-free alpha-MEM  supplemented with 16.5% fetal bovine serum, 2 mM L-glutamine, 100 U/ml of penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated from Trizol with DNase treatment using the Direct-zol RNA mini-prep kit (Zymo Research #R2050).
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) using standard protocols.
Barcoded libraries were loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the The Vermont Integrative Genomics Resource (VIGR).


title: iaa9_4DAF_Pol biological rep3 [SK145]


title: hMSC-hTERT20_Day14_R6


title: Sample_31: genomic DNA from PDB case 31

description: Blood Sample

source_name: White blood cells_31

value: Paget’s disease of bone (PDB)


title: hMSC-hTERT20_Day14_R4


title: Sample_30: genomic DNA from PDB case 30

description: Blood Sample

source_name: White blood cells_30


title: MicroTom-J_0DAF biological rep2 [SK141]

source_name: Ovary of tomato MicroTom-J harvested on flowering day

value: MicroTom-J


title: MicroTom-J_0DAF biological rep1 [SK140]

value: 0 DAF


title: MicroTom-J_0DAF biological rep3 [SK142]


title: Sample_29: genomic DNA from PDB case 29

description: Blood Sample

source_name: White blood cells_29

value: Male

value: White blood cells


title: Sample_33: genomic DNA from PDB case 33

description: Blood Sample

source_name: White blood cells_33


title: DG2Heart

value: Heart


title: DG2Kidney


title: Sample_28: genomic DNA from PDB case 28

description: Blood Sample

source_name: White blood cells_28


title: hMSC-hTERT20_control_Day0_R1

value: control


title: hMSC-hTERT20_Day14_R2


title: hMSC-hTERT20_Day14_R3


title: DG2Brain

value: Brain


title: DG2Skin

source_name: Skin

value: Skin


title: MicroTom-J_2DAF_Pol biological rep2 [SK138]

source_name: Ovary of tomato MicroTom-J harvested 2 days after flowering

value: ovary


title: MicroTom-J_2DAF_Pol biological rep3 [SK139]


title: iaa9_4DAF_Pol biological rep1 [SK143]


title: hMSC-hTERT20_Day14_R1


title: DG1Skin


title: Sample_27: genomic DNA from PDB case 27

description: Blood Sample

source_name: White blood cells_27

value: Date _1


title: MicroTom-J_-2DAF biological rep1 [SK152]

source_name: Ovary of tomato MicroTom-J harvested two days before flowering

value: -2 DAF


title: CM9Skin

organism: Tamias striatus


title: hMSC-hTERT20_Day7_R6


title: Sample_26: genomic DNA from PDB case 26

description: Blood Sample

source_name: White blood cells_26

value: Female

value: Blood


title: MicroTom-J_2DAF_Pol biological rep1 [SK137]

value: Pollinated

value: 2 DAF


title: Sample_25: genomic DNA from PDB case 25

description: Blood Sample

source_name: White blood cells_25


title: MicroTom-J_4DAF_Pol biological rep2 [SK135]

source_name: Ovary of tomato MicroTom-J harvested 4 days after flowering

value: 4 DAF


title: CM9Lung

source_name: Lung

value: Lung


title: Sample_23: genomic DNA from PDB case 23

description: Blood Sample

source_name: White blood cells_23

value: Paget’s disease of bone (PDB)


title: Sample_24: genomic DNA from PDB case 24

description: Blood Sample

source_name: White blood cells_24


title: CM9Liver

source_name: Liver

value: Liver


title: MicroTom-J_4DAF_Pol biological rep3 [SK136]

value: MicroTom-J


title: MicroTom-J_4DAF_Pol biological rep1 [SK134]


title: hMSC-hTERT20_Day7_R3

source_name: mesenchymal stromal cell

value: marrow stromal cell


title: CM9Kidney

source_name: Kidney

value: Kidney


title: hMSC-hTERT20_Day7_R4


title: DM20Kidney


title: hMSC-hTERT20_Day7_R2


title: Sample_22: genomic DNA from PDB case 22

description: Blood Sample

source_name: White blood cells_22

value: Male

value: White blood cells


title: CM9Heart

source_name: Heart

value: Heart


title: Sample_21: genomic DNA from PDB case 21

description: Blood Sample

source_name: White blood cells_21


title: hMSC-hTERT20_Day0_R6


title: hMSC-hTERT20_Day7_R1


title: CM8Lung


title: Sample_20: genomic DNA from PDB case 20

description: Blood Sample

source_name: White blood cells_20


title: hMSC-hTERT20_Day7_R5


title: hMSC-hTERT20_Day0_R5


title: CM8Kidney


title: Sample_19: genomic DNA from PDB case 19

description: Blood Sample

source_name: White blood cells_19


title: CM8Heart


title: CM8Liver


title: hMSC-hTERT20_Day0_R4


title: Sample_18: genomic DNA from PDB case 18

description: Blood Sample

source_name: White blood cells_18

value: Date _3


title: hMSC-hTERT20_Day0_R3


title: Non-tumor 15N

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

country: Brazil

institute: University of São Paulo

description: patient 58

data_processing:
Quality control of reads was performed using FastQC v0.10.1. Adapters and low quality sequences were filtered out with Trimmomatic (sliding window 4:15, minlen: 35).
Reads were aligned against the human genome reference (hg19 version) using TopHat2 software
Tumor and non-tumor samples were assembled using SringTie
Gene and transcript abundance levels were estimated using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Length, effective length, expected count, TPM and FPKM values for each sample

source_name: pancreas non-tumor

extract_protocol:
Surgical fragments of PDAC and peritumoral nonmalignant tissues were collected and snap frozen in liquid nitrogen. RNA was isolated using the Trizol reagent (ThermoFisher) and purified according to the manufacturer’s protocol.
RNA-Seq libraries were generated using the Illumina TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (Cat# RS-122-2001) according to the standard manufacturer’s protocol (Part no. 15031048 Rev. D April 2013).

tag: subject status

value: pancreatic ductal adenocarcinoma (PDAC) patient

value: Non-tumor adjacent pancreatic tissue


title: Tumor 15T

description: patient 58

source_name: pancreas tumor

value: Female

value: PDAC


title: hMSC-hTERT20_Day0_R2


title: Sample_16: genomic DNA from PDB case 16

description: Blood Sample

source_name: White blood cells_16

value: Blood


title: CM7Lung


title: hMSC-hTERT20_Day0_R1


title: CM7SKin

source_name: SKin

value: SKin


title: KO5

city: Daejeon

first: Hyun

middle: Ahm

last: Sohn

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

data_processing:
base calling was conducted through an integrated primary analysis software called RTA (Real Time  Analysis).
The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq
Adapters are trimmed away with Trim Galore 0.6.4 (>Q30)
Reads are mapped with paired end mapping of STAR 2.7.3a
Mapped reads are quantified and normalized with cufflinks 2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: KO5 liver tissue

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using  RNA Prep Kit (Qiagen) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Ndrg3 exon4 deletion

tag: food

value: Ad libitum

tag: strain background


title: KO4

source_name: KO4 liver tissue


title: Sample_15: genomic DNA from PDB case 15

description: Blood Sample

source_name: White blood cells_15

value: Paget’s disease of bone (PDB)

value: Date _1


title: Sample_14: genomic DNA from PDB case 14

description: Blood Sample

source_name: White blood cells_14


title: KO3

source_name: KO3 liver tissue

value: Liver


title: KO2

source_name: KO2 liver tissue


title: CM7Heart


title: Tumor 14T

description:
14T_CTTGTA_L001
patient 06

data_processing:
Quality control of reads was performed using FastQC v0.10.1. Adapters and low quality sequences were filtered out with Trimmomatic (sliding window 4:15, minlen: 35). Reads were aligned against the human genome reference (hg19 version) using TopHat2 software. Tumor and non-tumor samples were assembled separately using SringTie and merged with Cuffmerge to generate a final pancreatic transcriptome reference. Gene and transcript abundance levels in each sample were estimated using RSEM. Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Length, effective length, expected count, TPM and FPKM values for each sample

tag: Sex


title: Non-tumor 14N

description:
14N_CAGATC_L001
patient 06


title: Tumor 13T

description:
13T_GTGAAA_L002
patient 56


title: KO1

source_name: KO1 liver tissue


title: Sample_17: genomic DNA from PDB case 17

description: Blood Sample

source_name: White blood cells_17


title: CM1Skin

source_name: Skin

value: Skin


title: Non-tumor 13N

description:
13N_GTCCGC_L002
patient 56


title: Wild5

source_name: Wild5 liver tissue

value: wild type


title: Sample_11: genomic DNA from PDB case 11

description: Blood Sample

source_name: White blood cells_11


title: CM1Lung

source_name: Lung

value: Lung


title: Tumor 12T

description:
12T_CCGTCC_L002
patient 50


title: CM7Liver

source_name: Liver


title: CM1Liver


title: Sample_10: genomic DNA from PDB case 10

description: Blood Sample

source_name: White blood cells_10

value: Male

value: White blood cells


title: Non-tumor 12N

description:
12N_ATGTCA_L002
patient 50


title: CM7Kidney

source_name: Kidney

value: Kidney


title: Tumor 11T

description:
11T_GCCAAT_L001
patient 04

value: pancreatic ductal adenocarcinoma (PDAC) patient


title: CM1Kidney


title: Sample_8: genomic DNA from PDB case 8

description: Blood Sample

source_name: White blood cells_8


title: Sample_9: genomic DNA from PDB case 9

description: Blood Sample

source_name: White blood cells_9


title: Sample_13: genomic DNA from PDB case 13

description: Blood Sample

source_name: White blood cells_13


title: CM1Heart

source_name: Heart

value: Heart


title: Wild2

source_name: Wild2 liver tissue


title: Sample_12: genomic DNA from PDB case 12

description: Blood Sample

source_name: White blood cells_12


title: Sample_7: genomic DNA from PDB case 7

description: Blood Sample

source_name: White blood cells_7


title: Wild1

source_name: Wild1 liver tissue


title: Non-tumor 11N

description:
11N_ACAGTG_L001
patient 04

value: Non-tumor adjacent pancreatic tissue


title: CM10Skin


title: Tumor 10T

description:
10T_AGTTCC_L002
patient 47

value: Female

value: PDAC


title: Sample_6: genomic DNA from PDB case 6

description: Blood Sample

source_name: White blood cells_6

value: Blood


title: CM10LUNG

source_name: LUNG

value: LUNG


title: EVAld2

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

country: China

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome
Sam format files were output by HISAT2. Samtools was used to convert these sam format files to bam format files and resort these bam format files. Then the gene reads were counted by HTSeq and analysis by DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: txt files of normalized gene counts for each sample

extract_protocol:
Livers were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: male

value: 9 weeks

value: Lieber-DeCarli liquid diet containing 5% (w/v) alcohol (EtOH)


title: Sample_5: genomic DNA from PDB case 5

description: Blood Sample

source_name: White blood cells_5

tag: gender

value: Paget’s disease of bone (PDB)


title: Non-tumor 10N

description:
10N_AGTCAA_L002
patient 47


title: CM10Liver

value: Liver


title: Wild4

source_name: Wild4 liver tissue

value: wild type

value: Ad libitum


title: Wild3

source_name: Wild3 liver tissue


title: Tumor 9T

description:
9T_CTTGTA_L002
patient 44

value: Male


title: CM10Kidney


title: Sample_4: genomic DNA from PDB case 4

description: Blood Sample

source_name: White blood cells_4

tag: sample type

value: White blood cells


title: Non-tumor 9N

description:
9N_TGACCA_L002
patient 44


title: CM10Heart


title: EVCtrl1

source_name: Liver

value: isocaloric maltose dextrin (Ctrl)


title: Sample_2: genomic DNA from PDB case 2

description: Blood Sample

source_name: White blood cells_2

tag: disease state


title: Non-tumor 8N

description:
8N_ACAGTG_L002
patient 39

value: pancreatic ductal adenocarcinoma (PDAC) patient


title: Tumor 8T

description:
8T_GCCAAT_L002
patient 39


title: WTAld1


title: Sample_1: genomic DNA from PDB case 1

description: Blood Sample

source_name: White blood cells_1

tag: cell type


title: Non-tumor 7N

description:
7N_CCGTCC_L001
patient 38

tag: age


title: WTCtrl2


title: EVAld1


title: U5Skin

organism: Cavia porcellus

source_name: Skin

value: Skin


title: U5Kidney

source_name: Kidney

value: Kidney


title: Tumor 7T

description:
7T_CGATGT_L001
patient 38


title: U5Lung

source_name: Lung

value: Lung


title: U4Skin


title: Sample_3: genomic DNA from PDB case 3

description: Blood Sample

source_name: White blood cells_3

tag: array


title: control male3, Riboseq

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

description: ribosome protected fragments

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt (Martin 2011)
Trimmed sequence reads were mapped to rRNA using  bowtie2 (Langmead, 2012) v2.4.4, and remaining reads were maped to mm10 supplied with GENCODE22 annotation using STAR v2.7.9a (Dobin, 2013).
Alignment file quality control metrics and read count matrices were obtained using RibosomeProfilingQC (Jianghong Ou 2021) and RiboseQC (Calviello  2019). DESeq2 (Love, 2014) was used to perform differential analysis.
ORFquant (Calviello, 2021) was used to perform de novo ORF detection and quantification.
Assembly: mm10
Supplementary files format and content: excel files include average log2FC and average CPM for ctrl and cKO conditions
Library strategy: Ribo-seq

source_name: E11.5 neocortex

extract_protocol:
RNA-seq: RNA was harvested using the RNAeasy kit (Qiagen, 74034). 50 ng of total RNA was used for the construction of sequencing libraries.
Riboseq: Ribosome protected fragments were isolated on a 15% denaturing urea gel followed by gel extraction and Trizol-based RNA isolation.
RNAseq: cDNA libraries for RNA-seq were prepared using the Kapa mRNA HyperPrep kit with mRNA capture (KapaBiosystems, KR1352)
Riboseq: cDNA libraries for Ribo-seq were prepared using the Qiagen miRNA library prep kit (331502)

tag: tissue

value: E11.5 neocortex

value: WT

tag: assay

value: Riboseq


title: EVCtrl2

value: male

tag: genotype

tag: treatment


title: Tumor 6T

description:
6T_ATGTCA_L001
patient 35

value: PDAC


title: WTCtrl1

value: 9 weeks


title: control female3, Riboseq

description: ribosome protected fragments

value: female


title: control male1, Riboseq

description: ribosome protected fragments


title: U5Liver

value: Liver


title: control male2, Riboseq

description: ribosome protected fragments


title: U4Liver


title: INS-1E cell_cyanidin-3-o-glucoside treated_rep3

city: Guangzhou

first: Yunan

last: Chen

state: Guangdong

address: Guangzhou, Guangdong Province, P.R. China.

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: INS-1E cell

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: pancreas

value: treated with the mixture of palmitic acid and cyanidin-3-o-glucosidefor 24 h

value: Insulin secreting beta cell derived line.


title: WTAld2

value: wild type

value: Lieber-DeCarli liquid diet containing 5% (w/v) alcohol (EtOH)


title: control female2, Riboseq

description: ribosome protected fragments


title: INS-1E cell_cyanidin-3-o-glucoside treated_rep2


title: INS-1E cell_cyanidin-3-o-glucoside treated_rep1


title: Tumor 5T

description:
5T_AGTCAA_L001
patient 30

value: pancreatic ductal adenocarcinoma (PDAC) patient

value: Male


title: Non-tumor 6N

description:
6N_AGTTCC_L001
patient 35

value: Non-tumor adjacent pancreatic tissue


title: Non-tumor 5N

description:
5N_CTTGTA_L001
patient 30


title: CKO male3, Riboseq

description: ribosome protected fragments

value: cKO


title: Tumor 4T

description:
4T_TGACCA_L001
patient 02


title: INS-1E cell_palmitic acid treated_rep3

value: treated with palmitic acid for 24 h


title: Non-tumor 4N

description:
4N_CGATGT_L001
patient 02


title: Tumor 3T

description:
3T_CAGATC_L001
patient 29

value: Female


title: Non-tumor 3N

description:
3N_GCCAAT_L001
patient 29


title: CKO female2, Riboseq

description: ribosome protected fragments

value: E11.5 neocortex

value: Riboseq


title: Tumor 2T

description:
2T_ACAGTG_L001
patient 25

value: PDAC


title: U3Skin

value: Skin


title: U4Kidney

value: Kidney


title: HFpEF_4

city: Los Angeles

first: Thassio

last: Mesquita

state: California

address: 8700 Beverly Boulevard

department: Smidt Heart Institute

institute: Cedars-Sinai Medical Center

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: sinoatrial node

extract_protocol:
Sinoatrial node was dissected, flash frozen on LN2, and RNA extracted using RNeasy kit (QIAzol, Qiagen).
Total RNA-Seq library construction was performed using the Swift Biosciences RNA Library Kit (Swift Biosciences, Ann Arbor, MI), following rRNA depletion using Lexogen RiboCop Depletion Kit Human/Mouse/Rat v2 (Lexogen Inc., Greenland, NH).
Final library concentration was measured via the Qubit 1X dsDNA HS Assay kit (ThermoFisher Scientific) and library size was evaluated on the 4200 TapeStation using the Agilent D1000 ScreenTape System (Agilent Technologies).

treatment_protocol: Dahl salt-sensitive rats fed with normal salt diet (0.4% NaCl, control group) or high-salt diet (8% NaCl, HFpEF group) for 11 weeks.

value: sinoatrial node

value: Dahl/Salt Sensitive Rat (SS/JrHsdMcwiCrl)

value: High salt diet 8% NaCl for 11 weeks


title: control male3 RNAseq

data_processing:
Sequence reads were trimmed for adaptor sequence using cutadapt (Martin 2011)
Trimmed sequence reads were mapped to rRNA using  bowtie2 (Langmead, 2012) v2.4.4, and remaining reads were maped to mm10 supplied with GENCODE22 annotation using STAR v2.7.9a (Dobin, 2013).
Alignment file quality control metrics and read count matrices were obtained using RibosomeProfilingQC (Jianghong Ou 2021) and RiboseQC (Calviello  2019). DESeq2 (Love, 2014) was used to perform differential analysis.
ORFquant (Calviello, 2021) was used to perform de novo ORF detection and quantification.
Assembly: mm10
Supplementary files format and content: excel files include average log2FC and average CPM for ctrl and cKO conditions

value: male

value: WT

value: RNAseq


title: HFpEF_3


title: INS-1E cell_palmitic acid treated_rep1

value: pancreas

value: Insulin secreting beta cell derived line.


title: INS-1E cell_palmitic acid treated_rep2


title: control male1, RNAseq


title: CKO male2, Riboseq

description: ribosome protected fragments


title: U3Liver

data_processing:
raw fastq reads files were cleaned by Trimmomatic-0.36
gene expression (reads counts) were calculated by salmon 1.4.0
Supplementary_files_format_and_content: gene expression

value: Liver


title: CKO female3 Riboseq

description: ribosome protected fragments

value: female

value: cKO


title: control female3, RNAseq


title: CKO male1, Riboseq

description: ribosome protected fragments


title: INS-1E cell_control_rep2

value: treated with fatty acid-free BSA for 24 h


title: GypSkin


title: U4Heart

source_name: Heart

value: Heart


title: Non-tumor 1N

description:
1N_AGTCAA_L001
patient 12

value: pancreatic ductal adenocarcinoma (PDAC) patient

value: Male

value: Non-tumor adjacent pancreatic tissue


title: INS-1E cell_control_rep3


title: control female2, RNAseq

value: E11.5 neocortex


title: U3Kidney

value: Kidney


title: U2Heart


title: U2Kidney


title: Tumor 1T

description:
1T_AGTTCC_L001
patient 12

value: PDAC


title: CKO female1, Riboseq

description: ribosome protected fragments

value: Riboseq


title: U2Lung

value: Lung


title: U2Skin

value: Skin


title: INS-1E cell_control_rep1


title: HFpEF_2

value: sinoatrial node

value: Dahl/Salt Sensitive Rat (SS/JrHsdMcwiCrl)

value: High salt diet 8% NaCl for 11 weeks


title: HFpEF_1


title: Non-tumor 2N

description:
2N_TGACCA_L001
patient 25


title: GypLung


title: Control_2

value: Normal salt diet 0.4% NaCl for 11 weeks


title: GypLiver

value: Liver


title: control male2 RNAseq

value: male

value: WT

value: RNAseq


title: U2Liver


title: CKO male3, RNAseq

value: cKO


title: Control_3


title: Control_4


title: GpyHeart

value: Heart


title: GypKidney


title: CKO male2, RNAseq


title: CKO female2, RNAseq

value: female


title: CKO male1, RNAseq

value: E11.5 neocortex


title: CKO female3, RNAseq


title: Control_1


title: Hypothalamus female oriented ram3

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description: female oriented ram 3

data_processing:
Quality check was performed on the sequenced data using FastQC and MultiQC, followed by trimming using TrimGalore to get high quality reads.
The trimmed sequences were aligned to sheep reference genome “Oar_v3.1” and methylation profile extracted from the same, using Bismark with bowtie2 option chosen for alignment.
Further quality checks, normalization  and differential methylation analysis were performed using R bioconductoR package, methylKit.
Annotation was done with genomation.
Functional annotation was performed using gProfileR (Raudvere et al. 2019). Visualization are done using methylKit, ViewBS (Huang et al. 2018) and GOplot(Walter et al. 2015).
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Methylation Report Data in text format.

organism: Ovis aries

source_name: Hypothalamus

extract_protocol:
Genomic DNA was isolated from hypothalami using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer instructions.  The gDNA was then concentrated using the Genomic DNA Clean & Concentrator Kit (Zymo Research) as directed by the manufacturer.  The concentration and quality of gDNA was veri¬fied with absorbance spectroscopy and Qubit fluorimetry (ThermoFisher Scientific).
To generate RRBS libraries, ~150ng of sheep genomic DNA extracted as described above was digested overnight with the restriction enzyme MspI (New England Biolabs) cutting the sequence CCGG producing sticky ends which enables every read to start with a CpG. Clean up was performed with AMPure XP magnetic beads (Beckman Coulter) before use with the NEXTflex Bisulfite-Seq Kit (BiooScientific) for library preparation. The digested DNA was end repaired, A-tailed and then ligated with the NEBNext Methylated Adaptor (New England Biolabs). The ligated DNA was size-selected using AMPure XP magnetic beads to produce a final library size of 350bp. Bisulfite conversion was performed with the EZ DNA Methylation-Gold Kit (Zymo Research) before carrying out PCR amplification with NEBNext Multiplex Oligos (New England Biolabs) to barcode each library. A final AMPure XP bead clean was performed and the resulting libraries were quantified with the Qubit High Sensitivity double stranded (dsDNA) Assay (Life Technologies) and the Bioanalyzer High Sensitivity Analysis (Agilent). Libraries were multiplexed and sequenced on the Illumina NextSeq or HiSeq2500 to obtain ~30 million single end, 75 bp reads.

tag: ram number


title: Hypothalamus female oriented ram4

description: female oriented ram 4


title: Hypothalamus female oriented ram2

description: female oriented ram 2


title: CKO female1, RNAseq


title: Hypothalamus male oriented ram5

description: male oriented ram 5


title: Hypothalamus female oriented ram1

description: female oriented ram 1


title: 010nuc, replicate 1, snRNAseq

city: Cambridge

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

institute: Broad Institute

library_source: transcriptomic single cell

data_processing:
BCL files were converted to FASTQ using bcl2fastq2-v2.20.
CellRanger v3.0.2 was used to demultiplex the FASTQ reads, align them to the hg38 human transcriptome (pre-mRNA) reference and extract the UMI and nuclei barcodes.
We used CellBender remove-background to remove ambient RNA and other technical artifacts from the count matrices.
Nuclei with over 10,000 UMI counts were filtered.
UMI counts were normalized by the total number of UMIs per nucleus and converted to transcripts-per-10,000 (TP10K) as the final expression unit.
Assembly: Hg38
Supplementary files format and content: H5ad file of aggregated processed single-nuclei RNA sequencing data from all 45 human specimens; found in totaldata-final-toshare.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (untreated); found in adata_010nuc_10x.h5ad
Supplementary files format and content: H5ad file of processed single-nuclei RNA sequencing data from the patient-derived organoid (treated with 5-FU, SM38, and oxaliplatin); found in adata_010orgCRT_10x.h5ad

source_name: Pancreas

extract_protocol:
Resected primary tumor samples were snap frozen and stored at -80°C. Selected tissue was transferred into an NSTcPA buffer and manually minced.
Nuclei from each sample were loaded into each channel of a Chromium single-cell 3’ chip according to the manufacturer’s instructions. Single nuclei were partitioned into droplets with gel beads in the Chromium Controller to form emulsions, after which nuclear lysis, barcoded reverse transcription of mRNA, cDNA amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment were performed according to manufacturer’s instructions.
The snRNA-seq sample libraries were pooled (3-4 samples per flow cell line) and sequenced on the HiSeq X Version 2.5 (Illumina) with the following paired end read configuration: read 1, 26-28 nt; read 2, 96-98 nt; index read, 8 nt.

value: Pancreas

tag: cell line

value: Patient-derived organoid

value: Tumor

value: Untreated


title: Normal_2517, replicate 3, snRNAseq

value: Normal


title: 010orgCRT, replicate 1, snRNAseq

value: CRT


title: anterior segments, mutant, rep6

city: San Francisco

first: Douglas

last: Gould

state: CA

address: Room 235, 10 Koret Way

department: Ophthalmology

institute: UCSF

data_processing:
Illumina sequencing libraries were prepared and sequenced (150 bp  pair-ended) on an Illumina Novaseq6000 sequencer.
Filtered reads were aligned to mouse reference genome assembly (GRCm38) using STAR v2.6.1 and the read count table was generated  using HTseq v0.6.1.
Differential gene expression analysis was performed using the  DEseq2 v1.6.3 R package.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file including count values of all samples

source_name: tissue

extract_protocol:
Anterior segments were dissected in PBS by cutting along the limbus with scissors. After removing the lens, the remaining anterior segment (cornea, iris, ciliary body and ocular drainage structures) was collected. Samples were stabilized in RNAlater (ThermoFisher Scientific, USA) and stored at −80 °C until use. Each sample were pooled from 4 eyes from 2 mice. Total RNA was extracted using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tissue

value: anterior segments

value: Mut


title: anterior segments, mutant, rep5


title: Normal_2517, replicate 2, snRNAseq


title: spinal cord cells, HBOT 1d 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from spinal cord cells from an animal given a cSCI followed by one hyperbaric oxygen treatment (HBOT) at day 10.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Rat Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray ragene20strnentrezgcdf R package (version 17.0.0).

source_name: spinal cord cells, animal given cSCI followed by one hyperbaric oxygen treatment (HBOT) only on day 1 post-injury

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: All procedures were approved by the University of Florida Institutional Animal Care and Use Committee.  Rats were housed in an Assessment and Accreditation of Laboratory Animal Care (AAALAC)-accredited facility with a 12:12 light/dark cycle with ad libitum access to rodent chow and water. Adult female Sprague-Dawley rats (200-250g, Harlan Laboratories, Indianapolis, IN, USA) were studied.

extract_protocol: Rats were injected intraperitoneally with beuthanasia solution. After the loss of the hind-limb withdrawal reflex, cervical spinal tissues (C3-C5) were harvested, placed into RNA Later (Life Technologies, Carlsbad, CA, USA), and stored at -80°C. RNA extraction was performed using TRIzol and isolated total RNA was purified using an RNeasy Mini kit (Qiagen, Valencia, CA), according to manufacturer’s instructions. The resulting quantity and purity of total RNA was tested through absorbance spectrophotometry at 230, 260 and 280 nm.

treatment_protocol: For spinal surgery, anesthesia was induced in a closed chamber with 3% isoflurane (balance O2) and maintained with 2-3% isoflurane (balance O2) via nose cone. A dorsal midline incision was made from the second to fifth cervical segment (C2–5) and the C3/4 laminae were removed.  Rats in the SCI groups underwent a left lateralized spinal contusion using the Infinite Horizon pneumatic impactor (Precision Systems & Instrumentation, Lexington, KY;22). The impactor probe (2.5 mm diameter tip) was positioned between midline and the left lateral edge of the spinal cord at C3/C4, and was raised 5mm above the intact dura. The cord was contused at a pre-set nominal force of 200 kilodynes (dwell time = 0). For HBO treatment:  HBO exposures began within the first four hours of anesthesia recovery and continued daily for 10 days. Rats were placed in a small hyperbaric chamber (volume = 17 L; PCCI Hyperbaric Systems, Alexandria, Virginia). The chamber was sealed and flushed with 100% O2 for 5 min prior to pressurization. The chamber was steadily pressurized over 6 min (~5 psi/min) until reaching 3.0 atmospheres (29.4 psi). The pressure was maintained for 60 min, and the chamber was continually flushed with 100% O2 (3 L/min). After the 60 min exposure, the chamber was steadily depressurized over 6 min (~5 psi/min).

value: Sprague-Dawley

tag: developmnetal stage

value: Adult

value: HBOT 1d

value: spinal cord cells


title: Normal_2517, replicate 1, snRNAseq


title: Normal_010N, replicate 1, snRNAseq


title: spinal cord cells, HBOT 10d 4

description: Gene expression data from spinal cord cells from an animal given a cSCI followed by daily hyperbaric oxygen treatment (HBOT) for 10 days.

source_name: spinal cord cells, animal given cSCI followed by daily hyperbaric oxygen treatment (HBOT) for 10 days

value: HBOT 10d


title: Normal_2548, replicate 1, snRNAseq


title: spinal cord cells, HBOT 10d 1


title: anterior segments, mutant, rep4


title: spinal cord cells, HBOT 10d 2


title: spinal cord cells, HBOT 1d 4


title: spinal cord cells, HBOT 10d 3


title: Hypothalamus male oriented ram4

description: male oriented ram 4

value: male


title: Normal_2540N, replicate 1, snRNAseq


title: anterior segments, mutant, rep3


title: Hypothalamus male oriented ram3

description: male oriented ram 3


title: Hypothalamus male oriented ram2

description: male oriented ram 2


title: Normal_2675N replicate 1, snRNAseq


title: anterior segments, mutant, rep2


title: Hypothalamus male oriented ram1

description: male oriented ram 1


title: spinal cord cells, HBOT 1d 1

value: female


title: spinal cord cells, cSCI 4

description: Gene expression data from spinal cord cells from an animal given a cervical spinal cord injury (cSCI) (contusion injury at C3/C4).

source_name: spinal cord cells, animal given cervical spinal cord injury (cSCI) (contusion injury at C3/C4)

value: cSCI


title: spinal cord cells, HBOT 1d 2


title: Normal_MGHR13, replicate 2, snRNAseq

value: Pancreas


title: anterior segments, mutant, rep1


title: anterior segments, wildtype, rep3

value: Wt


title: Normal_MGHR13, replicate 1, snRNAseq


title: spinal cord cells, cSCI 3


title: spinal cord cells, cSCI 2


title: MNKPL5 tumor HC CD34 CD56 scRNA-seq

description: MNKPL5 tumor HC CD34 CD56 scRNA-seq

source_name: Bone marrow, Bone marrow

extract_protocol:
The preparation of single cell suspension was performed using lymph node and bone marrow. The extraction of RNA and RNA libraries were generated by BD Rhapsody system and BD Rhapsody Whole Transcriptome Analysis kit.
RNA libraries were prepared for sequencing using standard BD protocols.

value: Male

value: Bone marrow, Bone marrow

tag: subgroup


title: spinal cord cells, cSCI 1


title: spinal cord cells, sham 2

description: Gene expression data from spinal cord cells from an animal that underwent a sham operation (C3/C4 laminectomy).

source_name: spinal cord cells, animal underwent sham operation (C3/C4 laminectomy)

value: sham


title: spinal cord cells, sham 1


title: PDAC_T_24, replicate 2, snRNAseq

value: Tumor

value: Gem/abraxane, Gy/cape


title: anterior segments, wildtype, rep1

value: tissue

value: anterior segments


title: PDAC_T_25, replicate 1, snRNAseq

value: Gy/cape


title: spinal cord cells, sham 4

value: Sprague-Dawley

value: Adult


title: PDAC_T_24, replicate 1, snRNAseq


title: IPA-1

first: LI

middle: YAN

last: LI

address: Changgang East Road

institute: The Second Affiliated Hospital of Guangzhou Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build:  hg19_GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: noninvasive pituitary adenoma

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: noninvasive pituitary adenoma


title: NIPA-3

source_name: invasive pituitary adenoma

value: invasive pituitary adenoma


title: IPA-2


title: spinal cord cells, naive 4

description: Gene expression data from spinal cord cells from a naive animal (no surgical intervention).

source_name: spinal cord cells, naive animal (no surgical intervention)

value: naive

value: spinal cord cells


title: spinal cord cells, naive 2

value: female


title: spinal cord cells, naive 3


title: NIPA-1


title: NIPA-2


title: PDAC_T_21, replicate 2, snRNAseq

value: Pancreas

value: CRTLN


title: spinal cord cells, sham 3


title: IPA-3


title: PDAC_T_21, replicate 1, snRNAseq


title: SMU_218 Xylose 3

city: Jonesboro

first: Robert

middle: Colquhoun

last: Shields

state: Arkansas

address: Lab Science East

department: Biological Sciences

institute: Arkansas State University

description:
Xylose 3
repeat 3 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Assembly: NC_004350.2
Supplementary files format and content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: bacterial cells

growth_protocol: Bacterial cells used for extraction of RNA were grown in CDM medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C. Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
Constructed by the Microbial Genome Sequencing Center

value: Pxyl-dcas9 sgRNA-218

tag: media

value: Chemically Defined Media

tag: growth point


title: PDAC_T_19, replicate 2, snRNAseq

value: CRTL


title: SMU_218 Control 3

description:
Control 3
repeat 3 of 3

tag: strain


title: PDAC_T_20, replicate 1, snRNAseq

value: Tumor

value: CRTN


title: SMU_218 Control 2

description:
Control 2
repeat 2 of 3


title: SMU_218 Xylose 1

description:
Xylose 1
repeat 1 of 3


title: SMU_218 Xylose 2

description:
Xylose 2
repeat 2 of 3


title: PDAC_T_19, replicate 1, snRNAseq


title: anterior segments, wildtype, rep2

value: tissue

value: Wt


title: SMU_218 Control 1

description:
Control 1
repeat 1 of 3


title: PDAC_T_23, replicate 1, snRNAseq

value: FOLFIRINOX, Gy/cisplatin


title: spinal cord cells, naive 1

value: Sprague-Dawley

tag: Sex


title: PDAC_T_15, replicate 2, snRNAseq

description:
10x Genomics
totaldata-final-toshare.h5ad