title: Kennebec_2232

source_name: Kennebec_foliage from field-grown plants

value: tetraploid variety

value: Kennebec


title: 15143-52_2222

status: Public on Dec 11 2018

type: SRA

city: Fredericton

first: Helen

middle: H.

last: Tai

state: New Brunswick

address: P. O. Box 20280, 850 Lincoln Rd.

department: Potato Research Centre

country: Canada

institute: Agriculture and Agri-Food Canada

library_source: transcriptomic

data_processing:
*_arn*.txt: Adapter and barcode sequences were trimmed
*1x3.txt: Sequences that were not present in at least one of the three replicates were removed (1X3 tags)
Tag count data were transformed into a data matrix using in-house Perl scripts and transformed to the relative unit of counts per million.
Supplementary_files_format_and_content: tab delimited txt file with tag sequence and tag counts

molecule: total RNA

organism: Solanum tuberosum

source_name: 15143-52_foliage from field-grown plants

extract_protocol:
The smallest leaflet from the 4th fully expanded compound leaf was removed from each of the five plants per plot and pooled for each replicate plot.  Leaf tissue was ground in the Lysing Matrix D tubes using a Geno Grinder 2000 (SPEX CertiPrep) machine for 2 min at speed 5. Samples were kept frozen. One ml RNA lysis buffer (200 mM sodium borate decahydrate (Borax), pH 9.0, 30 mM ethylene glygol bis (aminoethyl ether)-N-N’-tetraacetic acid (EGTA), 1% (w/v) sodium dodecyl sulfate (SDS), and 10 mM dithiothreitol) plus 1 % (w/v) sodium deoxycholate and 2% (w/v) polyvinylpyrrolidone (PVP) (Mr 40,000))  was added to ground leaf tissue in each tube.
Template DNA hybridization and sequencing on an Illumina Genome Analyzer II (Illumina, San Diego, USA) according to the manufacturer's instructions.

tag: genotype/variety

value: 15143 diploid mapping population clone

tag: clone id

tag: tissue

value: foliage from field-grown plants

tag: run

value: RunC

tag: adapter b barcode

value: TAG

tag: channel


title: 15143-60_2224

source_name: 15143-60_foliage from field-grown plants


title: 15143-53_2220

source_name: 15143-53_foliage from field-grown plants


title: 15143-86_2221

source_name: 15143-86_foliage from field-grown plants


title: 15143-64_2219

source_name: 15143-64_foliage from field-grown plants

value: TCC


title: 15143-92_2225

source_name: 15143-92_foliage from field-grown plants


title: Green Mountain_2218

source_name: Green Mountain_foliage from field-grown plants

value: Green Mountain


title: 15143-74_2223

source_name: 15143-74_foliage from field-grown plants


title: 15143-15_2230

source_name: 15143-15_foliage from field-grown plants

value: TGT


title: 15143-39_2229

source_name: 15143-39_foliage from field-grown plants


title: 15143-26_2227

source_name: 15143-26_foliage from field-grown plants


title: 15143-25_2189

source_name: 15143-25_foliage from field-grown plants

value: RunB

value: GTT


title: 15143-68_2205

source_name: 15143-68_foliage from field-grown plants

value: TTA


title: 15143-66_2208

source_name: 15143-66_foliage from field-grown plants


title: 15143-06_2210

source_name: 15143-06_foliage from field-grown plants


title: 15143-59_2195

source_name: 15143-59_foliage from field-grown plants


title: 15143-66_2192


title: 15143-17_2201

source_name: 15143-17_foliage from field-grown plants

value: AAT


title: 15143-24_2191

source_name: 15143-24_foliage from field-grown plants


title: 15143-42_2194

source_name: 15143-42_foliage from field-grown plants


title: 15143-03_2190

source_name: 15143-03_foliage from field-grown plants


title: 15143-14_2217

source_name: 15143-14_foliage from field-grown plants


title: 15143-93_2214

source_name: 15143-93_foliage from field-grown plants


title: 15143-97_2211

source_name: 15143-97_foliage from field-grown plants


title: 15143-24_2215


title: 15143-34_2202

source_name: 15143-34_foliage from field-grown plants


title: 12120-03_2187

source_name: 12120-03_foliage from field-grown plants

value: parental clone

value: AGC


title: 15143-83_2213

source_name: 15143-83_foliage from field-grown plants


title: 15143-20_2209

source_name: 15143-20_foliage from field-grown plants


title: 15143-17_2188


title: 15143-75_2200

source_name: 15143-75_foliage from field-grown plants


title: Atlantic-1_2197

source_name: Atlantic-1_foliage from field-grown plants


title: 15143-86_2193

source_name: 15143-86_foliage from field-grown plants


title: 15143-07_2204

source_name: 15143-07_foliage from field-grown plants


title: 15143-56_2216

source_name: 15143-56_foliage from field-grown plants


title: 15143-85_2206

source_name: 15143-85_foliage from field-grown plants


title: 15143-23_2199

source_name: 15143-23_foliage from field-grown plants


title: 15143-16_2212

source_name: 15143-16_foliage from field-grown plants


title: 15143-77_2207

source_name: 15143-77_foliage from field-grown plants


title: 15143-46_2183

source_name: 15143-46_foliage from field-grown plants


title: 15143-48_2182

source_name: 15143-48_foliage from field-grown plants


title: Green Mountain_2186

source_name: Green Mountain_foliage from field-grown plants


title: 15143-39_2184

source_name: 15143-39_foliage from field-grown plants


title: 15143-76_2181

source_name: 15143-76_foliage from field-grown plants


title: 15143-92_2180

source_name: 15143-92_foliage from field-grown plants


title: 15143-08_2185

source_name: 15143-08_foliage from field-grown plants


title: 07506-01_2176

source_name: 07506-01_foliage from field-grown plants

value: ACA


title: 15143-78_2177

source_name: 15143-78_foliage from field-grown plants


title: Kennebec_2179

source_name: Kennebec_foliage from field-grown plants


title: 15143-61_2171

source_name: 15143-61_foliage from field-grown plants

value: ATG


title: 15143-20_2174

source_name: 15143-20_foliage from field-grown plants


title: 15143-91_2165

source_name: 15143-91_foliage from field-grown plants


title: 15143-70_2178

source_name: 15143-70_foliage from field-grown plants


title: 15143-47_2166

source_name: 15143-47_foliage from field-grown plants


title: 15143-09_2173

source_name: 15143-09_foliage from field-grown plants


title: 15143-26_2170

source_name: 15143-26_foliage from field-grown plants


title: 15143-97_2159

source_name: 15143-97_foliage from field-grown plants

value: CGG


title: 15143-04_2168

source_name: 15143-04_foliage from field-grown plants


title: 15143-31_2167

source_name: 15143-31_foliage from field-grown plants


title: 15143-57_2157

source_name: 15143-57_foliage from field-grown plants


title: 15143-40_2156

source_name: 15143-40_foliage from field-grown plants


title: 15143-18_2153

source_name: 15143-18_foliage from field-grown plants

value: CAA


title: 15143-44_2155

source_name: 15143-44_foliage from field-grown plants

value: 15143 diploid mapping population clone


title: 15143-96_2154

source_name: 15143-96_foliage from field-grown plants

value: foliage from field-grown plants


title: 15143-22_2169

source_name: 15143-22_foliage from field-grown plants


title: 15143-14_2172

source_name: 15143-14_foliage from field-grown plants


title: 15143-79_2152

source_name: 15143-79_foliage from field-grown plants


title: 15143-28_2175

source_name: 15143-28_foliage from field-grown plants


title: 15143-56_2161

source_name: 15143-56_foliage from field-grown plants


title: 15143-77_2151

source_name: 15143-77_foliage from field-grown plants


title: 15143-43_2164

source_name: 15143-43_foliage from field-grown plants


title: 15143-74_2160

source_name: 15143-74_foliage from field-grown plants


title: 15143-58_2163

source_name: 15143-58_foliage from field-grown plants


title: 15143-27_2162

source_name: 15143-27_foliage from field-grown plants


title: 15143-07_2150

source_name: 15143-07_foliage from field-grown plants


title: 15143-49_2158

source_name: 15143-49_foliage from field-grown plants


title: 15143-16_2149

source_name: 15143-16_foliage from field-grown plants


title: 15143-88_2147

source_name: 15143-88_foliage from field-grown plants

value: CTC


title: 15143-38_2146

source_name: 15143-38_foliage from field-grown plants


title: 15143-21_2138

source_name: 15143-21_foliage from field-grown plants


title: 15143-64_2140

source_name: 15143-64_foliage from field-grown plants


title: 15143-68_2137

source_name: 15143-68_foliage from field-grown plants


title: Russet Burbank_2143

source_name: Russet Burbank_foliage from field-grown plants

value: tetraploid variety

value: Russet Burbank


title: 15143-29_2141

source_name: 15143-29_foliage from field-grown plants


title: 15143-60_2139

source_name: 15143-60_foliage from field-grown plants


title: 15143-72_2144

source_name: 15143-72_foliage from field-grown plants


title: 15143-36_2131

source_name: 15143-36_foliage from field-grown plants


title: 15143-52_2129

source_name: 15143-52_foliage from field-grown plants

value: TAG


title: 15143-01_2134

source_name: 15143-01_foliage from field-grown plants

value: TGT


title: 15143-32_2132

source_name: 15143-32_foliage from field-grown plants

value: RunB


title: 15143-89_2133

source_name: 15143-89_foliage from field-grown plants


title: Green Mountain_2130

source_name: Green Mountain_foliage from field-grown plants

value: Green Mountain


title: 15143-06_2122

source_name: 15143-06_foliage from field-grown plants


title: 15143-33_2126

source_name: 15143-33_foliage from field-grown plants


title: 15143-51_2125

source_name: 15143-51_foliage from field-grown plants


title: 15143-19_2127

source_name: 15143-19_foliage from field-grown plants


title: 15143-98_2148

source_name: 15143-98_foliage from field-grown plants


title: 15143-73_2128

source_name: 15143-73_foliage from field-grown plants


title: 15143-87_2145

source_name: 15143-87_foliage from field-grown plants


title: 15143-54_2123

source_name: 15143-54_foliage from field-grown plants


title: 15143-90_2120

source_name: 15143-90_foliage from field-grown plants

value: TCC


title: 15143-85_2119

source_name: 15143-85_foliage from field-grown plants


title: 15143-65_2117

source_name: 15143-65_foliage from field-grown plants


title: 15143-71_2121

source_name: 15143-71_foliage from field-grown plants


title: 15143-67_2118

source_name: 15143-67_foliage from field-grown plants


title: Hindenburg_2135

source_name: Hindenburg_foliage from field-grown plants

value: Hindenburg


title: 15143-69_2115

source_name: 15143-69_foliage from field-grown plants


title: 15143-63_2114

source_name: 15143-63_foliage from field-grown plants


title: 15143-84_2116

source_name: 15143-84_foliage from field-grown plants


title: 15143-90_2087

value: RunA


title: 15143-34_2088

source_name: 15143-34_foliage from field-grown plants

value: AGC


title: 15143-08_2090

source_name: 15143-08_foliage from field-grown plants

value: GTT


title: 15143-54_2089


title: 07506-01_2094

source_name: 07506-01_foliage from field-grown plants

value: parental clone


title: 15143-95_2107

source_name: 15143-95_foliage from field-grown plants

value: TTA


title: 15143-15_2102

source_name: 15143-15_foliage from field-grown plants

value: AAT


title: 15143-98_2096

source_name: 15143-98_foliage from field-grown plants

value: 15143 diploid mapping population clone


title: 15143-55_2103

source_name: 15143-55_foliage from field-grown plants

value: foliage from field-grown plants


title: 12120-03_2095

source_name: 12120-03_foliage from field-grown plants


title: 15143-37_2113

source_name: 15143-37_foliage from field-grown plants


title: 15143-02_2111

source_name: 15143-02_foliage from field-grown plants


title: 15143-05_2106

source_name: 15143-05_foliage from field-grown plants


title: 15143-18_2099

source_name: 15143-18_foliage from field-grown plants


title: 15143-35_2108

source_name: 15143-35_foliage from field-grown plants


title: 15143-58_2100

source_name: 15143-58_foliage from field-grown plants


title: 15143-94_2109

source_name: 15143-94_foliage from field-grown plants


title: 15143-93_2112

source_name: 15143-93_foliage from field-grown plants


title: 15143-83_2104

source_name: 15143-83_foliage from field-grown plants


title: 15143-45_2105

source_name: 15143-45_foliage from field-grown plants


title: 15143-34_2101

source_name: 15143-34_foliage from field-grown plants


title: 15143-86_2092

source_name: 15143-86_foliage from field-grown plants


title: 15143-32_2093

source_name: 15143-32_foliage from field-grown plants


title: 15143-35_2091


title: Shepody_2110

source_name: Shepody_foliage from field-grown plants

value: Shepody


title: 15143-75_2084

source_name: 15143-75_foliage from field-grown plants


title: 15143-14_2085

source_name: 15143-14_foliage from field-grown plants


title: Russet Burbank_2083

source_name: Russet Burbank_foliage from field-grown plants

value: tetraploid variety


title: 15143-89_2086

source_name: 15143-89_foliage from field-grown plants


title: 15143-57_2082

source_name: 15143-57_foliage from field-grown plants


title: 15143-04_2081

source_name: 15143-04_foliage from field-grown plants

value: ACA


title: Atlantic-1_2078

source_name: Atlantic-1_foliage from field-grown plants


title: 15143-68_2080

source_name: 15143-68_foliage from field-grown plants


title: 15143-94_2073

value: ATG


title: 15143-16_2077

source_name: 15143-16_foliage from field-grown plants


title: 15143-22_2076

source_name: 15143-22_foliage from field-grown plants


title: 15143-74_2075

source_name: 15143-74_foliage from field-grown plants


title: 15143-51_2074

source_name: 15143-51_foliage from field-grown plants


title: 15143-65_2071

source_name: 15143-65_foliage from field-grown plants


title: Kennebec_2058

source_name: Kennebec_foliage from field-grown plants

value: Kennebec

value: CGG


title: 15143-27_2063

source_name: 15143-27_foliage from field-grown plants


title: 15143-44_2059

source_name: 15143-44_foliage from field-grown plants


title: 15143-36_2061

source_name: 15143-36_foliage from field-grown plants


title: Green Mountain_2067

source_name: Green Mountain_foliage from field-grown plants

value: Green Mountain


title: 15143-59_2066

source_name: 15143-59_foliage from field-grown plants


title: 15143-76_2072

source_name: 15143-76_foliage from field-grown plants


title: 15143-71_2057

source_name: 15143-71_foliage from field-grown plants

value: CAA


title: 15143-83_2056

source_name: 15143-83_foliage from field-grown plants


title: 15143-47_2060

source_name: 15143-47_foliage from field-grown plants


title: Green Mountain_2069


title: 15143-67_2064

source_name: 15143-67_foliage from field-grown plants


title: 15143-72_2055

source_name: 15143-72_foliage from field-grown plants


title: 15143-48_2054

source_name: 15143-48_foliage from field-grown plants


title: 15143-23_2053

source_name: 15143-23_foliage from field-grown plants


title: 15143-09_2079

source_name: 15143-09_foliage from field-grown plants


title: 15143-15_2070

source_name: 15143-15_foliage from field-grown plants


title: 15143-79_2062

source_name: 15143-79_foliage from field-grown plants


title: 15143-20_2065

source_name: 15143-20_foliage from field-grown plants


title: 15143-01_2052

source_name: 15143-01_foliage from field-grown plants


title: 15143-85_2051

source_name: 15143-85_foliage from field-grown plants


title: 15143-29_2050

source_name: 15143-29_foliage from field-grown plants


title: 15143-56_2049

source_name: 15143-56_foliage from field-grown plants

value: CTC


title: 15143-28_2047

source_name: 15143-28_foliage from field-grown plants

value: RunA


title: 15143-39_2044

source_name: 15143-39_foliage from field-grown plants


title: 15143-02_2041

source_name: 15143-02_foliage from field-grown plants

value: TGT


title: 15143-66_2048

source_name: 15143-66_foliage from field-grown plants


title: 15143-41_2046

source_name: 15143-41_foliage from field-grown plants


title: 15143-03_2034

source_name: 15143-03_foliage from field-grown plants


title: 15143-73_2043

source_name: 15143-73_foliage from field-grown plants


title: 15143-06_2035

source_name: 15143-06_foliage from field-grown plants


title: 15143-05_2042

source_name: 15143-05_foliage from field-grown plants


title: 15143-87_2036

source_name: 15143-87_foliage from field-grown plants


title: 15143-21_2031

source_name: 15143-21_foliage from field-grown plants

value: TAG


title: 15143-95_2040

source_name: 15143-95_foliage from field-grown plants


title: 15143-96_2045

source_name: 15143-96_foliage from field-grown plants


title: 15143-42_2038

source_name: 15143-42_foliage from field-grown plants


title: Hindenburg_2028

source_name: Hindenburg_foliage from field-grown plants

value: Hindenburg


title: 15143-43_2030

source_name: 15143-43_foliage from field-grown plants


title: 15143-61_2032

source_name: 15143-61_foliage from field-grown plants


title: 15143-17_2027

source_name: 15143-17_foliage from field-grown plants


title: 15143-26_2033

source_name: 15143-26_foliage from field-grown plants


title: 15143-40_2029

source_name: 15143-40_foliage from field-grown plants


title: 15143-55_2026

source_name: 15143-55_foliage from field-grown plants


title: 15143-63_2037

source_name: 15143-63_foliage from field-grown plants


title: 15143-24_2024

source_name: 15143-24_foliage from field-grown plants

value: TCC


title: 15143-33_2021

source_name: 15143-33_foliage from field-grown plants


title: 15143-38_2025

source_name: 15143-38_foliage from field-grown plants


title: 15143-80_2020

source_name: 15143-80_foliage from field-grown plants


title: 15143-92_2022

source_name: 15143-92_foliage from field-grown plants


title: 15143-69_2023

source_name: 15143-69_foliage from field-grown plants


title: Drp1-KO_T cells_rep3

city: Rome

first: Silvia

last: Campello

state: <None>

address: Via della Ricerca Scientifica

department: Department of Biology

country: Italy

institute: University of Rome, Tor Vergata

data_processing:
Libraries were quantified using the 4200 TapeStation (Agilent Technologies) and pooled such that each index-tagged sample was present in equimolar amounts, with final concentration of the pooled samples of 2nM. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq500 (Illumina) in a 1x75 single end (mRNA-seq) format
The raw sequence files generated (.fastq files) underwent quality control analysis using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then aligned to the mouse genome (mm10 assembly) using STAR v.2.5.2 [Dobin et al., 2012], with standard parameters
Raw counts were computed with HTSeq-count v.0.6.1[Anders et al., 2014] and differentially expressed mRNAs were identified using DESeq2 v.1.12[Love et al., 2014].  FPKM counts were computed using Cufflinks [Trapnell et al., 2010]
Genome_build: mm10
Supplementary_files_format_and_content: raw count

organism: Mus musculus

source_name: Drp1-KO_T cells

growth_protocol: T-cells were purified from Spleen

extract_protocol:
RNA was harvested using Promega ReliaPrep RNA Cell Miniprep System. Indexed libraries were prepared from 1 ug/ea purified RNA with TruSeq Stranded mRNA (Illumina) Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T-cells were activated in vitro using anti-CD3 and anti- CD28 antibodies, with IL-2

tag: strain background

tag: age

tag: genotype

value: Spleen

tag: cell type

value: T-cell


title: Drp1-KO_T cells_rep2


title: Wt_T cells_rep3

source_name: Wt_T cells

value: wild type


title: Wt_T cells_rep2


title: Shepody_2018

source_name: Shepody_foliage from field-grown plants

value: Shepody

value: foliage from field-grown plants


title: 15143-77_2016

source_name: 15143-77_foliage from field-grown plants

value: 15143 diploid mapping population clone

value: TTA


title: 15143-52_2012

source_name: 15143-52_foliage from field-grown plants


title: 15143-81_2014

source_name: 15143-81_foliage from field-grown plants


title: 15143-70_2015

source_name: 15143-70_foliage from field-grown plants


title: Wt_T cells_rep1


title: Drp1-KO_T cells_rep1


title: 15143-91_2013

source_name: 15143-91_foliage from field-grown plants


title: 15143-37_2011

source_name: 15143-37_foliage from field-grown plants


title: 15143-31_2010

source_name: 15143-31_foliage from field-grown plants


title: 15143-49_2009

source_name: 15143-49_foliage from field-grown plants


title: shSetdb1 rep#3 (ATAC-seq)

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the mouse (mm10) genome using bowtie2
Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Processed peak (BED) files and bigWig tracks

molecule: genomic DNA

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESCs were grown in serum+LIF medium: DMEM-HIGH GLUCOSE (SH30022.01, HyClone), 15% fetal bovine serum (S1580-500, Biowest), 1% L-Glutamine (35050-061, GIBCO), 1% sodium pyruvate (25-000-CIR, Corning), 1% non-essential amino acids (25-025-CI, Corning), 0.5% penicillin-streptomycin solution (SV30010, HyClone), 0.1 mM 2-mercaptoethanol (21985-023, GIBCO), 0.01% mLIF (ESG1107, Millipore).

extract_protocol:
ATAC-seq was performed as described (Buenrostro et al., 2015). In brief, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina). Samples were then PCR amplified and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen). ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described (Buenrostro et al., 2015), and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column and were quantified using a KAPA Library Quantification kit (KK4824, Kapa Biosystems) according to the manufacturer’s instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturer’s instructions.
According to the extract protocol

treatment_protocol: pLKO lentiviruses, generated with Plat-E cells, were added to ESCs and medium was changed after 8 hours. Cells were selected with 2 μg/ml puromycin for 2 days, and harvested after a further 2 days.

value: mouse embryonic stem cell

tag: cell line

tag: knockdown


title: shSetdb1 rep#1 (ATAC-seq)


title: shSetdb1 rep#2 (ATAC-seq)


title: shUhrf1 rep#2 (ATAC-seq)


title: shUhrf1 rep#1 (ATAC-seq)


title: shRrp8 rep#2 (ATAC-seq)


title: 15143-64_2017

source_name: 15143-64_foliage from field-grown plants


title: 15143-07_2007

source_name: 15143-07_foliage from field-grown plants

value: AAT


title: 15143-25_2008

source_name: 15143-25_foliage from field-grown plants


title: 15143-46_2019

source_name: 15143-46_foliage from field-grown plants


title: shRnf2 rep#2 (ATAC-seq)


title: shRrp8 rep#1 (ATAC-seq)


title: shPrmt5 rep#1 (ATAC-seq)


title: 15143-78_2001

source_name: 15143-78_foliage from field-grown plants


title: 15143-93_2004

source_name: 15143-93_foliage from field-grown plants


title: 15143-60_2002

source_name: 15143-60_foliage from field-grown plants


title: shPrmt5 rep#2 (ATAC-seq)


title: shNcor2 rep#2 (ATAC-seq)


title: 15143-45_2003

source_name: 15143-45_foliage from field-grown plants


title: 15143-50_2006

source_name: 15143-50_foliage from field-grown plants


title: shRnf2 rep#1 (ATAC-seq)


title: shNcor2 rep#1 (ATAC-seq)


title: Contol human single cell, replicate 39

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description:
Human_single39
GEO_rpkms_human.txt
GEO_counts_human.txt

data_processing:
Raw read counts were extracted using the GenomicAlignments package in R, with the function SummarizeOverlaps, mode set to "Union"
Genome_build: hg38
Supplementary_files_format_and_content: wo processed data files are added, providing raw counts and normalized abundance measurements (RPKM), respectively.

molecule: polyA RNA

organism: Homo sapiens

source_name: Stem cell-derived motor neuron culture

growth_protocol: Human induced pluriportent stem cells (iPS) were differentiated into motor neurons in an embryoid body protocol. After embryoid body formation combined with neural induction for 2 days, cells were patterned with retinoic acid and SAG (agonist for the Shh pathway) for 8 days. Embryoid bodies were then dissociated and the neurons were seeded in microfluidic devices. Neuronal maturation and axonal growth was stimulated by Notch-signaling inhibition with DAPT, and trophic factor support with GDNF and BDNF. A gradient of trophic factors was used to recruit axons to cross microgrooves. Cells were cultured in these devices for 14 days, after which they were lysed and RNA was collected for RNAseq.

extract_protocol:
Cell culture material was lysed in the presence of RNAse inhibitor and immediately frozen down. Library preparation occurred in the lysis buffer directly, without RNA-extraction.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.

tag: disease status

value: Control

tag: cell part

value: Single cell

tag: day after seeding

value: Day 14


title: shLuc rep#2 (ATAC-seq)

value: shLuc


title: Contol human single cell, replicate 38

description:
Human_single38
GEO_rpkms_human.txt
GEO_counts_human.txt


title: shRnf2 rep#3 (ATAC-seq)


title: shLuc rep#3 (ATAC-seq)


title: Contol human single cell, replicate 37

description:
Human_single37
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 36

description:
Human_single36
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 35

description:
Human_single35
GEO_rpkms_human.txt
GEO_counts_human.txt


title: shKat5 rep#1 (ATAC-seq)


title: shKat5 rep#2 (ATAC-seq)


title: shLuc rep#1 (ATAC-seq)


title: Contol human single cell, replicate 34

description:
Human_single34
GEO_rpkms_human.txt
GEO_counts_human.txt


title: 15143-19_2005

source_name: 15143-19_foliage from field-grown plants

value: RunA


title: shGFP (ATAC-seq)

value: shGFP


title: cold_20d_poly(A)+

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

description:
20Vrep0
processed data file: lncRNA_exp.xlsx.gz

data_processing:
RNAseq:The adapter or low quality reads were removed by Trimmomatic( Bolger, 2014) .Clean reads were aligned to the Arabidopsis reference genome (TAIR10) by using TopHat version 2.0.10(Trapnell,2009). Parameters were set for strand-specific mapping and up to 5 different alignments were allowed for a given read. The mapped reads which are associated with unique molecular identifiers were further removed PCR duplicates by STL (BIOO SCIENTIFIC) as according to the manufacturer's instructions.
sRNA-seq:After removing bacodes, adapters and low-quality reads, clean reads of size 18-30 nt or 30-60 nt were mapped to the Arabidopsis genome (TAIR10 version) with Bowtie (Langmead et al., Genome Biology, 2009, 10, R25) allowing no mismatches
Genome_build: TAIR10
Supplementary_files_format_and_content: For RNA-Seq processed dataset，our provided file is the expression matrix of our identified lncRNA. The abundance of lncRNAs are estimated FPKM. For sRNA-seq processed datasets, our provided files contain genome match small RNA sequences and their counts.,

organism: Arabidopsis thaliana

growth_protocol: For ABA and dehydration treatment, plants were grown in a standard chamber under long-day conditions (16 h of light/8 h of darkness, 22°C). For cold treatment, plants were grown in short-day conditions(8 h of light/16 h of darkness, 22°C).

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN).
Libraries for RNA-seq were generated using NEXTflex Directional RNA-Seq Kit (dUTP based)  according to the manufacturer's instructions.

treatment_protocol: For ABA treatment, 2-week-old seedlings were transferred to 1/2 MS liquid medium with 100 μM ABA for 0, 2, 4, 6, 8 hours. For dehydration treatment, 2-week-old seedlings were removed from the agar and desiccated in dishes for 0, 2, 4, 6, 8 hours. For cold treatment, 2-week-old seedlings (grown under SD conditions) were transferred to 4°C and cultured under SD conditions for 20 days.

tag: ecotype

value: Columbia

tag: genotype/variation

value: Wild type

tag: treatment

value: 2-week-old seedlings

tag: molecule subtype

value: poly(A)+ RNA


title: Contol human single cell, replicate 33

description:
Human_single33
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 32

description:
Human_single32
GEO_rpkms_human.txt
GEO_counts_human.txt


title: cold_0d_poly(A)+

description:
0Vrep0
processed data file: lncRNA_exp.xlsx.gz

tag: tissue


title: Contol human single cell, replicate 27

description:
Human_single27
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_8h_poly(A)-

description:
dry8hrep0NA
processed data file: lncRNA_exp.xlsx.gz

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (Ambion). Polyadenylated [poly(A)+] RNAs were isolated from total RNA through two rounds of purification with oligo(dT) beads (QIAGEN). The poly(A)+ RNA depleted fraction from the first round of purification was collected as crude non-polyadenylated [(poly(A)-] RNA sample, which was subjected to another two rounds of treatment with oligo(dT) beads. Ribosomal RNAs were removed by two rounds of treatment with the Ribo-minus kit (Invitrogen).
Libraries for RNA-seq were generated using NEXTflex Directional RNA-Seq Kit (dUTP based)  according to the manufacturer's instructions.

value: 8 hour post drought treatment

value: rRNA-depleted poly(A)- RNA


title: Contol human single cell, replicate 30

description:
Human_single30
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_6h_poly(A)+

description:
dry6hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: 6 hour post drought treatment


title: Contol human single cell, replicate 31

description:
Human_single31
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_8h_poly(A)+

description:
dry8hrep0PA
processed data file: lncRNA_exp.xlsx.gz


title: drought_6h_poly(A)-

description:
dry6hrep0NA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 29

description:
Human_single29
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 28

description:
Human_single28
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 26

description:
Human_single26
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_2h_poly(A)+

description:
dry2hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: 2 hour post drought treatment


title: drought_4h_poly(A)+

description:
dry4hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: 4 hour post drought treatment


title: Contol human single cell, replicate 23

description:
Human_single23
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_4h_poly(A)-

description:
dry4hrep0NA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 24

description:
Human_single24
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 22

description:
Human_single22
GEO_rpkms_human.txt
GEO_counts_human.txt


title: drought_0h_poly(A)+

description:
dry0hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: 0 hour post drought treatment


title: drought_0h_poly(A)-

description:
dry0hrep0NA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 20

description:
Human_single20
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 21

description:
Human_single21
GEO_rpkms_human.txt
GEO_counts_human.txt


title: ABA_8h_poly(A)+

description:
ABA8hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: 8 hour post ABA treatment


title: ABA_8h_poly(A)-

description:
ABA8hrep0NA
processed data file: lncRNA_exp.xlsx.gz


title: drought_2h_poly(A)-

description:
dry2hrep0NA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 19

description:
Human_single19
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Control


title: Contol human single cell, replicate 18

description:
Human_single18
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Single cell


title: ABA_6h_poly(A)-

description:
ABA6hrep0NA
processed data file: lncRNA_exp.xlsx.gz

value: 6 hour post ABA treatment


title: ABA_6h_poly(A)+

description:
ABA6hrep0PA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 25

description:
Human_single25
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Day 14


title: Contol human single cell, replicate 17

description:
Human_single17
GEO_rpkms_human.txt
GEO_counts_human.txt


title: ABA_4h_poly(A)-

description:
ABA4hrep0NA
processed data file: lncRNA_exp.xlsx.gz

value: 4 hour post ABA treatment


title: ABA_4h_poly(A)+

description:
ABA4hrep0PA
processed data file: lncRNA_exp.xlsx.gz


title: Contol human single cell, replicate 16

description:
Human_single16
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 15

description:
Human_single15
GEO_rpkms_human.txt
GEO_counts_human.txt


title: ABA_2h_poly(A)-

description:
ABA2hrep0NA
processed data file: lncRNA_exp.xlsx.gz

value: 2 hour post ABA treatment


title: Contol human single cell, replicate 13

description:
Human_single13
GEO_rpkms_human.txt
GEO_counts_human.txt


title: ABA_2h_poly(A)+

description:
ABA2hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: Columbia


title: Contol human single cell, replicate 12

description:
Human_single12
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 10

description:
Human_single10
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 11

description:
Human_single11
GEO_rpkms_human.txt
GEO_counts_human.txt


title: IL4 and IL6 treated macrophages_2

city: Frankfurt am Main

first: Dmitry

last: Namgaladze

state: Hessen

address: Theodor-Stern-Kai 7, Building 74

department: Faculty of Medicine

country: Germany

institute: Goethe University Frankfurt

data_processing:
Fastqc analysis with Qc score >93%
Quality trimming using trimmomatic from trinity using ILLUMINACLIP:/~Trimmomatic- 0.32/adapters/TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDING WINDOW :4:15.
Mapping to STAR aligner using --outFilterMultimapNmax 1 --   outSAMtype BAM SortedByCoordinate mapped to hg19 genome with >91% unique reads
Mapping results are summarized with feature counts using gencode.v19.annotations
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited excel sheet of normalized read counts

source_name: IL4 and IL6 treated macrophages

growth_protocol: differentiated in 3% human plasma in RPMI, P/S

extract_protocol:
4µg of total RNA extracted from Macherey-Nagel NucleoSpin RNA extraction kit   (#740955.250)
Libraries were prepared using TruSeq Stranded mRNA LT - SetB library preparation kit (Illumina #RS-122-2102). cDNA was  prepared for single end (SE) sequencing on NextSeq 500/550 High Output Kit v2 (75 cycles, Illumina # FC-404-2005).

treatment_protocol: Treated with individual cytokines on Day 7 for 24hrs

value: human monocyte-derived primary macrophages

tag: Stage

value: 7 days differentiation from monocytes

value: IL-4/IL-6 co-stimulation


title: ABA_0h_poly(A)-

description:
ABA0hrep0NA
processed data file: lncRNA_exp.xlsx.gz

value: Wild type

value: 0 hour post ABA treatment

value: 2-week-old seedlings


title: ABA_0h_poly(A)+

description:
ABA0hrep0PA
processed data file: lncRNA_exp.xlsx.gz

value: poly(A)+ RNA


title: Contol human single cell, replicate 9

description:
Human_single9
GEO_rpkms_human.txt
GEO_counts_human.txt


title: IL4 and IL6 treated macrophages_3


title: IL6 treated macrophages_2

source_name: IL6 treated macrophages


title: Contol human single cell, replicate 8

description:
Human_single8
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 6

description:
Human_single6
GEO_rpkms_human.txt
GEO_counts_human.txt


title: IL6 treated macrophages_1


title: Contol human single cell, replicate 7

description:
Human_single7
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 5

description:
Human_single5
GEO_rpkms_human.txt
GEO_counts_human.txt


title: IL6 treated macrophages_3


title: IL4 treated macrophages_3

source_name: IL4 treated macrophages


title: Contol human single cell, replicate 14

description:
Human_single14
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 4

description:
Human_single4
GEO_rpkms_human.txt
GEO_counts_human.txt


title: IL4 treated macrophages_2


title: IL4 treated macrophages_1


title: Contol human single cell, replicate 3

description:
Human_single3
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Contol human single cell, replicate 2

description:
Human_single2
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Untreated macrophages_repl 3

source_name: Untreated macrophages

value: untreated control


title: Contol human single cell, replicate 1

description:
Human_single1
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Control human soma, replicate 6

description:
Ctrl_soma6
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Soma (bulk culture)


title: Control human axons, replicate 6

description:
Ctrl_axon6
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Axon (isolated from bulk)


title: SOD1G93A mutant mouse single cell, replicate 22

description:
G93A_single22
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

data_processing:
Raw read counts were extracted using the GenomicAlignments package in R, with the function SummarizeOverlaps, mode set to "Union"
Differential gene expression analysis was performed on the read counts using DESeq2 version 1.12.4. Only genes with reads in 4 samples or more were considered in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Two processed data files are added, providing raw counts and normalized abundance measurements (RPKM), respectively.

growth_protocol: Mouse embryonic stem cells (mES) were differentiated into motor neurons in an embryoid body protocol. After embryoid body formation for 2 days, cells were patterned with retinoic acid and SAG (agonist for the Shh pathway) for 4 days. Embryoid bodies were then dissociated and the neurons were seeded in microfluidic devices. Neuronal maturation and axonal growth was stimulated with trophic factors GDNF, BDNF, NT3 and CNTF, and a gradient of trophic factors was used to recruit axons to cross microgrooves. Cells were cultured in these devices for 7 days, after which they were lysed and RNA was collected for RNAseq.

value: Amyotrophic lateral sclerosis

value: Day 0


title: IL4 and IL6 treated macrophages_1


title: SOD1G93A mutant mouse single cell, replicate 20

description:
G93A_single20
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Single cell


title: Control human soma, replicate 5

description:
Ctrl_soma5
GEO_rpkms_human.txt
GEO_counts_human.txt

value: Control

value: Day 14


title: SOD1G93A mutant mouse single cell, replicate 19

description:
G93A_single19
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control human soma, replicate 4

description:
Ctrl_soma4
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Control human soma, replicate 3

description:
Ctrl_soma3
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Control human soma, replicate 2

description:
Ctrl_soma2
GEO_rpkms_human.txt
GEO_counts_human.txt


title: SOD1G93A mutant mouse single cell, replicate 16

description:
G93A_single16
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control human soma, replicate 1

description:
Ctrl_soma1
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Control human axons, replicate 4

description:
Ctrl_axon4
GEO_rpkms_human.txt
GEO_counts_human.txt


title: SOD1G93A mutant mouse single cell, replicate 14

description:
G93A_single14
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Untreated macrophages_repl 2


title: Control human axons, replicate 3

description:
Ctrl_axon3
GEO_rpkms_human.txt
GEO_counts_human.txt


title: SOD1G93A mutant mouse single cell, replicate 15

description:
G93A_single15
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 12

description:
G93A_single12
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 13

description:
G93A_single13
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control human axons, replicate 1

description:
Ctrl_axon1
GEO_rpkms_human.txt
GEO_counts_human.txt


title: SOD1G93A mutant mouse single cell, replicate 11

description:
G93A_single11
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control human axons, replicate 5

description:
Ctrl_axon5
GEO_rpkms_human.txt
GEO_counts_human.txt


title: Control human soma, replicate 7

description:
Ctrl_soma7
GEO_rpkms_human.txt
GEO_counts_human.txt


title: SOD1G93A mutant mouse single cell, replicate 10

description:
G93A_single10
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: BWF--006_Human

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Quality control and subsequent trimming of the raw data was carried out using FastQC (Version 0.11.5) and Trim Galore! (Version 0.4.0)
Alignment was performed with STAR aligner (Version 2.5.1)
Transcript quantification was performed using RSEM (Version 1.2.26)
Rae counttable was further analyzed with DESeq2
Genome_build: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary_files_format_and_content: NASH_data_rlog_normalised_counttable.txt =normalised counttable

source_name: patient liver

extract_protocol:
RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel) according to manufacturer instructions including rDNAse digestion step
Library prep was performed using Illumina TruSeq Stranded mRNA Sample Preparation Kit

treatment_protocol: liver biopsy

tag: gender

value: M

tag: bmi

tag: group

value: NASH


title: SOD1G93A mutant mouse single cell, replicate 18

description:
G93A_single18
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: BWF--007_Human

tag: age


title: SOD1G93A mutant mouse single cell, replicate 7

description:
G93A_single7
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: BWF--008_Human


title: BWF--004_Human

value: NAFLD


title: SOD1G93A mutant mouse single cell, replicate 21

description:
G93A_single21
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 17

description:
G93A_single17
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 6

description:
G93A_single6
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 8

description:
G93A_single8
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse single cell, replicate 5

description:
G93A_single5
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Untreated macrophages_repl 1

value: human monocyte-derived primary macrophages

value: 7 days differentiation from monocytes


title: SOD1G93A mutant mouse single cell, replicate 9

description:
G93A_single9
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control human axons, replicate 2

description:
Ctrl_axon2
GEO_rpkms_human.txt
GEO_counts_human.txt


title: BWF--003_Human


title: SOD1G93A mutant mouse single cell, replicate 4

description:
G93A_single4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: BWF--002_Human

value: heathy


title: BWF--001_Human


title: SOD1G93A mutant mouse single cell, replicate 3

description:
G93A_single3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: BWF--000_Human


title: shZmynd11.rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (version 2.2.5) and RSEM.
The gene expression level was calculated by using  EDASeq GC-normalize method
Genome_build: mm10
Supplementary_files_format_and_content: csv files with GC-normalised read counts from RSEM

source_name: mouse embryonic stem cell

extract_protocol: VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

value: mouse embryonic stem cell


title: SOD1G93A mutant mouse single cell, replicate 2

description:
G93A_single2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shZmynd11.rep1


title: SOD1G93A mutant mouse single cell, replicate 1

description:
G93A_single1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shUhrf1.rep1


title: BWF--005_Human


title: shSirt2.rep1


title: shSmyd3.rep1


title: shSirt2.rep2


title: Control mouse single cell, replicate 12

description:
Ctrl_single12
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse single cell, replicate 11

description:
Ctrl_single11
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shSetdb1.rep2


title: H1299_WT_neg_d4_rep3

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

country: France

institute: Institut Imagine

data_processing:
Mapping with hisat2 2.0.4 (–dta)
Sort with samtools 1.4 sort
Deduplication with Picard 1.9.2 MarkDuplicates (AS=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true)
Sort with samtools 1.4 sort (-n)
Assign to features using featureCounts 1.5.0 (-p -F GTF)
Genome_build: Human v37 (hg19)
Supplementary_files_format_and_content: Tab-delimited table of raw read counts for Ensembl genes and for each sample (P180240_final_gene_count_table.txt)
Supplementary_files_format_and_content: Tab-delimited table with the layout for processing (P180240_layout.txt)

source_name: Human non-small cell lung carcinoma

growth_protocol: Human non-small cell lung carcinoma H1299 cells and human invasive ductal breast cancer MDA-MB-231 cells, wild type (American Type Culture Collection) or carrying a doxycycline (DOX)-inducible BRCA2 shRNA4, were cultivated in monolayers in DMEM medium (Sigma) supplemented with 10% tetracycline free foetal bovine serum (Clontech).

extract_protocol:
Cells were collected for RNA extraction and processed using the RNeasy® Mini Kit (Qiagen, #74104) according to the manufacturer’s guidelines. RNA samples were quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 2200 or 4200 TapeStation (Agilent, RNA ScreenTape).
Poly(A) transcript enrichment and strand specific library preparation were performed using TruSeq Stranded mRNA kit (Illumina) following manufacturer’s instructions. Libraries were amplified (15 cycles) on a Tetrad (Bio-Rad) using in-house unique dual indexing primers27. Individual libraries were normalised using Qubit and size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were pooled together and pooled libraries were diluted to ~10 nM for storage. Each library aliquot was denatured and further diluted prior to loading on the sequencer.

treatment_protocol: For induction of shBRCA2, 2 µg/ml DOX (D9891, Sigma) was added to growth medium.

tag: genotype

value: WT

tag: time point

value: 4 days


title: shRrp8.rep2

tag: cell type

tag: cell line


title: Control mouse single cell, replicate 9

description:
Ctrl_single9
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

tag: disease status


title: H1299_WT_neg_d28_rep3

value: 28 days


title: shRnf2.rep2

tag: knockdown


title: H1299_shBRCA2_neg_d28_rep2


title: H1299_shBRCA2_neg_d4_rep2


title: shRnf8.rep1


title: Control mouse single cell, replicate 8

description:
Ctrl_single8
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

tag: cell part

tag: day after seeding


title: H1299_shBRCA2_neg_d28_rep3


title: shUhrf1.rep2


title: shRnf2.rep1


title: shPrmt5.rep2


title: H1299_WT_neg_d28_rep2


title: H1299_WT_neg_d4_rep2


title: 15143-67_2284

source_name: 15143-67_foliage from field-grown plants

tag: genotype/variety

value: 15143 diploid mapping population clone

tag: clone id

value: foliage from field-grown plants

tag: run

value: RunC

tag: adapter b barcode

value: GTT

tag: channel


title: shPrmt5.rep1


title: Control mouse single cell, replicate 7

description:
Ctrl_single7
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Single cell

value: Day 0


title: Control mouse single cell, replicate 6

description:
Ctrl_single6
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Control


title: H1299_shBRCA2_neg_d4_rep3

tag: treatment


title: shPrdm4.rep1


title: Control mouse single cell, replicate 5

description:
Ctrl_single5
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: H1299_shBRCA2_neg_d28_rep1


title: shSetdb1.rep1


title: shPhf19.rep1


title: H1299_shBRCA2_neg_d4_rep1


title: shRrp8.rep1


title: shRnf8.rep2


title: Control mouse single cell, replicate 10

description:
Ctrl_single10
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shNcor2.rep3


title: shNcor2.rep2


title: shNcor2.rep1


title: shNcor1.rep1


title: Control mouse single cell, replicate 3

description:
Ctrl_single3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shMtf2.rep1


title: shMtf2.rep2


title: Control mouse single cell, replicate 2

description:
Ctrl_single2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: H1299_WT_neg_d4_rep1


title: shMcrs1.rep2


title: Control mouse single cell, replicate 1

description:
Ctrl_single1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shMcrs1.rep1


title: shLuc.rep2

value: shLuc


title: H1299_shBRCA2_pos_d4_rep3

value: +DOX


title: shLuc.rep3


title: Control mouse somas, replicate 3

description:
Ctrl_soma3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Soma (bulk culture)

value: Day 7


title: shPhf19.rep2


title: H1299_WT_pos_d28_rep3


title: shLrwd1.rep2


title: H1299_WT_pos_d4_rep3


title: shKmt2b.rep1


title: shLrwd1.rep1


title: shKdm3b.rep1


title: Control mouse single cell, replicate 4

description:
Ctrl_single4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: H1299_WT_neg_d28_rep1


title: H1299_shBRCA2_pos_d28_rep2


title: Control mouse axons, replicate 3

description:
Ctrl_axon3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

source_name: Stem cell-derived motor neuron axons

value: Axon (isolated from bulk)


title: Control mouse somas, replicate 2

description:
Ctrl_soma2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shKdm2a.rep2


title: Control mouse axons, replicate 2

description:
Ctrl_axon2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: H1299_shBRCA2_pos_d4_rep2


title: shKdm2a.rep1


title: Control mouse axons, replicate 1

description:
Ctrl_axon1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shKdm1a.rep1


title: H1299_WT_pos_d28_rep2


title: shKdm1a.rep2


title: H1299_WT_pos_d4_rep2


title: shKat5.rep2


title: shLuc.rep1


title: shKat5.rep1


title: SOD1G93A mutant mouse cell somas, replicate 6

description:
G93A_soma6
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Amyotrophic lateral sclerosis


title: H1299_shBRCA2_pos_d28_rep1


title: SOD1G93A mutant mouse cell somas, replicate 5

description:
G93A_soma5
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shHdac6.rep1

value: mouse embryonic stem cell


title: shHdac7.rep1


title: H1299_shBRCA2_pos_d4_rep1


title: shHdac6.rep2


title: SOD1G93A mutant mouse cell somas, replicate 3

description:
G93A_soma3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse cell somas, replicate 4

description:
G93A_soma4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shIng5.rep1


title: shHdac3.rep2


title: shHdac5.rep1


title: shHdac3.rep1


title: H1299_WT_pos_d28_rep1

value: WT


title: H1299_WT_pos_d4_rep1

value: 4 days


title: shHdac2.rep2


title: SOD1G93A mutant mouse cell somas, replicate 2

description:
G93A_soma2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: SOD1G93A mutant mouse axons, replicate 4

description:
G93A_axon4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: MDA_shBRCA2_neg_d28_rep3

source_name: Invasive ductal breast cancer

value: 28 days


title: SOD1G93A mutant mouse axons, replicate 3

description:
G93A_axon3
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shHdac1.rep2


title: MDA_shBRCA2_neg_d4_rep3


title: SOD1G93A mutant mouse axons, replicate 2

description:
G93A_axon2
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: shHdac1.rep1


title: MDA_WT_neg_d28_rep3


title: shEhmt1.rep2


title: shEhmt1.rep1


title: shHdac5.rep2


title: shDzip3.rep1


title: MDA_WT_neg_d4_rep3


title: Isolated brain microvascular fragments (heterozygous Ins2-AKITA mutant 1)

city: Uppsala

first: L.

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

data_processing:
The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4).
The duplicated reads were removed using the picard tool (version 1.92).
FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample

source_name: brain

extract_protocol:
Microvascular fragments were isolated from male heterozygous Ins2-AKITA mice and littermate wild-type controls. RNA integrity and concentration of the isolated microvasculature was checked with the Agilent RNA 6000 pico kit and the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).
For conversion of the RNA to a cDNA library for Illumina sequencing, the SMARTer® Stranded Total RNA Sample Prep Kit - Low Input Mammalian kit from Clontech was used according to the manufacturer’s protocol. The total RNA was depleted from rRNA and tRNA’s with the RiboGone- Mammalian kit (Clontech) prior to library construction.

tag: background strain

value: heterozygous Ins2-AKITA

tag: tissue

value: brain

tag: tissue compartment

value: microvasculature

value: between 26 to 38 weeks of age

tag: Sex

value: male


title: Isolated brain microvascular fragments (wildtype control 3)

description: Isolated brain microvascular fragments (control 3)

tag: genotype

value: wildtype

tag: age


title: MDA_shBRCA2_neg_d28_rep2

tag: cell line

tag: time point


title: shChd4.rep2

tag: cell type

tag: knockdown


title: shChd5.rep1


title: shChd4.rep1


title: shCbx5.rep2


title: MDA_shBRCA2_neg_d4_rep2


title: shCbx6.rep1


title: Isolated brain microvascular fragments (heterozygous Ins2-AKITA mutant 2)


title: shHdac2.rep1


title: Isolated brain microvascular fragments (wildtype control 1)

description: Isolated brain microvascular fragments (control 1)


title: shCbx5.rep1


title: Isolated brain microvascular fragments (wildtype control 2)

description: Isolated brain microvascular fragments (control 2)


title: shBrd7.rep1


title: shBaz2a.rep2


title: shEzh1.rep1


title: shBaz2a.rep1


title: shBap1.rep1


title: MDA_WT_neg_d4_rep2


title: shBahd1.rep2


title: MDA_shBRCA2_neg_d28_rep1


title: MDA_shBRCA2_neg_d4_rep1


title: MDA_WT_neg_d28_rep1


title: shBahd1.rep1


title: MDA_WT_neg_d28_rep2


title: MDA_shBRCA2_pos_d28_rep3


title: shCbx2.rep1


title: shAsh2l.rep1


title: shAsh2l.rep2


title: MDA_shBRCA2_pos_d4_rep3


title: MDA_WT_neg_d4_rep1


title: MDA_WT_pos_d4_rep3


title: MDA_shBRCA2_pos_d28_rep2


title: MDA_shBRCA2_pos_d4_rep2


title: MDA_WT_pos_d28_rep2


title: MDA_WT_pos_d28_rep3


title: MDA_WT_pos_d4_rep2


title: H1299_shBRCA2_pos_d28_rep3


title: MDA_shBRCA2_pos_d28_rep1


title: MDA_shBRCA2_pos_d4_rep1


title: MCF7_Alarid_Input

city: Madison

first: Elaine

middle: T

last: Alarid

state: WI

address: 1111 Highland Ave

department: McArdle Laboratory for Cancer Research

country: USA

institute: University of Wisconsin - Madison

data_processing:
All ChIP-seq runs were 50 bp. Barcodes were decoded by Illumina HiSeq2000 software automatically.  All samples were mapped from fastq files using BOWTIE [-m 1 -- best] to hg19 [UCSC human genome build 19].  Replicate lanes were analyzed separately for reproducibility and normalization of the peak calls.
Peaks were called by using HOMER [http://biowhat.ucsd.edu/homer/] and MACS.
HOMER analysis was run using the default settings for peak finding.
False Discovery Rate (FDR) cut off was 0.001 (0.1%) for all peaks.
Genome_build: hg19
Supplementary_files_format_and_content: *.bed files contain the ChIP-seq peak locations, *.bedgraph files are for display in the UCSC genome browser

growth_protocol: MCF-7 cells were maintained in high-glucose (4.5 g/L) Dulbecco’s modified Eagles Medium (DMEM; Mediatech, Manassas, VA) containing 10% fetal bovine serum (FBS), 100 U/mL penicillin and 100 µg/mL streptomycin incubated at 10% CO2 and 37°C. Prior to estrogen treatments, cells were grown at 37°C and 5% CO2 for three days in stripping media consisting of phenol-red free DMEM supplemented with 10% charcoal-stripped FBS, 100 U/mL penicillin, 100 µg/mL streptomycin, 4 mM L-glutamine, and 1 mM sodium pyruvate.

extract_protocol:
Post-treatment and fixation, nuclei were isolated from MCF-7 cells and sonicated to shear DNA. Protein-DNA complexes were then immunoprecipitated with antibodies specific to either pan-ER or pS118-ER followed by purification of DNA.
ChIP-seq libraries were prepared using the NEBNext DNA sample prep kit (NEB, #E6000L) with the Bioo NEXTflex ChIP-seq Barcodes (Bioo Scientific, Austin, TX, #514122) according to manufacturer’s protocols, with few exceptions.  During the NEBNext prep, the Illumina adapters were replaced with the Bioo Scientific Barcoded adapters according to Bioo protocols.  ChIP-DNA ligated libraries were cleaned up with Agencourt AMPureXP Magnetic Beads (Beckman-Coulter, #A63881).  A pre-size selection PCR was performed using Phusion polymerase, NEXTflex Primer Mix and purified ligation product for 4 cycles of PCR according to the Bioo Protocol.  Libraries were size selected using Invitrogen E-gels to a size of 400-500bp.  Samples were then PCR amplified for 14 cycles using Phusion polymerase, NEXTflex Primer mix and the size selected DNA as per Bioo protocol, followed by Agencourt bead clean up.  Libraries were validated for integrity using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).  Clusters were formed and sequenced on the Illumina HiSeq2000 sequencers by the University of Wisconsin-Madison DNA Sequencing Facility in the University of Wisconsin-Madison Biotechnology Center.  DNA clusters were generated using a cBot Single Read Cluster Generation kit (ver.  3) on an Illumina cBot (Illumina, Carlsbad, CA) according to the manufacturer's instructions, to obtain an average of 1.5×108 clusters for each lane on a flowcell.  All sequencing runs for 50mers were performed on an Illumina HiSeq2000 using the Illumina Sequencing kit (ver.  3). Fluorescent images were analyzed using the CASAVA 1.8.2 (Illumina Carlsbad, CA) to obtain FASTQ formatted sequence data.  Twelve barcoded libraries were run per lane and this was repeated over 4 lanes.  After which, the raw FASTQ for each sample was concatenated from the 4 lanes prior to mapping to create a single sample.  The ChIP samples were repeated in biological replicate in the same manner (3 replicates). Sequences were mapped to the human genome (hg19) using BOWTIE (--best –m 1) to yield unique alignments.

treatment_protocol: MCF-7 cells were stripped as described in growth protocol and then treated with either vehicle (0.01% EtOH) or 10 nM 17ß-estradiol for 30 min prior to ChIP assay

value: vehicle

tag: chip antibody


title: MCF7_Alarid_ER_Veh_rep3

value: ER (Santa Cruz, sc-543, lot F0316)


title: MCF7_Alarid_ER_Veh_rep1


title: MCF7_Alarid_ER_Veh_rep2


title: MDA_WT_pos_d28_rep1

value: +DOX


title: MCF7_Alarid_ER_E2_rep3


title: MDA_WT_pos_d4_rep1


title: rna_wt_b

city: Berkeley

first: Celeste

last: Riepe

state: California

address: 1 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Tophat v2.1.1 using GRCh38
Custom fp-count script using Gencode v25 basic annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count

source_name: HEK293 cells

growth_protocol: Cells cultured in DMEM, 10% FBS at 37'C and 5% CO2

extract_protocol:
Detergent lysis with Triton-X followed by centrifugation to remove cell debris
Denaturing RNA extraction, TruSeq stranded RNA-Seq library generation with Ribo-Zero Gold (Illumina)

value: HEK 293

tag: fraction

value: whole cell lysate


title: MCF7_Alarid_ER_E2_rep2


title: rna_wt_a


title: MCF7_Alarid_ER_E2_rep1


title: genomic DNA from paraganglioma 16

type: genomic

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

description: Paraganglioma/pheochromocytoma sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011

label: Cy5 and Cy3

source_name: Pheochromocytoma/paraganglioma 16

label_protocol: Standard Illumina Protocol

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

tag: gender

value: female

tag: sample type

value: autonomic lineage cell tumor


title: genomic DNA from paraganglioma carrying c.952C>T_DNMT3A mutation

description: Paraganglioma/pheochromocytoma sample carrying c.952C>T_DNMT3A mutation

source_name: Pheochromocytoma/paraganglioma 14


title: genomic DNA from paraganglioma 13

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 13


title: genomic DNA from paraganglioma 18

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 18


title: genomic DNA from paraganglioma 9

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 9


title: genomic DNA from paraganglioma 1

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 1


title: MCF7_Alarid_3pER_Veh_rep3

value: pS118-ER (Santa Cruz, sc-12915, lot A1614)


title: genomic DNA from paraganglioma 11

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 11


title: genomic DNA from paraganglioma 15

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 15


title: rna_ufsp2_b

source_name: UFSP2-KO HEK293 cells

treatment_protocol: Cas9 knockout with sgUFSP2

value: Clonal UFSP2-KO HEK293 cells generated with Cas9


title: rna_ufsp2_a


title: genomic DNA from paraganglioma carrying c.896A>T_DNMT3A mutation 2

description: Paraganglioma/pheochromocytoma sample carrying c.896A>T_DNMT3A mutation

source_name: Pheochromocytoma/paraganglioma 20


title: genomic DNA from HeLa cells 1

description: genomic DNA from HeLa cells 1

source_name: HeLa cells 1

value: Cell line


title: genomic DNA from paraganglioma 8

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 8


title: genomic DNA from paraganglioma carrying c.896A>T_DNMT3A mutation 1

source_name: Pheochromocytoma/paraganglioma 19

value: Tumor


title: genomic DNA from paraganglioma 17

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 17


title: genomic DNA from HeLa cells KI_DNMT3A_c.896A>T_1

source_name: HeLa cells 3


title: genomic DNA from paraganglioma 3

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 3


title: genomic DNA from HeLa cells KI_DNMT3A_c.896A>T_3

source_name: HeLa cells 5


title: genomic DNA from paraganglioma carrying c.896A>T_DNMT3A mutation 3

source_name: Pheochromocytoma/paraganglioma 21


title: genomic DNA from paraganglioma 2

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 2


title: MCF7_Alarid_3pER_Veh_rep1


title: Patient 5 Normal

type: RNA

city: Changsha

first: Zan

last: Liu

state: Hunan

address: Xiangya Road No. 81

institute: Xiangya Hospital, Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Patient 5 Normal

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: normal skin samples

value: Female

value: 49 years


title: genomic DNA from paraganglioma 12

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 12


title: genomic DNA from paraganglioma 10

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 10


title: Patient 5 Ca

source_name: Patient 5 Ca

value: Marjolin’s Ulcer samples


title: Patient 4 Ca

source_name: Patient 4 Ca

value: Male

value: 62 years


title: genomic DNA from paraganglioma 4

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 4

value: male


title: genomic DNA from HeLa cells KI_DNMT3A_c.896A>T_2

source_name: HeLa cells 4


title: genomic DNA from lymphocytes carrying c.952C>T_DNMT3A mutation

source_name: Lymphocites 5

value: Lymphocites


title: rna_ufm1_b

source_name: UFM1-KO HEK293 cells

treatment_protocol: Cas9 knockout with sgUFM1

value: Clonal UFM1-KO HEK293 cells generated with Cas9


title: Patient 5 Scar

source_name: Patient 5 Scar

value: para-cancerous scar samples


title: genomic DNA from HeLa cells 2

description: genomic DNA from HeLa cells 2

source_name: HeLa cells 2


title: MCF7_Alarid_3pER_E2_rep3


title: Patient 4 Scar

source_name: Patient 4 Scar


title: rna_ufm1_a

value: whole cell lysate


title: genomic DNA from paraganglioma 6

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 6

value: female


title: wt_cyto_a

data_processing:
Adapter trimming with fastx_clipper v0.0.14 -Q33 -a AGATCGGAAGAGCACACGTCTGAA -n -v
Tophat v2.1.1 using GRCh38, removing reads aligning to rRNA and tRNA
Custom fp-count script using Gencode v22 APPRIS principal splice isoforms
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count

source_name: Cytosolic fraction from HEK293 cells

extract_protocol:
Detergent lysis with digitonin, centrifugation to remove cell debris and organelles
RNase I footprinting, ultracentrifugation, denaturing RNA extraction, dephosphorylation, preadenylated inker ligation, reverse transcription, cDNA circularization, PCR amplification

value: HEK 293

value: cytosolic


title: genomic DNA from lymphocytes control 2

description: genomic DNA from lymphocytes control 2

source_name: Lymphocites 4


title: wt_cyto_b


title: MCF7_Alarid_3pER_E2_rep2

value: pS118-ER (Santa Cruz, sc-12915, lot A1614)


title: MCF7_Alarid_3pER_E2_rep1


title: wt_memb_b

source_name: Membrane fraction from HEK293 cells

extract_protocol:
Triton-X lysis of leftover pellet from cytosolic fractionation followed by centrifugation to remove cell debris
RNase I footprinting, ultracentrifugation, denaturing RNA extraction, dephosphorylation, preadenylated inker ligation, reverse transcription, cDNA circularization, PCR amplification

value: membrane


title: MCF7_Alarid_2pER_Veh_rep3

value: vehicle


title: Patient 4 Normal

source_name: Patient 4 Normal

value: normal skin samples


title: wt_memb_a


title: 729-AF-8

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

institute: Vanderbilt University

data_processing:
Alignment performed using STAR v2.5.3a
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene
FPKM values were calculated by normalizing the read counts by the total mapped reads and the transcript length
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for the Sample

source_name: iPS cells

extract_protocol:
Qiagen Rneasy Mini Kit
TruSeq mRNA

value: Cardiomyocytes cells


title: genomic DNA from paraganglioma 5

description: Paraganglioma/pheochromocytoma sample

source_name: Pheochromocytoma/paraganglioma 5

value: autonomic lineage cell tumor


title: Patient 3 Ca

source_name: Patient 3 Ca

value: Marjolin’s Ulcer samples

value: 42 years


title: MCF7_Alarid_2pER_Veh_rep2


title: Valproate.rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (version 2.2.5) and RSEM 。
The gene expression level was calculated by using  EDASeq GC-normalize method
Genome_build: mm10
Supplementary_files_format_and_content: csv file with GC-normalised read counts from RSEM

source_name: mouse embryonic stem cell

value: mouse embryonic stem cell

value: Valproate


title: genomic DNA from lymphocytes control 1

description: genomic DNA from lymphocytes control 1

source_name: Lymphocites 3

value: male

value: Lymphocites


title: Patient 3 Scar

source_name: Patient 3 Scar

value: para-cancerous scar samples

value: Male


title: Patient 3 Normal

source_name: Patient 3 Normal


title: UNC0379.rep2


title: Valproate.rep1


title: ufsp2_cyto_a

source_name: Cytosolic fraction from UFSP2-KO HEK293 cells

value: Clonal UFSP2-KO HEK293 cells generated with Cas9


title: MCF7_Alarid_2pER_Veh_rep1


title: MCF7_Alarid_2pER_E2_rep3


title: MCF7_Alarid_2pER_E2_rep2


title: rrbs_esc

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
fastq files were aligned by BS-Seeker2 and bowtie to generate bam file
methylation were called on the bam files by BS-Seeker2
Genome_build: mm9
Supplementary_files_format_and_content: Cgmap

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic fibroblasts that were induced to ectopically express the Yamanaka reprogramming factors OCT4 (O), SOX2 (S), KLF4 (K), and MYC (M; also known as ‘cMYC’)(25) for 48 hours, representing an early somatic cell reprogramming intermediate (EARLY).

extract_protocol: 5 μl of genomic DNA was digested with 50 units of MspI (NEB) in a 100 μl reaction for 6 hours at 37oC. Digested DNA was run on a 3% low-melt agarose gel (Lonza) and fragments of 25 to 300 bp were extracted and purified using a MinElute gel extraction kit (QIAGEN) according to the manufacturers instructions. DNA end-repair and adenylation was as described above with the exception of using a dNTP mix consistent of dATP, dGTP and 5medCTP. Ligation to methylated adapters and subsequent library construction was performed similarly to the WGBS protocol. Single-end sequencing for 100bp reads was performed on an Illumina Hiseq 2000.

value: mouse embryonic stem cells

tag: method

value: RRBS


title: OICR.rep2

value: OICR


title: ufsp2_memb_a

source_name: Membrane fraction from UFSP2-KO HEK293 cells

value: membrane


title: UNC0379.rep1


title: rrbs_early

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: ufsp2_cyto_b

value: cytosolic


title: ufm1_cyto_b

source_name: Cytosolic fraction from UFM1-KO HEK293 cells

value: Clonal UFM1-KO HEK293 cells generated with Cas9


title: ufsp2_memb_b


title: wgbs_esc

extract_protocol: Genomic DNA from induced MEFs (48h OSKM) and ESCs was isolated using the Blood and tissue DNeasy kit (Qiagen). Isolated DNA was treated with RNAseA for 30 min at 37oC and cleaned up using AMPure XP beads. 5 μg of treated DNA was fragmented to 100–500 bp using a Bioruptor Sonicator. 5 minutes in pulses of 30 sec on, 1 minute off. DNA fragments were visualized on 1% agarose gel, gel extracted and purified using a QIAGEN gel extraction minelute kit. End-repair reactions (50 μl) contained 1x T4 DNA ligase buffer (NEB), ATP, 0.4 mM dNTPs, 15 units T4 DNA polymerase, 5 units Klenow DNA polymerase, 50 units T4 polynucleotide kinase (all NEB) and were incubated for 30 min at 20°C. DNA clean-up was performed using a 2x volume of AMPure XP beads and eluted in 32 μl of dH2O. Adenylation was performed for 30 minutes at 37°C in 50 μl volumes that contained 5 μl 1x Klenow buffer, 0.2 mM dATP and 15 units Klenow exo− (NEB). Adenylated DNA fragments and methylated adapters (Illumina) were ligated for 15 min at 20oC in a 50 μl reaction containing 5,000 units quick ligase (NEB) and 5 μl of adapters. Adaptor-ligated DNA of 200-600 bp, was size-selected on a 2% agarose gel. Bisulfite conversion was performed with an EpiTect Bisulfite Kit (QIAGEN) following the manufactures conditions. Bisulfite converted DNA was amplified for 15 cycles with PfuTurboCx Hotstart DNA polymerase (Agilent technologies). The final library DNA was quantified using a Qubit fluorometer and a Quant-iT dsDNA HS Kit (Invitrogen).  Single-end sequencing for 100bp reads was performed on an Illumina Hiseq 2000.

value: WGBS


title: ufm1_cyto_a


title: genomic DNA from lymphocytes carrying c.896A>T_DNMT3A mutation 2

source_name: Lymphocites 2

value: female


title: MCF7_Alarid_1pER_Veh_rep3

value: vehicle

value: pS118-ER (Cell Signaling, #2511, lot 16J4)


title: MCF7_Alarid_1pER_Veh_rep2


title: ufm1_memb_b

data_processing:
Adapter trimming with fastx_clipper v0.0.14 -Q33 -a AGATCGGAAGAGCACACGTCTGAA -n -v
Tophat v2.1.1 using GRCh38, subtracted reads aligning to rRNA and tRNA
Custom fp-count script using Gencode v22 APPRIS principal splice isoforms
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count

source_name: Membrane fraction from UFM1-KO HEK293 cells


title: wgbs_early


title: genomic DNA from lymphocytes carrying c.896A>T_DNMT3A mutation 1

source_name: Lymphocites 1


title: MCF7_Alarid_1pER_Veh_rep1


title: mrebs_esc2

data_processing:
Library strategy: MREBS
fastq files were aligned by BS-Seeker2 and bowtie to generate bam file
methylation were called on the bam files by BS-Seeker2
Genome_build: mm9
Supplementary_files_format_and_content: Cgmap

extract_protocol: Three enzymatic digestions were performed on 1 μg of purified genomic DNA using 10 U of each one of the MRE restriction enzymes (HpaII, Hin6 and AciI - Fermentas) in a 50 μl final volume with TANGO buffer. 2.5 μl of RNase cocktail mix (Ambion) were added and the reaction was incubated overnight at 37°C. After the digestion, the three reactions were pooled and the DNA was purified using AMPure XP beads (Beckman Coulter). Subsequent reactions of DNA End Repair, A-tailing and Adapter Ligation were performed using Illumina TruSeq reagents, following manufacturer’s instructions and the DNA was size selected between 200 and 500 bp using AMPure XP beads. Size selected DNA was then treated with bisulfite using the EpiTect kit (QIAGEN) according to the protocol suggested from the manufacturer, except that the conversion step was performed twice, for a total time of 10 h. For each bisulfite-converted sample, two parallel PCR reactions were set up in a final volume of 50 μl using MyTaq HS Mix (Bioline) and 2.5 μl of Illumina TruSeq PCR Cocktail Primers. The amplification cycles were as follows: 98°C – 2 min; 12 cycles of: 98°C – 15 sec, 60°C – 30 sec, 72°C – 30 sec; 72°C – 5 min. The final PCR products were purified using AMPure XP beads and the final concentration of the libraries was measured using Qubit DNA BR Assay (Life Technologies). Single-end sequencing for 100bp reads was performed on an Illumina Hiseq 2000.

value: MREBS


title: MCF7_Alarid_2pER_E2_rep1


title: ufm1_memb_a

data_processing:
library strategy: ribosome profiling
Adapter trimming with fastx_clipper v0.0.14 -Q33 -a AGATCGGAAGAGCACACGTCTGAA -n -v
Tophat v2.1.1 using GRCh38, subtracted reads aligning to rRNA and tRNA
Custom fp-count script using Gencode v22 APPRIS principal splice isoforms
Genome_build: GRCh38
Supplementary_files_format_and_content: qexpr.txt files are tab-delimited text files with three columns: transcript id, CDS length, and read count


title: mrebs_esc1


title: NC.rep1

value: mouse embryonic stem cell

value: NC


title: MCF7_Alarid_1pER_E2_rep3


title: MS023.rep2


title: MCF7_Alarid_1pER_E2_rep2


title: NC.rep2


title: OICR.rep1


title: MCF7_Alarid_1pER_E2_rep1


title: MS023.rep1


title: Control mouse somas, replicate 13

description:
Ctrl_soma13
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

source_name: Stem cell-derived motor neuron culture

extract_protocol:
Cell culture material was lysed in the presence of RNAse inhibitor and immediately frozen down. Library preparation occurred in the lysis buffer directly, without RNA-extraction.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5 tagementation.

tag: disease status

value: Control

tag: cell part

value: Soma (bulk culture)

tag: day after seeding

value: Day 7


title: mrebs_early2


title: MCF7_Alarid_3pER_Veh_rep2

tag: treatment

value: pS118-ER (Santa Cruz, sc-12915, lot A1614)


title: Control mouse somas, replicate 12

description:
Ctrl_soma12
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: DZNep.rep2

value: DZNep


title: IOX1.rep1


title: Garcinol.rep2

value: Garcinol


title: Control mouse somas, replicate 9

description:
Ctrl_soma9
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: IOX1.rep2


title: DZNep.rep1


title: Garcinol.rep1


title: Control mouse somas, replicate 10

description:
Ctrl_soma10
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse somas, replicate 8

description:
Ctrl_soma8
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse somas, replicate 7

description:
Ctrl_soma7
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Chaetocin.rep2

value: Chaetocin


title: mrebs_early1

value: mouse embryonic fibroblasts


title: Control mouse somas, replicate 6

description:
Ctrl_soma6
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse somas, replicate 5

description:
Ctrl_soma5
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: CPTH2.rep1


title: Control mouse somas, replicate 4

description:
Ctrl_soma4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse somas, replicate 11

description:
Ctrl_soma11
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: CPTH2.rep2


title: Bromosporine.rep2

value: Bromosporine


title: Control mouse somas, replicate 1

description:
Ctrl_soma1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Control mouse axons, replicate 5

description:
Ctrl_axon5
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

source_name: Stem cell-derived motor neuron axons

value: Axon (isolated from bulk)


title: Control mouse axons, replicate 4

description:
Ctrl_axon4
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: HepaRG cells_0.8 µM CYN_24 hr_rep 1

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

institute: Anses

description:
CYN_220
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 1

hyb_protocol: For the experiments we used 4 X 44K Whole Human Genome 70-mer oligo-chips (G4112F; Agilent Technologies). Hybridisation of Cyanine-labeled cRNA samples was performed onto each microarray for 17 hrs at 65°C with an HSPro4800 hybridisation automatic station (Tecan) and using the Gene Expression Wash Pack kit (Agilent Technologies) and the “Stabilization and Drying Solution” kit (Agilent Technologies) according to the manufacturers’ protocols.

scan_protocol: The absorbance was measured at 532 nm (for cyanine-3-labeled cRNA samples) or 635 nm (for cyanine-5-labeled cRNA samples) with an Innoscan 900AL scanner (Innopsys, Carbonne, France).

data_processing: Raw data, corresponding to the median pixel intensity for each probe, were extracted with Mapix software, version 5.0. The quality of the extracted raw data was checked for signal homogeneity using the Pearson correlation. A Lowess normalisation was performed on the raw data with R software using the Linear Model for Microarray Data Bioconductor package. A background signal was calculated from the mean of the one hundred lowest values of each sample. Following this, the normalised data were filtered on threshold intensity (3 times the background signal): for each probe, values were selected if the median value for at least one experimental condition was higher than the threshold intensity. This dataset, including the 29 488 post-filtering probes, was labelled “filtered data”.

source_name: HepaRG cells, 0.8 µM CYN, 24 hours

label_protocol: For probe preparation, 200 ng of total RNA were reverse transcribed into double strand cDNA and then amplified and labelled into cRNA with either cyanine-3 CTP or cyanine-5 CTP using the “Low Input QuickAmp Labeling” kit according to the manufacturer’s protocol (Agilent Technologies, Massy, France). Cyanine-labeled cRNA was purified using the “RNeasy Mini” kit according to the manufacturer’s instructions (Qiagen, Courtaboeuf, France), cyanine incorporation was monitored with a NanoPhotometer (Implen, Munich, Germany), and cyanine-labeled cRNA was fragmented for 30 min at 60°C.

growth_protocol: HepaRG cells were seeded at 2.5 x 10e4 cells/cm2 in 12-well plates and grown in William’s E medium supplemented with 50 IU/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine, 5 μg/mL insulin, 25 µg/mL hydrocortisone hemisuccinate, and 10% fœtal calf serum for 28 days. The medium was changed three times a week.

extract_protocol: Following cell treatments, total RNA was isolated using the NucleoSpin® RNA II kit according to the manufacturer’s instructions with a final elution volume of 10 µL of RNase free water (Macherey-Nagel, Hoerd, France). RNA was quantified with the BioSpec-Nano (Shimadzu, Marne la Vallée, France), and RNA integrity was assessed with the “Experion RNA StdSens analysis” kit using the Experion automated electrophoresis system (Bio-Rad, Marnes-la-Coquette, France). Only RNA with an RNA quality indicator ≥ 9 was used for further experiments (Experion software 3.0; Bio-Rad).

treatment_protocol: Differentiated HepaRG cells were exposed for 24 hrs to 0.8 µM of cylindrospermopsin in medium at 37°C in an atmosphere containing 5% CO2. A vehicle control (sterile water) was also included for each experiment. Six independent experiments were performed.

value: HepaRG

value: differentiated HepaR hepatic cells

value: 0.8 uM cylindrospermopsin

value: 24 hrs


title: HepaRG cells_0.8 µM CYN_24 hr_rep 3

description:
CYN_250
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 3


title: HepaRG cells_0.8 µM CYN_24 hr_rep 4

description:
CYN_190
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 4


title: HepaRG cells_0.8 µM CYN_24 hr_rep 5

description:
CYN_200
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 5


title: HepaRG cells_0.8 µM CYN_24 hr_rep 6

description:
CYN_210
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 6


title: HepaRG cells_0.8 µM CYN_24 hr_rep 2

description:
CYN_230
Gene expression after 24hr in 0.8 µM CYN exposed HepaRG cells.
Biological replicate 2


title: Bromosporine.rep1


title: HepaRG cells_0 µM CYN_24 hr_rep 6

description:
NT_245
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 6

source_name: HepaRG cells, 0 µM CYN, 24 hours

value: 0 uM cylindrospermopsin


title: HepaRG cells_0 µM CYN_24 hr_rep 5

description:
NT_225
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 5


title: SOD1G93A mutant mouse cell somas, replicate 10

description:
G93A_soma10
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

data_processing:
Raw read counts were extracted using the GenomicAlignments package in R, with the function SummarizeOverlaps, mode set to "Union"
Differential gene expression analysis was performed on the read counts using DESeq2 version 1.12.4. Only genes with reads in 4 samples or more were considered in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Two processed data files are added, providing raw counts and normalized abundance measurements (RPKM), respectively.

value: Amyotrophic lateral sclerosis


title: SOD1G93A mutant mouse cell somas, replicate 8

description:
G93A_soma8
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: HepaRG cells_0 µM CYN_24 hr_rep 3

description:
NT_205
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 3


title: SOD1G93A mutant mouse cell somas, replicate 9

description:
G93A_soma9
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: Chaetocin.rep1

value: mouse embryonic stem cell


title: HepaRG cells_0 µM CYN_24 hr_rep 2

description:
NT_195
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 2


title: SOD1G93A mutant mouse cell somas, replicate 7

description:
G93A_soma7
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt


title: HepaRG cells_0 µM CYN_24 hr_rep 4

description:
NT_215
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 4


title: delta-fis rep2

city: Pune

first: Payel

last: Ghosh

state: Maharashtra

address: Ganeshkhind

department: Bioinformatics Centre

country: India

institute: Savitribai Phule Pune University

data_processing:
Sequenced reads were mapped onto the reference genome of E. coli K-12 MG1655 (NC_000913.2) using Bowtie2.2.6.
Cufflinks v2.2.1 was used to calculate fragments per kilobase of exon per million fragments (FPKM). Differentially expressed genes (DEGs) were identified using Cuffdiff v2.2.1 program and expression of gene with adjusted P-value <0.05 and log2 fold change ≥+1.0 or ≤-1  was considered as differentially expressed.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: An excel file, where cuffdiff  results are given including log2 fold change, p-value, q-value.

organism: Escherichia coli

source_name: Total RNA isolated from E. coli

growth_protocol: E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose.

extract_protocol:
Total RNA was extracted using the Analytik Jena RNA Mini kit, according to manufacturer’s guidelines.
cDNA libraries constructed, using standard Illumina protocols.

tag: strain

value: str. K-12 substr. MG1655

tag: material type

value: whole organism

tag: growth condition

value: mid-exponential growth phase

value: delta-fis

tag: phenotype

value: lack Fis protein


title: delta-hns rep2

tag: genotype

value: delta-hns

value: lack H-NS protein


title: delta-hns rep1


title: delta-fis rep1


title: WT rep2

value: wild-type

value: normal


title: SOD1G93A mutant mouse axons, replicate 1

description:
G93A_axon1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Axon (isolated from bulk)

value: Day 7


title: KO, Control

city: kobe

first: Yu

last: Hirata

address: chuo-ku, kusunoki-chou, 7-5-2

country: Japan

institute: Kobe University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: rma-gene-full-Signal

label: biotin

source_name: Gastrocnemius muscle at 3 weeks after vehicle treatment of skeletal muscle specific KLF15 knockout mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Gastrocnemius muscle collections of mice at 3 weeks after vehicle or STZ treatment.

extract_protocol: Total RNA was extracted from mouse skeletal muscle with the use of the RNeasy Mini Kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: Intraperitoneally with sodium citrate (control) or STZ [50 mg/kg (Wako, Osaka, Japan), dissolved in 50 mM sodium citrate (pH 4.5)] on five consecutive days.

tag: tissue

value: Gastrocnemius muscle tissue

tag: agent

value: control


title: SOD1G93A mutant mouse cell somas, replicate 1

description:
G93A_soma1
GEO_rpkms_mouse.txt
GEO_counts_mouse.txt

value: Soma (bulk culture)


title: WT, Control

source_name: Gastrocnemius muscle at 3 weeks after vehicle treatment of wild type

value: wild type


title: WT rep1


title: HepaRG cells_0 µM CYN_24 hr_rep 1

description:
NT_185
Gene expression after 24hr in 0 µM CYN exposed HepaRG cells.
Biological replicate 1

tag: cell line

value: HepaRG

tag: cell type

value: differentiated HepaR hepatic cells

value: 0 uM cylindrospermopsin

tag: time point

value: 24 hrs


title: WT, STZ

source_name: Gastrocnemius muscle at 3 weeks after STZ treatment of wild type

value: STZ


title: macrophages F4/80 high MHCII high, from uninfected spleen [UI_SP_Ma_2]

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

data_processing:
Paired-end reads were mapped to reference genome using STAR version 2.3
Mapped reads were summaried to gene level using featureCounts version 1.5 and with GENCODE GRCm38 vM10 gene annotation
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Bioconductor edgeR package with normalized library sizes option and log2 transformation
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level log2 transformed FPKM values for all samples

source_name: Healthy spleen

extract_protocol:
Tissue was digested with collagenase D. Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bionanlyser for quality assessment; RNA Integrity Number (RIN) range was 6.5-10 and a median of 9.2.
cDNA libraries were prepared starting with 2ng of total RNA and 1ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip. All 8 samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2500 Rapid mode (17 samples/lane).

treatment_protocol: P. yoelii infection, 10+6 infected red blood cells

tag: infected with

value: none (uninfected)

value: spleen

value: macrophages F4/80 high

tag: samplegroup

value: SP Ma


title: KO, STZ

source_name: Gastrocnemius muscle at 3 weeks after STZ treatment of skeletal muscle specific KLF15 knockout mice


title: macrophages F4/80 high MHCII high, from uninfected spleen [UI_SP_Ma_1]


title: 23_1608 Br-M_Lac10_37g(golden)

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

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

growth_protocol: Mouse grow in NIDDK animal core facility.

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

treatment_protocol: mRNA is obtained by Co-Ip with FLAG tagged PAB-1 expressed in seam cells and VPCs converted to cDNA and amplified using NuGEN pico amplification kit

value: FVB/129SVEV/Black Swiss at ratios:80%/10%/10%.

tag: genotype/variation

value: Mutant

tag: stage pregnancy


title: macrophages F4/80 high MHCII high, from uninfected lung [UI_LU_Ma_5]

source_name: Healthy lung

value: lung

value: LU Ma


title: 24_1770 Br-M _Lac10_25.29g(white)


title: 5_6-1(1647)Br-M_Virgin_25g

source_name: M-V

value: V


title: 6_6-2(1640)Br-M_Virgin_22g


title: macrophages F4/80 high MHCII high, from uninfected lung [UI_LU_Ma_2]


title: macrophages F4/80 high MHCII high, from uninfected lung [UI_LU_Ma_3]


title: macrophages F4/80 high MHCII high, from uninfected spleen [UI_SP_Ma_3]


title: macrophages F4/80 high MHCII high, from uninfected liver [UI_LI_Ma_4]

source_name: Healthy liver

value: liver

value: LI Ma


title: macrophages F4/80 high MHCII high, from uninfected liver [UI_LI_Ma_2]


title: 129S6/SvEvTac_9 LF_129 [jos2150]

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: 9 LF_129

hyb_protocol: 15 ug of cRNA were hybridized to Mu74Av2 arrays, which were then washed and stained with user-generated reagents.

scan_protocol: Chips were scanned using the GCS 3000 scanner from Affymetrix.

data_processing: Data were analyzed using Robust Multi-Array Average (RMA).

label_protocol: 25  g total RNA was pooled from two to three mice and biotin-labeled cRNA was made using the One Cycle Assay protocol.

extract_protocol: Total RNA was extracted and purified with RNeasy (Qiagen, Chatsworth, CA).

value: Epididymal fat pads

tag: diet

value: low-fat


title: 129S6/SvEvTac_11 LF_129 [jos2168]

description: 11 LF_129


title: 129S6/SvEvTac_12 HF_129 [jos2169]

description: 12 HF_129

value: high-fat


title: 129S6/SvEvTac_13 HF_129 [jos2170]

description: 13 HF_129


title: C57Bl/6_8 HF_B6 [jos2149]

description: 8 HF_B6


title: 10_Br-M1727_dp12_47g


title: C57Bl/6_7 HF_B6 [jos2148]

description: 7 HF_B6


title: C57Bl/6_2 HF_B6 [jos2142]

description: 2 HF_B6


title: 22_1439 Br-M_Lac10_30g(white)


title: 18_Br-M 1769_dp18_48g (white)


title: 4_Deng-5(1645)Br-M_Virgin_24g


title: macrophages F4/80 high MHCII high, from infected spleen [IN_SP_Ma_4]

source_name: infected spleen d35

value: parasitized P. yoelii erythrocytes


title: 12_Br-M 1729_dp12_29g


title: 129S6/SvEvTac_10 LF_129 [jos2167]

description: 10 LF_129


title: 129S6/SvEvTac_14 HF_129 [jos2171]

description: 14 HF_129


title: C57Bl/6_5 LF_B6 [jos2146]

description: 5 LF_B6