title: A384

description: blast percentage >90%


title: A380

status: Public on Sep 16 2019

type: RNA

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description: blast percentage >90%

hyb_protocol: Affymetrix hybridization kit was used including fragmentation according to Affymetrix's protocol. Arrays were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: The arrays were scanned using the Affymetrix Genechip scanner

data_processing: R-version 2.13.0 with Bioconductor packages affy version 1.30.0, vsn version 3.20.0 and biobase version 2.12.1 were used to extract data according to rma and to normalize using VSN. Combat was used to correct for different batches.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: leukemic blast

label_protocol: 8ul 125ng/ul was used as input for the Affymetrix in vitro one cycle kit, followed by IVT labelling (Affymetrix)

growth_protocol: Primairy human leukemic cells were isolated at initial diagnosis (blast percentage >90%)

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

tag: all subtype

tag: batch

value: E


title: A401

description: blast percentage >90%


title: A392

description: blast percentage >90%


title: A396

description: blast percentage >90%

value: Other BCP


title: A394

description: blast percentage >90%


title: A386

description: blast percentage >90%


title: A389

description: blast percentage >90%


title: A399

description: blast percentage >90%

value: T-ALL


title: A388

description: blast percentage >90%


title: A393

description: blast percentage >90%


title: A391

description: blast percentage >90%


title: A385

description: blast percentage >90%


title: A390

description: blast percentage >90%


title: A382

description: blast percentage >90%


title: A387

description: blast percentage >90%


title: A379

description: blast percentage >90%


title: A377

description: blast percentage >90%


title: A370

description: blast percentage >90%


title: A372

description: blast percentage >90%


title: A373

description: blast percentage >90%


title: A374

description: blast percentage >90%


title: A369

description: blast percentage >90%


title: A365

description: blast percentage >90%


title: A367

description: blast percentage >90%


title: A376

description: blast percentage >90%


title: A358

description: blast percentage >90%


title: A371

description: blast percentage >90%


title: A359

description: blast percentage >90%


title: A356

description: blast percentage >90%


title: A360

description: blast percentage >90%


title: A363

description: blast percentage >90%


title: A353

description: blast percentage >90%


title: A354

description: blast percentage >90%


title: A400

description: blast percentage >90%


title: A361

description: blast percentage >90%


title: A364

description: blast percentage >90%


title: A357

description: blast percentage >90%


title: A366

description: blast percentage >90%


title: A362

description: blast percentage >90%


title: A351

description: blast percentage >90%


title: A368

description: blast percentage >90%


title: A352

description: blast percentage >90%


title: A350

description: blast percentage >90%


title: A348

description: blast percentage >90%


title: A355

description: blast percentage >90%


title: A347

description: blast percentage >90%


title: A343

description: blast percentage >90%


title: A341

description: blast percentage >90%


title: A340

description: blast percentage >90%


title: A342

description: blast percentage >90%


title: A378

description: blast percentage >90%


title: A346

description: blast percentage >90%


title: A349

description: blast percentage >90%


title: A333

description: blast percentage >90%


title: A337

description: blast percentage >90%


title: A336

description: blast percentage >90%


title: A344

description: blast percentage >90%


title: A326

description: blast percentage >90%


title: A334

description: blast percentage >90%


title: A329

description: blast percentage >90%


title: A338

description: blast percentage >90%


title: A325

description: blast percentage >90%


title: A327

description: blast percentage >90%


title: A335

description: blast percentage >90%


title: A345

description: blast percentage >90%


title: A328

description: blast percentage >90%


title: A330

description: blast percentage >90%


title: A332

description: blast percentage >90%


title: A339

description: blast percentage >90%


title: A331

description: blast percentage >90%


title: A323

description: blast percentage >90%


title: A314

description: blast percentage >90%


title: A319

description: blast percentage >90%


title: A315

description: blast percentage >90%


title: A318

description: blast percentage >90%


title: A324

description: blast percentage >90%


title: A321

description: blast percentage >90%


title: A313

description: blast percentage >90%


title: A310

description: blast percentage >90%


title: A309

description: blast percentage >90%


title: A317

description: blast percentage >90%


title: A304

description: blast percentage >90%


title: A303

description: blast percentage >90%


title: A306

description: blast percentage >90%


title: A311

description: blast percentage >90%


title: A316

description: blast percentage >90%


title: A298

description: blast percentage >90%


title: A322

description: blast percentage >90%


title: A312

description: blast percentage >90%


title: A307

description: blast percentage >90%


title: A305

description: blast percentage >90%


title: A297

description: blast percentage >90%


title: A308

description: blast percentage >90%


title: A300

description: blast percentage >90%


title: A302

description: blast percentage >90%


title: A296

description: blast percentage >90%


title: A320

description: blast percentage >90%


title: A301

description: blast percentage >90%


title: A299

description: blast percentage >90%


title: A295

description: blast percentage >90%


title: A293

description: blast percentage >90%


title: A294

description: blast percentage >90%


title: A285

description: blast percentage >90%


title: A283

description: blast percentage >90%


title: A291

description: blast percentage >90%


title: A288

description: blast percentage >90%


title: A275

description: blast percentage >90%


title: A279

description: blast percentage >90%


title: A281

description: blast percentage >90%


title: A284

description: blast percentage >90%


title: A286

description: blast percentage >90%


title: A375

description: blast percentage >90%


title: A282

description: blast percentage >90%


title: A276

description: blast percentage >90%


title: A268

description: blast percentage >90%


title: A270

description: blast percentage >90%


title: A269

description: blast percentage >90%


title: A287

description: blast percentage >90%


title: A280

description: blast percentage >90%


title: A289

description: blast percentage >90%


title: A271

description: blast percentage >90%


title: A277

description: blast percentage >90%


title: A278

description: blast percentage >90%


title: A292

description: blast percentage >90%


title: A274

description: blast percentage >90%


title: A264

description: blast percentage >90%


title: A266

description: blast percentage >90%


title: A263

description: blast percentage >90%


title: A273

description: blast percentage >90%


title: A272

description: blast percentage >90%


title: A260

description: blast percentage >90%


title: A261

description: blast percentage >90%


title: A253

description: blast percentage >90%


title: A262

description: blast percentage >90%


title: A265

description: blast percentage >90%


title: A251

description: blast percentage >90%


title: A258

description: blast percentage >90%


title: A256

description: blast percentage >90%


title: A250

description: blast percentage >90%


title: A246

description: blast percentage >90%


title: A254

description: blast percentage >90%


title: A259

description: blast percentage >90%


title: A249

description: blast percentage >90%


title: A243

description: blast percentage >90%


title: A257

description: blast percentage >90%


title: A244

description: blast percentage >90%


title: A252

description: blast percentage >90%


title: A248

description: blast percentage >90%


title: A247

description: blast percentage >90%


title: A255

description: blast percentage >90%


title: A239

description: blast percentage >90%


title: A242

description: blast percentage >90%


title: A237

description: blast percentage >90%


title: A241

description: blast percentage >90%


title: A236

description: blast percentage >90%


title: A245

description: blast percentage >90%


title: A232

description: blast percentage >90%


title: A229

description: blast percentage >90%


title: A224

description: blast percentage >90%


title: A231

description: blast percentage >90%


title: A234

description: blast percentage >90%


title: A225

description: blast percentage >90%


title: A227

description: blast percentage >90%


title: A240

description: blast percentage >90%


title: A222

description: blast percentage >90%


title: A228

description: blast percentage >90%


title: A233

description: blast percentage >90%


title: A226

description: blast percentage >90%


title: A267

description: blast percentage >90%


title: A235

description: blast percentage >90%


title: A219

description: blast percentage >90%


title: A218

description: blast percentage >90%


title: A223

description: blast percentage >90%


title: A215

description: blast percentage >90%


title: A221

description: blast percentage >90%


title: A220

description: blast percentage >90%


title: A216

description: blast percentage >90%


title: A230

description: blast percentage >90%


title: A214

description: blast percentage >90%


title: A213

description: blast percentage >90%


title: A211

description: blast percentage >90%


title: A210

description: blast percentage >90%


title: A212

description: blast percentage >90%


title: A217

description: blast percentage >90%


title: A209

description: blast percentage >90%


title: A208

description: blast percentage >90%


title: A207

description: blast percentage >90%


title: A206

description: blast percentage >90%


title: A204

description: blast percentage >90%


title: A202

description: blast percentage >90%


title: A201

description: blast percentage >90%


title: A196

description: blast percentage >90%


title: A195

description: blast percentage >90%


title: A203

description: blast percentage >90%


title: A185

description: blast percentage >90%


title: A190

description: blast percentage >90%


title: A189

description: blast percentage >90%


title: A200

description: blast percentage >90%


title: A183

description: blast percentage >90%


title: A194

description: blast percentage >90%


title: A187

description: blast percentage >90%


title: A191

description: blast percentage >90%


title: A192

description: blast percentage >90%


title: A199

description: blast percentage >90%


title: A205

description: blast percentage >90%


title: A181

description: blast percentage >90%


title: A197

description: blast percentage >90%


title: A184

description: blast percentage >90%


title: A188

description: blast percentage >90%


title: A193

description: blast percentage >90%


title: A198

description: blast percentage >90%


title: A178

description: blast percentage >90%


title: A182

description: blast percentage >90%


title: A179

description: blast percentage >90%


title: A176

description: blast percentage >90%


title: A180

description: blast percentage >90%


title: A177

description: blast percentage >90%


title: A173

description: blast percentage >90%


title: A175

description: blast percentage >90%


title: A171

description: blast percentage >90%


title: A161

description: blast percentage >90%


title: A238

description: blast percentage >90%


title: A166

description: blast percentage >90%


title: A164

description: blast percentage >90%


title: A174

description: blast percentage >90%


title: A160

description: blast percentage >90%


title: A165

description: blast percentage >90%


title: A170

description: blast percentage >90%


title: A154

description: blast percentage >90%


title: A158

description: blast percentage >90%


title: A172

description: blast percentage >90%


title: A152

description: blast percentage >90%


title: A167

description: blast percentage >90%


title: A290

description: blast percentage >90%


title: A151

description: blast percentage >90%


title: A155

description: blast percentage >90%


title: A148

description: blast percentage >90%


title: A168

description: blast percentage >90%


title: A150

description: blast percentage >90%


title: A156

description: blast percentage >90%


title: A153

description: blast percentage >90%


title: A157

description: blast percentage >90%


title: A162

description: blast percentage >90%


title: A163

description: blast percentage >90%


title: A149

description: blast percentage >90%


title: A159

description: blast percentage >90%


title: A146

description: blast percentage >90%


title: IS6_5 [sLHb_VTA_D2]

type: SRA

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (ENS_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

organism: Mus musculus

source_name: Lateral Habenula

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

tag: cell type

tag: quality control

value: Passed

tag: stress

value: Yes Stress

tag: andehonia

value: No Anhedonia

tag: despair

value: Yes Despair

tag: anxiety

value: Yes Anxiety

tag: projection

value: VTA Projecting


title: IS6_6 [sLHb_VTA_D2]


title: IS6_4 [sLHb_VTA_D2]


title: A142

description: blast percentage >90%


title: IS6_2 [sLHb_VTA_D2]


title: A144

description: blast percentage >90%


title: A141

description: blast percentage >90%


title: IS5_5 [sLHb_VTA_D2]

value: Yes Anhedonia

value: No Anxiety


title: IS6_1 [sLHb_VTA_D2]


title: IS5_4 [sLHb_VTA_D2]


title: A145

description: blast percentage >90%


title: A143

description: blast percentage >90%


title: IS5_3 [sLHb_VTA_D2]


title: A137

description: blast percentage >90%


title: IS5_2 [sLHb_VTA_D2]


title: A140

description: blast percentage >90%


title: A147

description: blast percentage >90%


title: A135

description: blast percentage >90%


title: A136

description: blast percentage >90%


title: A134

description: blast percentage >90%


title: A138

description: blast percentage >90%


title: A130

description: blast percentage >90%


title: A129

description: blast percentage >90%


title: A133

description: blast percentage >90%


title: A131

description: blast percentage >90%


title: IS4_6 [sLHb_VTA_DX]

value: Unknown


title: A128

description: blast percentage >90%


title: IS4_7 [sLHb_VTA_D2]


title: IS4_2 [sLHb_VTA_DX]


title: IS4_4 [sLHb_VTA_DX]


title: A139

description: blast percentage >90%


title: IS4_3 [sLHb_VTA_DX]


title: IS4_1 [sLHb_VTA_DX]


title: IS5_1 [sLHb_VTA_D2]


title: IS3_6 [sLHb_VTA_D3]


title: IS4_5 [sLHb_VTA_DX]


title: A132

description: blast percentage >90%


title: IS3_5 [sLHb_VTA_D3]


title: A122

description: blast percentage >90%


title: A125

description: blast percentage >90%


title: A121

description: blast percentage >90%


title: IS3_3 [sLHb_VTA_D3]


title: IS3_2 [sLHb_VTA_D3]


title: IS3_4 [sLHb_VTA_D3]


title: A127

description: blast percentage >90%


title: IS3_1 [sLHb_VTA_D3]


title: A169

description: blast percentage >90%


title: A126

description: blast percentage >90%


title: IS2_2 [sLHb_VTA_D3]


title: A123

description: blast percentage >90%


title: IS2_3 [sLHb_VTA_D3]


title: A116

description: blast percentage >90%


title: A124

description: blast percentage >90%


title: A117

description: blast percentage >90%


title: A115

description: blast percentage >90%


title: A120

description: blast percentage >90%


title: A119

description: blast percentage >90%


title: IS2_1 [sLHb_VTA_D3]


title: A114

description: blast percentage >90%


title: IS1_1 [sLHb_VTA_D3]


title: IC7_4 [LHb_raphe]

value: No Stress

value: DR Projecting


title: IC7_3 [LHb_raphe]


title: IC7_1 [LHb_raphe]


title: IC6_4 [LHb_raphe]

value: No Despair


title: IC6_2 [LHb_raphe]


title: IC6_1 [LHb_raphe]


title: A112

description: blast percentage >90%


title: A113

description: blast percentage >90%


title: A118

description: blast percentage >90%


title: IC5_6 [LHb_VTA]


title: A110

description: blast percentage >90%


title: IC7_2 [LHb_raphe]


title: A109

description: blast percentage >90%


title: IC5_4 [LHb_VTA]


title: IC5_3 [LHb_VTA]


title: A111

description: blast percentage >90%


title: A108

description: blast percentage >90%


title: A107

description: blast percentage >90%


title: IC5_2 [LHb_VTA]


title: IC6_3 [LHb_raphe]


title: IC4_2 [LHb_VTA]


title: IC3_3 [LHb_VTA]


title: IC4_1 [LHb_VTA]


title: A105

description: blast percentage >90%


title: A104

description: blast percentage >90%


title: IC3_2 [LHb_VTA]


title: IC2_6 [LHb_VTA]


title: A100

description: blast percentage >90%


title: A102

description: blast percentage >90%


title: A95

description: blast percentage >90%


title: A96

description: blast percentage >90%


title: A101

description: blast percentage >90%


title: IC2_3 [LHb_VTA]


title: A106

description: blast percentage >90%


title: I4_6 [LHb_VTA]


title: I4_5 [LHb_VTA]


title: I4_3 [LHb_VTA]


title: A98

description: blast percentage >90%


title: A99

description: blast percentage >90%


title: IC2_5 [LHb_VTA]


title: A103

description: blast percentage >90%


title: A94

description: blast percentage >90%


title: I3_6 [LHb_VTA]


title: I4_1 [LHb_VTA]


title: I3_7 [LHb_VTA]


title: A97

description: blast percentage >90%


title: I3_5 [LHb_VTA]


title: A92

description: blast percentage >90%


title: A93

description: blast percentage >90%


title: A91

description: blast percentage >90%


title: A90

description: blast percentage >90%


title: I3_3 [LHb_VTA]

value: Failed


title: A88

description: blast percentage >90%


title: A87

description: blast percentage >90%


title: I2_1 [LHb_raphe]


title: A89

description: blast percentage >90%


title: I1_1 [LHb_VTA]


title: C [LHb_raphe]


title: 4_3 [LHb_raphe]


title: 4_4 [LHb_raphe]


title: 4_1 [LHb_raphe]


title: 3_4 [LHb_raphe]


title: A85

description: blast percentage >90%


title: 4_5 [LHb_raphe]


title: A82

description: blast percentage >90%


title: 3_3 [LHb_raphe]


title: 3_2 [LHb_raphe]


title: 2_4 [LHb_VTA]


title: 2_3 [LHb_VTA]


title: 3_5 [LHb_raphe]


title: A83

description: blast percentage >90%


title: 2_2 [LHb_VTA]


title: A78

description: blast percentage >90%


title: 2_1 [LHb_VTA]


title: A75

description: blast percentage >90%


title: A80

description: blast percentage >90%


title: A72

description: blast percentage >90%


title: A77

description: blast percentage >90%


title: A81

description: blast percentage >90%


title: A74

description: blast percentage >90%


title: A69

description: blast percentage >90%


title: A79

description: blast percentage >90%


title: A70

description: blast percentage >90%


title: A73

description: blast percentage >90%


title: A76

description: blast percentage >90%


title: 1_2 [LHb_VTA]


title: A86

description: blast percentage >90%


title: 1_1 [LHb_VTA]


title: 1_3 [LHb_VTA]


title: 3_1 [LHb_raphe]


title: A71

description: blast percentage >90%


title: BMDM KLA1h csRNAinput r2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

description: small RNA-seq in KLA stimulated (1h) mouse macrophages as a control for csRNA-seq

data_processing:
Adapter sequences were first removed from the 3' end of reads for csRNA-seq and small RNA-seq libraries (AGATCGGAAGAGCACACGTCT). Reads were then aligned to the appropriate genome using HISAT2 (v2.1.0) with default settings. Normalized, single nucleotide resolution bigWig files and TSS cluster calls were generated using HOMER's makeUCSCfile and findcsRNATSS.pl tools, respectively (v4.11). findcsRNATSS.pl uses small RNA sequencing and total RNA-seq data as controls to remove non-TSS artifacts in the csRNA-seq data when identifying TSS clusters. http://homer.ucsd.edu/homer/ngs/csRNAseq/
Genome_build: hg38, mm10, ASM20922v1, NC12, IRGSP-1.0, C_owczarzaki_V2
Supplementary_files_format_and_content: BigWig files (.bigWig/.bw) were generated by constructing normalized, single-nucleotide resolution bedGraph files based on 5' read positions using HOMER and converted to bigWigs using UCSC's bedGraphToBigWig utility. TSS text files contain TSS cluster positions defined using HOMER's findcsRNATSS.pl command (tab-delimited text files).

source_name: Bone Marrow Derived Macrophages

extract_protocol:
K562 cells were grown in RPMI1640+L‐Glutamine with heat inactivated 10% FBS (Biowest Cat No.S1620, Lot 61N16) and 1x Pen/Strep (Gibco15140-163) and 1x L-Glutamine (Gibco25030164) in T75 flasks at 37°C with 5% CO2. HCT116 CMV-osTIR1 RAD21-mAC cells were obtained from Masato T. Kanemaki (Natsume et al., 2016) and cultured in McCoy’s 5A medium supplemented with 10% FBS. Cells were washed twice in 1x cold PBS (Gibco 10010023) and RNA isolated using Trizol LS. Human H9 cell RNA was provided by Yuanyuan Li and Mark H. Tuszynski (UC San Diego). H9 cells were grown as described in (Lu et al. 2017) and RNA isolated using the Qiagen RNA kit. Murine BMDMs were isolated, cultured and RNA extracted as described (Link et al. 2018). Nematostella vectensis (planula stage) was kindly provided by Drs. James Gahan and Fabian Rentzsch (University of Bergen). Neurospora crassa was provided by Dr. Jason Stajich (University of California, Riverside) and grown in Vogels media under constant light and gentle agitation (Wang et al. 2015). Rice was grown in the SALK greenhouse with 12 h light and leaves from adult plants provided by Dr. Joanne Chory (Salk Institute for Biological Studies). All non-mammalian samples were flash frozen in liquid N2, pulverized with a mortar and pestle and RNA extracted using Trizol LS as described by the manufacturer. Capsaspora owczarzaki RNA (Sebé-Pedrós et al. 2016) was gifted by Dr. Iñaki Ruiz-Trillo (Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra).
Small RNAs of ~20-60 nt were size selected form 2-15 µg of total RNA by denaturing gel electrophoresis.  A 10% input sample was taken aside and the remainder enriched for 5’Caped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.  Following cDNA synthesis, libraries were amplified for 12-14 cycles and sequenced SE75 on the Illumina NextSeq500. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina HiSeq 2500. A comprehensive description of the csRNA-seq method and analysis software can be found in the supplement as well as under http://homer.ucsd.edu/homer/ngs/csRNAseq/.

tag: tissue

value: Bone Marrow Derived Macrophages

tag: treatment

value: KLA 1h

tag: assay

value: small RNA input

tag: genome build

tag: library id

tag: assayed molecule

value: total short RNA (20-65nt)

tag: library strategy

value: small RNA-seq


title: BMDM notx csRNAinput r2

description: small RNA-seq in untreated mouse macrophages as a control for csRNA-seq


title: BMDM KLA1h csRNAinput r1


title: BMDM KLA1h csRNA-seq r2

description: csRNA-seq in KLA stimulated (1h) mouse macrophages to identify TSS

value: csRNA-seq

value: capped short RNA (20-65nt)

value: capped short RNA-seq (csRNA-seq)


title: BMDM KLA1h csRNA-seq r1


title: BMDM notx csRNA-seq r2

description: csRNA-seq in untreated mouse macrophages to identify TSS


title: A68

description: blast percentage >90%

value: Other BCP

value: E


title: A65

description: blast percentage >90%


title: A67

description: blast percentage >90%


title: A62

description: blast percentage >90%


title: BMDM notx csRNA-seq r1


title: A64

description: blast percentage >90%


title: A63

description: blast percentage >90%


title: dWAT-1

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

country: China

institute: Wuhan University

description:
AMTed_skin_fibroblast
CD31-CD45-Pdgfra+GFP- and CD31-CD45-Pdgfra+GFP+ cells.
The I1 and R1 raw data files include technical reads, and the R2 raw data files include biological reads.

data_processing:
BCL files were demultiplexed using Cell Ranger (v2.1.0).
Alignment, barcode counting, UMI counting were performed using Cell Ranger (v2.1.0).
PCA, clustering, and differential expression were performed using Seurat.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.mtx: Count matrix in a sparse matrix format.
Supplementary_files_format_and_content: barcodes.tsv: Barcode id of the sample.
Supplementary_files_format_and_content: genes.tsv: Gene ids of the sample.

source_name: Cells isolated from skin

extract_protocol:
Harvest skin at the second telogen, CD31-CD45-Pdgfra+GFP- and CD31-CD45-Pdgfra+GFP+ cells were sorted by FACS from the skin cell suspension.
The library was generated according to manufacturer's instructions (10X Genomics).

treatment_protocol: Dermal adipocytes were labeled with GFP by doxycycline at the second anagen in Adipose chaser mice, then traced the cells to pro-longed second telogen. Mouse used for this experiment contained homo mTmG, so some adipocytes will be GFP and Tdtomato double positive as the results of one allele excision.

tag: strain/background

value: Skin fibroblasts and de-differentiated adipocytes

tag: age


title: A57

description: blast percentage >90%

tag: all subtype

tag: batch


title: A61

description: blast percentage >90%


title: Control Activated cells

city: Atlanta

first: Leszek

last: Ignatowicz

state: GA

address: 100 Piedmont Ave SE

department: Institute for Biomedical Sciences

institute: Georgia State University

data_processing:
Illumina sequencer base call files (BCL) were processed and demultiplexed with CellRanger (v2.2) that used Illumina conversion software bcl2fastq2 (v2.2).
FASTQ files were processed using CellRanger software, which performed alignment, filtering, barcode counting and UMI counting.
Low-quality cells were excluded in an initial quality control (QC) step by removing genes expressed in fewer than three cells.
Cells with less than 200 genes expressed or that express more than 2500 genes were removed.
Cells that had more than 0.05% of mitochondrial-associated genes among their expressed genes were removed.
Genome_build: For single-cell expression profiling, reads were aligned to the mouse genome (mm10-2.2), with CellRanger counts software, for their assignment as murine sequences.
Supplementary_files_format_and_content: Cloupe files compatible with Loupe Cell Browser from 10x Genomics.

source_name: Inguinal Lymph Nodes

extract_protocol:
Single-cell suspensions were prepared from inguinal and mesenteric lymph nodes by mechanical disruption and passed through 100 μm filter; stained with monoclonal antibodiec cells were sorted on Sony SH800 sorted. All further steps were done according to Chromium 10x manual.
To prepare the cDNA libraries for 10x Genomics Chromium controller we used the single-cell 3′ v2 kit, next, up to 50ng cDNA was used for 5’ gene expression library construction according to manufacturer protocol.

tag: strain

tag: genotype

tag: population


title: CT6_Grp2

city: Montreal

first: Nicolas

last: Cermakian

state: QC

address: 6875 LaSalle blvd

department: Douglas Institute Research Centre

country: Canada

institute: McGill University

data_processing:
Basecalls performed using Illumina RTA 2.4.11
Samples demultiplexed using bcl2fastq 2.19
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic 0.35 and then mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version M13
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M13 annotations (based on Ensembl 88)
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output (first line identifies the column)

molecule: polyA RNA

source_name: CD8+ T cells (from lymph nodes)

extract_protocol:
TriZol + RNeasy kit
KAPA RNA HyperPrep PolyA

tag: gender

value: male

tag: cell type

value: CD8+ T cells

value: lymph node

tag: time point

value: Circadian time 6, day 2


title: A60

description: blast percentage >90%


title: A59

description: blast percentage >90%


title: BMDM notx csRNAinput r1

tag: tissue


title: A55

description: blast percentage >90%


title: A58

description: blast percentage >90%


title: CT6_Grp1

value: Circadian time 6, day 1


title: CT2_Grp2

value: Circadian time 2, day 2


title: A53

description: blast percentage >90%


title: CT22_Grp2

value: Circadian time 22, day 2


title: CT22_Grp1

value: Circadian time 22, day 1


title: CT2_Grp1

value: Circadian time 2, day 1


title: A66

description: blast percentage >90%


title: CT18_Grp1

value: Circadian time 18, day 1


title: CT18_Grp2

value: Circadian time 18, day 2


title: A54

description: blast percentage >90%


title: CT14_Grp2

value: Circadian time 14, day 2


title: A50

description: blast percentage >90%


title: A49

description: blast percentage >90%


title: CT14_Grp1

value: Circadian time 14, day 1


title: A48

description: blast percentage >90%


title: A56

description: blast percentage >90%


title: CT10_Grp2

value: Circadian time 10, day 2


title: A46

description: blast percentage >90%


title: CT10_Grp1

value: Circadian time 10, day 1


title: A47

description: blast percentage >90%

value: Other BCP

value: E


title: A44

description: blast percentage >90%


title: A43

description: blast percentage >90%


title: Scurfy Activated cells


title: RNAseq.Muscle.28M-2

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

country: South Korea

institute: KRIBB

description: RNAseq.cntNorm.Muscle.csv

data_processing:
Raw reads were trimmed using 'Trim_galore'
Mapped on mm10 using 'bowtie2' for MBDseq data and 'TopHat' for RNAseq data with default options
For MBDseq, genome wide read enrichemnts were calculated with 'makewindows' and 'intersect' commands in the bedtools suit. For RNAseq, 'htseq-count' with intersection strict was used to count reads on transcripts.
Normalization and differential methylation/expression analyses were performed using 'DESeq2'
Genome_build: mm10
Supplementary_files_format_and_content: A csv file containing DESeq2 normalized count data

source_name: muscle

extract_protocol:
gDNAs and total RNAs were extracted from muscles (hind limbs) and splenic T cells using Dneasy Blood and Tissue kit.
For preparation of MBD capture, MBD-Biotin proteins from MethylMiner Methylated DNA Enrichment Kit (Thermo) were first incubated with pre-cleared Dynabeads (Thermo) at RT for 1 h. Methylated DNAs were captured by incubating sonicated gDNA fragments with MBD-beads at 4 °C for overnight. Beads were washed twice, and captured DNA fragments were eluted using 2 M NaCl and precipitated using ethanol. Enrichment of methylated DNA fragments were checked by PCR for control sets of methylated and non-methylated DNAs (Thermo) that were premixed as spike-ins. Using the enriched methylated DNA fragments, Illumina sequencing libraries were generated. All the captured DNAs were end-repaired by reacting with T4 DNA polymerase (NEB), Klenow (NEB), and T4 Polynucleotide kinase (NEB) in the presence of dNTP at 20 °C for 2 h, and then 3’-end adenylated using Klenow Fragment (NEB) at 30 °C for 2 h. Finally, the end-repaired DNA fragments were ligated with NEBNext adapters (NEB) and were enriched by 18 cycles of PCR. The resulting libraries were subjected to Illumina sequencing with NEXTseq 500. For RNA-seq library construction, 30 mg of the powdered muscle tissues in liquid nitrogen were homogenized and lysed with 200 μl of tissue isolation buffer (RTL) of RNeasy Plus Mini Kit (QIAGEN) in biomasher II (DWK Life Sciences). RNAs were then obtained using the RNeasy Plus Mini Kit according to the manufacturer’s protocol. Poly-A tailed RNAs were isolated from 1 μg of total RNAs using Dynabeads mRNA DIRECT kit (Thermo) and using First Strand Buffer (NEB) in the library construction kit, the captured RNAs were eluted. RNA-seq libraries were constructed using NEBNext Ultra RNA library prep kit for Illumina (NEB). Isolated poly-A tailed RNAs were incubated at 94°C for 15 min for fragmentation. First strand cDNA was synthesized with fragmented RNAs using ProtoScript II Reverse Transcriptase and their second strands were synthesized using Second Strand Synthesis Enzyme Mix in the kit before purification. After the end repair of the double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20 °C for 30 m and 65 °C for 30 m, the products were incubated with NEBNext Adaptor and Blunt/TA Ligase Master Mix (NEB) at 20 °C for 15 m. The resulting ligates were enriched by 13 cycles of PCR using NEBNext Q5 Hot Start HiFi PCR Master Mix and index primers. Enriched RNA-seq libraries were purified and sequenced using NextSeq 500 (Illumina).

value: 28 month

value: muscle


title: RNAseq.Muscle.28M-1

description: RNAseq.cntNorm.Muscle.csv


title: RNAseq.Muscle.28M-3

description: RNAseq.cntNorm.Muscle.csv


title: RNAseq.Muscle.20M-3

description: RNAseq.cntNorm.Muscle.csv

value: 20 month


title: A39

description: blast percentage >90%


title: A45

description: blast percentage >90%


title: A42

description: blast percentage >90%


title: OPMD Immortalized Clone rep 3

city: Londonderry

first: William

middle: John

last: Duddy

address: C-TRIC building, Altnagelvin Hospital Campus

department: Northern Ireland Centre for Stratified Medicine

country: United Kingdom

institute: Ulster University

description:
OPMD Immortalized Clone rep 3
OPMD Cloned C

hyb_protocol: 4 µg labelled cDNA was hybridized to a NimbleGen 12-plex microarray chip (Roche-NimbleGen) in the presence of hybridisation cocktail on a dedicated NimbleGen workstation (16 h at 42°C).

scan_protocol: Arrays were scanned on an MS200 system (Roche-NimbleGen), and decoded using NimbleScan software (Roche-NimbleGen) to obtain raw intensity values.

data_processing: Robust Multi-Array Analysis (RMA) to give normalized expression values was carried out on raw intensity values (‘pair’ files) using DEVA software (Roche-NimbleGen).

source_name: Cultured cells

label_protocol: 300 ng of total RNA was used for cDNA synthesis using the kit WTA1 TransPlex Whole Transcriptome Amplication kit (Sigma). This kit uses the WTA Library Synthesis Enzyme (incubation 15 min at 24°C, then 2 h at 42°C and 5 min at 95°C, after which cDNA were amplified using JumpStart Taq DNA polymerase (15 cycles of 20 sec at 95°C and 5 min at 65°C). cDNA was purified using GenElute™ Clean-Up (Sigma) and eluted in 50 µL DPEC H2O, then labelled with Cy3 dye (2 h at 37°C).

extract_protocol: Cell pellets were dissolved in TRIzol (1 mL).

tag: clonal state

value: Immortalized Clone

tag: pathology state

value: Oculopharyngeal Muscular Dystrophy (OPMD)


title: A84

description: blast percentage >90%


title: A40

description: blast percentage >90%


title: RNAseq.Muscle.20M-2

description: RNAseq.cntNorm.Muscle.csv


title: OPMD Immortalized Clone rep 2

description:
OPMD Immortalized Clone rep 2
OPMD Cloned B


title: OPMD Immortalized rep 1

description:
OPMD Immortalized rep 1
OPMD Immort A

value: Immortalized


title: OPMD Primaries rep 3

description:
OPMD Primaries rep 3
OPMD Prim C

value: Primary


title: OPMD Immortalized rep 2

description:
OPMD Immortalized rep 2
OPMD Immort B


title: OPMD Immortalized Clone rep 1

description:
OPMD Immortalized Clone rep 1
OPMD Cloned A


title: OPMD Primaries rep 2

description:
OPMD Primaries rep 2
OPMD Prim B


title: RNAseq.Muscle.20M-1

description: RNAseq.cntNorm.Muscle.csv


title: OPMD Immortalized rep 3

description:
OPMD Immortalized rep 3
OPMD Immort C


title: OPMD Primaries rep 1

description:
OPMD Primaries rep 1
OPMD Prim A


title: RNAseq.Muscle.02m-3

description: RNAseq.cntNorm.Muscle.csv

value: 2 month


title: A35

description: blast percentage >90%


title: FSH Immortalized Clone rep 2

description:
FSH Immortalized Clone rep 2
FSH Cloned B

value: Facioscapulohumeral Muscular Dystrophy (FSHD)


title: A38

description: blast percentage >90%


title: A36

description: blast percentage >90%


title: FSH Immortalized Clone rep 3

description:
FSH Immortalized Clone rep 3
FSH Cloned C


title: A41

description: blast percentage >90%


title: FSH Immortalized rep 2

description:
FSH Immortalized rep 2
FSH Immort B


title: FSH Immortalized Clone rep 1

description:
FSH Immortalized Clone rep 1
FSH Cloned A


title: FSH Immortalized rep 3

description:
FSH Immortalized rep 3
FSH Immort C


title: RNAseq.Muscle.02m-2

description: RNAseq.cntNorm.Muscle.csv


title: A37

description: blast percentage >90%


title: MBDseq.Tcell.28m

description: MBDseq.cntNorm.Muscle.Tcell.csv

library_source: genomic

molecule: genomic DNA

source_name: T cells

value: T cells


title: E12.5 TrkCcre;Tom

city: Stockholm

first: Francois

last: Lallemend

state: Stockholm

address: Tomtebodavägen 16

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: corresponding raw files include "384" in the file name

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include individual counts aligning to each gene per cell

source_name: Dorsal root ganglion neurons

extract_protocol:
Brachial DRGs were dissected and collected in Leibovitz L-15 medium (Life technologies) on ice. Then the DRGs were incubated in 0.05% trypsin-EDTA (1x) (Life technologies) for 5, 7, and 10 mins for DRGs from E9.5, E10.5 and E11.5, respectively, at 37 °C, shaking at 700 RPM. After spinning down the samples at 100 RCF for 5 mins, the supernatant was removed and replaced by Leibovitz L-15 medium (Life technologies). DRGs were physically triturated using 2 different sizes of pipettes previously coated with 0.2% bovine serum albumin until the solution homogenized. The cell suspension was then filtered through 70 ?m cell strainer (BD Biosciences) to remove clusters of cells.
RNA libraries were prepared according to Smart-seq2 protocol.

value: TrkCcre;Tom

tag: developmental stage

value: dorsal root ganglia


title: E11.5 TrkCcre;Tom

description: corresponding raw files include "385" in the file name


title: EBs_RA_Neil2_KO_rep3

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: RA treated EBs derived from Neil2 knockout mESCs clone #14

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina's bcl2fastq Conversion Software v.1.8.4.
RNA-seq reads were quality assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The raw reads were aligned to the mm9 genome with TopHat v.2.0.9 (https://ccb.jhu.edu/software/tophat) and Bowtie v.2.1.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with a GTF transcript annotation file from Ensemble release 67.
The mapped reads were summarized on gene level using the tool htseq-count from package HTSeq v.0.5.4 (http://www-huber.embl.de/HTSeq).
Differential expression analysis was performed using the Bioconductor package DESeq2 v.1.6.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from htseq-count

source_name: embryoid bodies (EBs) treated with retinoic acid (RA)

growth_protocol: Mouse E14TG2a (ATCC number CRL-1821) embryonic stem cells (mESCs) were cultured on plates coated with 0.1% Gelatin (Millipore) in DMEM supplemented with 15% PANSera ES FBS (PAN Biotech), 2 mM L-Glutamine, 100 µM non-essential amino acids (NEAA, Gibco), 1 mM sodium pyruvate (Gibco), 100 µM 2-mercaptoethanol (Sigma), 1000 U/ml Leukemia inhibitory factor (LIF, Millipore), 100 U/ml PEN-STREP at 37 °C in 5% CO2 and 20% O2. mESCs cells were seeded and transfected the next day with either empty or gRNA encoding pX330-U6-Chimeric_BB-CBh-hSpCas9 (Addgene #42230) mixed with the selection plasmid pPGKPuro (Addgene #11349) using Lipofectamine 2000 (Thermo Fisher) according to manufacturer’s instruction. Cells were selected with 2 µg/ml puromycin for 6 days, colonies picked, passaged and subjected to genotyping PCR. Three independent clones per genotype were expanded for further analyses, except for Apex1 where a single mESC mutant clone was analysed in technical duplicates.

extract_protocol:
Total RNA was isolated from mESCs and EBs using the RNeasy mini kit (Qiagen) with on-column DNase I digest following the manufacturer's protocol, quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.
NGS libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s recommendations and amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). The NGS libraries were sequenced on a HiSeq 2000 Illumina sequencer, for 51 cycles plus seven cycles for the index read.

treatment_protocol: Embryoid body (EB) differentiation was performed essentially as described before (Bibel et al. 2007; doi: 10.1038/nprot.2007.147). Briefly, on day 0 mESCs were plated at a density of 3.5x106 cells per 10 cm non-adherent bacteriological Petri dish in CA medium (15 ml DMEM supplemented with 10% PANSera ES FBS (PAN Biotech), 2 mM L-Glutamine, 100 µM non-essential amino acids (NEAA, Gibco), 143 µM 2-mercaptoethanol (Sigma), 100 U/ml PEN-STREP). After medium exchange on day 2, EBs were subdivided on day 4 with each half of the cells treated thereafter with CA medium (EB differentiation) and CA medium supplemented with 5 µM retinoic acid (EB + RA differentiation), respectively. After a medium exchange on day 6 embryoid bodies were harvested on day 8.

tag: cell line

value: Neil2 knockout


title: MBDseq.Tcell.02m

description: MBDseq.cntNorm.Muscle.Tcell.csv


title: MBDseq.Tcell.20m

description: MBDseq.cntNorm.Muscle.Tcell.csv


title: RNAseq.Muscle.02m-1

description: RNAseq.cntNorm.Muscle.csv


title: EBs_RA_Neil2_KO_rep2

description: RA treated EBs derived from Neil2 knockout mESCs clone #11


title: FSH Immortalized rep 1

description:
FSH Immortalized rep 1
FSH Immort A


title: EBs_RA_Apex1_KO_rep2

description: RA treated EBs derived from Apex1 knockout mESCs clone #46 (replicate 2)

value: Apex1 knockout


title: FSH Primaries rep 3

description:
FSH Primaries rep 3
FSH Prim C


title: A33

description: blast percentage >90%


title: FSH Primaries rep 2

description:
FSH Primaries rep 2
FSH Prim B


title: A34

description: blast percentage >90%


title: A32

description: blast percentage >90%


title: FSH Primaries rep 1

description:
FSH Primaries rep 1
FSH Prim A


title: A31

description: blast percentage >90%


title: DYSF Immortalized Clone rep 3

description:
DYSF Immortalized Clone rep 3
DYSF Cloned C

value: Limb Girdle Muscular Dystrophy Type 2B (LGMD2B)


title: A30

description: blast percentage >90%

value: Other BCP


title: A52

description: blast percentage >90%

value: E


title: MBDseq.Muscle.rep.28m

description: MBDseq.cntNorm.Muscle.Tcell.csv

value: 28 month


title: EBs_RA_Apex1_KO_rep1

description: RA treated EBs derived from Apex1 knockout mESCs clone #46 (replicate 1)


title: EBs_RA_Neil2_KO_rep1

description: RA treated EBs derived from Neil2 knockout mESCs clone #1


title: MBDseq.Muscle.rep.20m

description: MBDseq.cntNorm.Muscle.Tcell.csv

value: muscle


title: A29

description: blast percentage >90%


title: EBs_RA_Neil1_KO_rep3

description: RA treated EBs derived from Neil1 knockout mESCs clone #11

value: Neil1 knockout


title: MBDseq.Muscle.rep.02m

description: MBDseq.cntNorm.Muscle.Tcell.csv


title: EBs_RA_Neil1_KO_rep2

description: RA treated EBs derived from Neil1 knockout mESCs clone #9


title: MBDseq.Muscle.28m

description: MBDseq.cntNorm.Muscle.Tcell.csv


title: EBs_RA_Neil1_KO_rep1

description: RA treated EBs derived from Neil1 knockout mESCs clone #7


title: MBDseq.Muscle.20m

description: MBDseq.cntNorm.Muscle.Tcell.csv

value: 20 month


title: MBDseq.Muscle.02m

description: MBDseq.cntNorm.Muscle.Tcell.csv


title: A28

description: blast percentage >90%


title: DYSF Immortalized Clone rep 2

description:
DYSF Immortalized Clone rep 2
DYSF Cloned B

value: Immortalized Clone


title: EBs_RA_Control_rep2

description: RA treated EBs derived from wild-type mESCs clone #4

value: wild-type


title: EBs_RA_Control_rep3

description: RA treated EBs derived from wild-type mESCs clone #7


title: DYSF Immortalized Clone rep 1

description:
DYSF Immortalized Clone rep 1
DYSF Cloned A


title: A26

description: blast percentage >90%


title: EBs_RA_Control_rep1

description: RA treated EBs derived from wild-type mESCs clone #1


title: H9 csRNAinput r1

description: small RNA-seq in H9 cells as a control for csRNA-seq

source_name: H9 cells

value: H9 cells

tag: treatment

value: DMSO

tag: assay

value: small RNA input

tag: genome build

tag: library id

tag: assayed molecule

value: total short RNA (20-65nt)

value: small RNA-seq


title: H9 csRNAinput r2

tag: library strategy


title: A27

description: blast percentage >90%

tag: all subtype

tag: batch


title: A51

description: blast percentage >90%


title: DYSF Immortalized rep 3

description:
DYSF Immortalized rep 3
DYSF Immort C

value: Immortalized


title: A25

description: blast percentage >90%


title: EBs_Apex1_KO_rep1

description: EBs derived from Apex1 knockout mESCs clone #46 (replicate 1)

source_name: embryoid bodies (EBs)

tag: genotype


title: EBs_Apex1_KO_rep2

description: EBs derived from Apex1 knockout mESCs clone #46 (replicate 2)


title: H9 csRNA-seq r2

description: csRNA-seq in H9 cells to identify TSS

value: csRNA-seq

value: capped short RNA (20-65nt)

value: capped short RNA-seq (csRNA-seq)


title: A24

description: blast percentage >90%


title: A23

description: blast percentage >90%


title: DYSF Immortalized rep 2

description:
DYSF Immortalized rep 2
DYSF Immort B

value: Limb Girdle Muscular Dystrophy Type 2B (LGMD2B)


title: DYSF Primaries rep 3

description:
DYSF Primaries rep 3
DYSF Prim C

value: Primary


title: DYSF Primaries rep 2

description:
DYSF Primaries rep 2
DYSF Prim B


title: H9 csRNA-seq r1

description: csRNA-seq in H9 cells to identify TSS


title: EBs_Neil2_KO_rep3

description: EBs derived from Neil2 knockout mESCs clone #14

value: Neil2 knockout


title: A21

description: blast percentage >90%

value: E


title: DYSF Primaries rep 1

description:
DYSF Primaries rep 1
DYSF Prim A


title: DYSF Immortalized rep 1

description:
DYSF Immortalized rep 1
DYSF Immort A


title: EBs_Neil2_KO_rep2

description: EBs derived from Neil2 knockout mESCs clone #11


title: HCT116 csRNAinput r2

description: small RNA-seq in HCT116 cells as a control for csRNA-seq

source_name: HCT116 CMV-osTIR1 RAD21-mAC (no auxin)

value: HCT116 CMV-osTIR1 RAD21-mAC (no auxin)


title: A20

description: blast percentage >90%

value: Other BCP


title: HCT116 csRNAinput r1


title: EBs_Neil2_KO_rep1

description: EBs derived from Neil2 knockout mESCs clone #1


title: EBs_Neil1_KO_rep3

description: EBs derived from Neil1 knockout mESCs clone #11

value: Neil1 knockout


title: HCT116 csRNA-seq r1

description: csRNA-seq in HCT116 cells to identify TSS


title: Healthy C25 Immortalized Clone rep 3

description:
Healthy C25 Immortalized Clone rep 3
CTL Cloned C

value: Immortalized Clone

value: Healthy


title: A18

description: blast percentage >90%


title: Healthy C25 Immortalized Clone rep 1

description:
Healthy C25 Immortalized Clone rep 1
CTL Cloned A


title: Healthy C25 Immortalized Clone rep 2

description:
Healthy C25 Immortalized Clone rep 2
CTL Cloned B


title: EBs_Neil1_KO_rep2

description: EBs derived from Neil1 knockout mESCs clone #9


title: K562 csRNAinput r2

description: small RNA-seq in K562 cells as a control for csRNA-seq

source_name: K562 cells

value: K562 cells


title: A19

description: blast percentage >90%


title: Healthy C25 Immortalized rep 1

description:
Healthy C25 Immortalized rep 1
CTL Immort A


title: EBs_Control_rep3

description: EBs derived from wild-type mESCs clone #7

value: wild-type


title: A16

description: blast percentage >90%


title: Healthy C25 Immortalized rep 3

description:
Healthy C25 Immortalized rep 3
CTL Immort C


title: K562 csRNAinput r1

value: small RNA input

value: total short RNA (20-65nt)


title: A17

description: blast percentage >90%


title: Healthy C25 Primaries rep 2

description:
Healthy C25 Primaries rep 2
CTL Prim B


title: Healthy C25 Primaries rep 3

description:
Healthy C25 Primaries rep 3
CTL Prim C


title: Healthy C25 Immortalized rep 2

description:
Healthy C25 Immortalized rep 2
CTL Immort B

value: Immortalized


title: A14

description: blast percentage >90%


title: A15

description: blast percentage >90%


title: EBs_Control_rep2

description: EBs derived from wild-type mESCs clone #4


title: EBs_Neil1_KO_rep1

description: EBs derived from Neil1 knockout mESCs clone #7


title: EBs_Control_rep1

description: EBs derived from wild-type mESCs clone #1


title: K562 csRNA-seq r2

description: csRNA-seq in K562 cells to identify TSS

value: csRNA-seq


title: K562 csRNA-seq r1

description: csRNA-seq in K562 cells to identify TSS

value: capped short RNA (20-65nt)


title: A22

description: blast percentage >90%


title: S80A 3hr n1

city: Glasgow

first: Emma

last: Smith

address: 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

data_processing:
Read quality was checked for each sample using FastQC
Reads were aligned to human reference sequence iGenome NCBI GRCh38 using HISAT
Aligned reads were assembled into transcripts using Stringtie
Aligned reads were counted using htseq-count
Differential gene expression was determined using DESeq2
Genome_build: iGenome NCBI GRCh38
Supplementary_files_format_and_content: Reads counts generated using htseq-count; DESeq2 differential gene expression testing

source_name: HEK293T_S80A 3hr

growth_protocol: Human embryonic kidney 293T (HEK293T) cells were cultured in high glucose Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2mM L-glutamine, and 100 units/ml of streptomycin and penicillin. Cells were sub-cultured by enzymatic detachment with 0.05% Trypsin-EDTA solution. Cells were maintained at 37ºC in a humidified environment with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using RNeasy kits (Qiagen), according to the manufacturer’s instructions.
1 μg of total RNA was used for library construction. For PolyA selection, the TruSeq stranded mRNA sample prep kit was used. Illumina NextSeq™500 platform was used to sequence single-end 75bp reads to a depth of 20 million.

treatment_protocol: HEK293T cells were either left untreated or were treated with 10ng/ml TNFα for 3 hours prior to RNA extraction.

tag: cell line background

tag: genotype/variation

value: 10ng/ml TNFα for 3 hours


title: S80A 3hr n2

tag: cell type

value: Human embryonic kidney 293T (HEK293T) cells


title: A13

description: blast percentage >90%


title: S80A 0hr n3

source_name: HEK293T_S80A 0hr

value: none (untreated control)


title: S80A 0hr n2


title: mESCs_Apex1_KO_rep2

description: Apex1 knockout mESCs clone #46 (replicate 2)

source_name: undifferentiated mESCs

value: Apex1 knockout


title: S80A 0hr n1


title: HCT116 csRNA-seq r2

tag: tissue

value: DMSO

value: capped short RNA-seq (csRNA-seq)


title: WT 3hr n3

source_name: HEK293T_WT 3hr

value: wild type


title: A12

description: blast percentage >90%

source_name: leukemic blast

value: Other BCP

value: E


title: mESCs_Neil1_KO_rep3

description: Neil1 knockout mESCs clone #11

value: Neil1 knockout


title: mESCs_Neil1_KO_rep1

description: Neil1 knockout mESCs clone #7


title: mESCs_Neil2_KO_rep1

description: Neil2 knockout mESCs clone #1

value: Neil2 knockout


title: mESCs_Neil2_KO_rep3

description: Neil2 knockout mESCs clone #14


title: mESCs_Neil2_KO_rep2

description: Neil2 knockout mESCs clone #11


title: mESCs_Neil1_KO_rep2

description: Neil1 knockout mESCs clone #9


title: mESCs_Apex1_KO_rep1

description: Apex1 knockout mESCs clone #46 (replicate 1)


title: mESCs_Control_rep3

description: wild-type mESCs clone #7

value: wild-type


title: mESCs_Control_rep2

description: wild-type mESCs clone #4


title: A11

description: blast percentage >90%


title: WT 3hr n1


title: WT 0hr n3

source_name: HEK293T_WT 0hr


title: WT 3hr n2


title: 6h WT R2: 6 hour wildtype C57BL/6J Replicate 2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: uterus

growth_protocol: C57BL6/J females were maintained under standard light-dark conditions and fed 16% Protein Rodent Diet (Teklad Global 2016)

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions from 3 individual mice per replicate per time point.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate RNA-seq libraries. The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina Nextseq.
75bp single end polyA-RNA-seq

treatment_protocol: Adult females (6-8 weeks old) were ovariectomized to deplete endogenous hormones. Following 2 weeks of rest, females received sub cutaneous injection of 250 ng 17beta estradiol in corn oil for 0.5, 1,2, or 6 hours. Vehicle control animals received an injection of ethanol (vehicle) in corn oil for 0.5 hour. Whole uterine horns where collected under avertin anesthesia and flash frozen until further processing.

tag: strain

value: uterus

value: 250 ng 17beta-estradiol 6 hour


title: WT 0hr n2


title: 6h WT R1: 6 hour wildtype C57BL/6J Replicate 1


title: A7

description: blast percentage >90%


title: A10

description: blast percentage >90%


title: Teratoma_Neil_TKO_rep3

description: pool of 3 technical replicates of teratomas derived from Neil TKO mESC clone #93

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina's bcl2fastq Conversion Software v.1.8.4.
RNA-seq reads were quality assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The raw reads were aligned to the mouse mm9 genome with TopHat v.2.0.9 (https://ccb.jhu.edu/software/tophat) and Bowtie v.2.1.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with a GTF transcript annotation file from Ensemble release 67.
The mapped reads were summarized on gene level using the tool htseq-count from package HTSeq v.0.5.4 (http://www-huber.embl.de/HTSeq).
Differential expression analysis was performed using the Bioconductor package DESeq2 v.1.6.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: tab-delimited text file with summarised read counts per gene from htseq-count

source_name: teratoma

growth_protocol: Mouse E14TG2a (ATCC number CRL-1821) embryonic stem cells (mESCs) were cultured on plates coated with 0.1% Gelatin (Millipore) in DMEM supplemented with 15% PANSera ES FBS (PAN Biotech), 2 mM L-Glutamine, 100 µM non-essential amino acids (NEAA, Gibco), 1 mM sodium pyruvate (Gibco), 100 µM 2-mercaptoethanol (Sigma), 1000 U/ml Leukemia inhibitory factor (LIF, Millipore), 100 U/ml PEN-STREP at 37 °C in 5% CO2 and 20% O2. mESCs cells were seeded and transfected the next day with either empty or gRNA encoding pX330-U6-Chimeric_BB-CBh-hSpCas9 (Addgene #42230) mixed with the selection plasmid pPGKPuro (Addgene #11349) using Lipofectamine 2000 (Thermo Fisher) according to manufacturer’s instruction. Cells were selected with 2 µg/ml puromycin for 6 days, colonies picked, passaged and subjected to genotyping PCR. Three independent clones per genotype were expanded for further analyses.

extract_protocol:
Teratoma samples were homogenized with an Ultra-TURRAX disperser (IKA) in presence of 2 ml TRIzol reagent (Invitrogen) using approximately 200 mg tissue per tumor. After clearance of supernatant by centrifugation for 5 min at 12.000 x g at 4°C, 0.4 ml of chloroform was added and the solution centrifuged for 15 min at 12.000 x g at 4°C. RNA from aqueous phase was precipitated with 1 ml isopropanol, washed with 75 % ethanol, air dried and resuspended in RNase-free water. Contaminating DNA was digested with DNase I followed by an RNA cleanup (RNeasy kit, Qiagen) according to manufacturer’s instructions. RNA was quantified with a Thermo NanoDrop and quality tested on Agilent Bioanalyzer.
NGS libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s recommendations and amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA chip on a 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies). The NGS libraries were sequenced on a HiSeq 2000 Illumina sequencer, for 51 cycles plus seven cycles for the index read.

treatment_protocol: mESCs were mixed with Matrigel (Corning) and subcutaneously injected into the left flank of immunodeficient (NSG) mice essentially as described (Wesselschmidt, 2011; doi: 10.1007/978-1-61779-201-4_17). Teratomas of approximately 1 cm3 size were harvested and snap frozen for further analysis.

value: Neil1,2,3 triple knockout (Neil TKO)


title: mESCs_Control_rep1

description: wild-type mESCs clone #1


title: WT 0hr n1


title: 2h WT R3: 2 hour wildtype C57BL/6J Replicate 3

value: 250 ng 17beta-estradiol 2 hour


title: S80A 3hr n3


title: A2

description: blast percentage >90%


title: A5

description: blast percentage >90%


title: Vehicle Control 062619AFE01

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

description: Vehicle Control

hyb_protocol: Standard Affymatrix hybridization protocol

scan_protocol: Standard Affymatrix scan protocol

data_processing: RMA Express normalization and background

source_name: J774 macrophage control

label_protocol: Standard Affymatrix label protocol

growth_protocol: Macrophages, murine cell line J774, were maintained in 100-mm Petri dishes in DMEM free of phenol red, supplemented with 10% FBS, 2mM L-glutamine, penicillin (100 U/mL), streptomycin (100 µg/mL) and 10 mM HEPES.

extract_protocol: RNA extraction was conducted through a RNeasy Mini Kit (Qiagen).

treatment_protocol: Macrophages were plated in 24 well-plate and exposed to 10 µg/well of particles and 2 µg/mL of estrogen for 24 hrs.


title: Teratoma_Neil_TKO_rep2

description: pool of 3 technical replicates of teratomas derived from Neil TKO mESC clone #85


title: A3

description: blast percentage >90%


title: 2h WT R2: 2 hour wildtype C57BL/6J Replicate 2


title: A4

description: blast percentage >90%


title: A8

description: blast percentage >90%


title: A6

description: blast percentage >90%


title: Talc and estrogen 062619AFE11

description: Talc and estrogen

source_name: J774 macrophage exposed to talc and estrogen


title: Healthy C25 Primaries rep 1

description:
Healthy C25 Primaries rep 1
CTL Prim A

source_name: Cultured cells

tag: clonal state

value: Primary

tag: pathology state

value: Healthy


title: Teratoma_Neil_TKO_rep1

description: pool of 3 technical replicates of teratomas derived from Neil TKO mESC clone #23

tag: cell line


title: 2h WT R1: 2 hour wildtype C57BL/6J Replicate 1

tag: treatment


title: Estrogen 062619AFE04

description: Estrogen

source_name: J774 macrophage exposed to estrogen


title: A9

description: blast percentage >90%


title: A1

description: blast percentage >90%


title: Talc 062619AFE07

description: Talc

source_name: J774 macrophage exposed to talc


title: Vehicle Control 062619AFE02

description: Vehicle Control


title: Vehicle Control 062619AFE03

description: Vehicle Control


title: Talc and estrogen 062619AFE12

description: Talc and estrogen


title: ∆SMR1_T42h_male_replicate 4 (RID-SMR1)

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description: Biological replicate 4 of 4 of timepoint T42h of sexual reproduction time course with ∆SMR1_T42h Mat- as female

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: To facilitate biological materials collecting, S strains from mating type mat+ (female strain) were grown on cheesecloth (Sefar Nitex 03-48/31 Heiden) previously placed on Petri-dishes containing M2 medium. S mat- strain (Wild type or ∆SMR1) has been used as male gamete donor and S mat+ ((Wild type or ∆RID) as female. the S mat- male gamete donor strains were grown on M2 Petri-dishes.  For each points of the time course materials, number of Petri-dishes has been adjusted (5 were used for T12h, T24h, 4 for T30h, 2 for T42) to collect 20 to 100 mg of biological. All the time points were grown on cheesecloth. One to five Petri-dishes per time course experiment were thus inoculated simultaneously with a growing the male gamete donor strain and spermatia were collected by washing with 1.5 ml of H2O 6 days later. The collected spermatia (around 104 spermatia per ml) were pooled and then used to fertilize corresponding number of Petri-dishes of the S mat+ strain which was growing since 4 days. Time just prior the fertilization process was considered as the T0 (0h). The biological material was then collected 12h, 18h, 30h, 42h (for the mutant strains) after fertilization. The RNA pool used as a reference was assembled by combining equal amount of RNA issued from various growth and crosses conditions and has already been described (Bidard et al., BMC research notes, 2010).

extract_protocol: Strains were grown on cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: female strain

value: Wild type S mat+

tag: growth condition

value: harvested after 138h at 28°C and 42 hours after fertilization with microconidia of a S strain ∆SMR1 mat+, M2 media covered with a cheesecloth

tag: male strain

value: S ∆SMR1 mat-

source_name: Common reference

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name of biosource 4


title: Teratoma_Control_rep3

description: pool of 3 technical replicates of teratomas derived from Control mESC clone #7

tag: genotype


title: 1h WT R2: 1 hour wildtype C57BL/6J Replicate 2

tag: strain

tag: tissue

value: 250 ng 17beta-estradiol 1 hour


title: Talc 062619AFE09

description: Talc


title: 1h WT R1: 1 hour wildtype C57BL/6J Replicate 1


title: 0.5h WT R2: 0.5 hour wildtype C57BL/6J Replicate 2

value: 250 ng 17beta-estradiol 0.5 hour


title: Teratoma_Control_rep1

description: pool of 3 technical replicates of teratomas derived from Control mESC clone #1


title: Estrogen 062619AFE06

description: Estrogen


title: miRNA_WT_L_2

city: Aurora

first: Xiying

last: Fan

state: CO

department: Dermatology

institute: University of Colorado Anschutz Medical Campus

description:
microRNA
processed data file: blast_results_reads.xlsx

data_processing:
Libraries are sequenced by Illumina HiSeq 2000. Sequencing reads are mapped to customized miRNAs database with BLAST.
genome build: mapped to customized miRNAs database with BLAST.
processed data files format and content: column names are sample names, and sample names are miRNA name.

source_name: prostate luminal cells

extract_protocol:
mouse prostate is dissected and treated with Collagenase and Trypsin to get single cells. Luminal cells are purified through FACS by antibody staining and gating of Sca-1(+), lin(-) and CD49f(low) cells.
Followed the methods described in Zhang et al. Genome Biology 2013, 14:R112

value: prostate

tag: cell type

value: luminal cells

tag: age

value: 10 weeks

value: WT

tag: background strain

tag: gender

value: male


title: 0.5h WT R1: 0.5 hour wildtype C57BL/6J Replicate 1

value: uterus

tag: treatment


title: Talc 062619AFE08

description: Talc

tag: cell line


title: 0h WT R3: 0 hour wildtype C57BL/6J Replicate 3

value: ethanol vehicle


title: ∆SMR1_T42h_male_replicate 3 (RID-SMR1)

description: Biological replicate 3 of 4 of timepoint T42h of sexual reproduction time course with ∆SMR1_T42h Mat- as female

tag: female strain

tag: growth condition

tag: male strain

tag: biosource 1


title: miRNA_WT_B_2

source_name: prostate basal cells

extract_protocol:
mouse prostate is dissected and treated with Collagenase and Trypsin to get single cells. Basal cells are purified through FACS by antibody staining and gating of Sca-1(+), lin(-) and CD49f(high) cells.
Followed the methods described in Zhang et al. Genome Biology 2013, 14:R110

value: basal cells


title: 0h WT R2: 0 hour wildtype C57BL/6J Replicate 2


title: Teratoma_Control_rep2

description: pool of 3 technical replicates of teratomas derived from Control mESC clone #4

value: wild-type


title: Talc and estrogen 062619AFE10

description: Talc and estrogen


title: Estrogen 062619AFE05

description: Estrogen


title: Titanium dioxide 062619AFE13

description: Titanium dioxide

source_name: J774 macrophage exposed to titanium dioxide


title: ∆SMR1_T42h_male_replicate 1 (RID-SMR1)

description: Biological replicate 1 of 4 of timepoint T42h of sexual reproduction time course with ∆SMR1_T42h Mat- as female

value: Wild type S mat+

value: harvested after 138h at 28°C and 42 hours after fertilization with microconidia of a S strain ∆SMR1 mat+, M2 media covered with a cheesecloth

tag: name of biosource 1

tag: biosource 2

tag: name of biosource 2

tag: biosource 3


title: miRNA_WT_B_1

extract_protocol:
mouse prostate is dissected and treated with Collagenase and Trypsin to get single cells. Basal cells are purified through FACS by antibody staining and gating of Sca-1(+), lin(-) and CD49f(high) cells.
Followed the methods described in Zhang et al. Genome Biology 2013, 14:R109

tag: genotype


title: Intestinal tumor tissues of  mice gavage with feces from CRC patients, biological rep1  [FMT_AC6]

city: Tianjin

first: Lu

last: Li

address: 154 Anshan Road in Heping District

department: Department of Gastroenterology and Hepatology

institute: General Hospital, Tianjin Medical University

data_processing:
Read quality was checked for each sample using NGS QC Toolkit v2.3.3.
High-quality reads were then imported into TopHat v2.0.13 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline, RSEM (version v1.2.22) to count transcript abundance.
Genome_build: Genome_build: Alignment was initially to the transcriptome (GRCm38), and then to the genome (GRCm38).
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM for each sample.

growth_protocol: The Apcmin/+ mice gavage with feces from healthy controls or CRC patients after antibiotic cocktails. The intestinal tissues were isolated for RNA-seq.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The qualified libraries were sequenced on a HiSeq X-Ten (Illumina).

treatment_protocol: The intestine was isolated and rinsed with ice-cold sterile PBS solution. The proximal tissue of each intestinal  was snap frozen in liquid nitrogen and kept at −80 °C later.

tag: strain

value: Apcmin/+ mice

value: Intestinal tumor tissues

tag: sample group

value: FMT-AC group (gavage of fecal samples from patients with CRC)


title: Intestinal tumor tissues of  mice gavage with feces from CRC patients, biological rep3  [FMT_AC9]

tag: tissue


title: Intestinal tumor tissues of  mice gavage with feces from CRC patients, biological rep2  [FMT_AC8]


title: ∆SMR1_T42h_male_replicate 2 (RID-SMR1)

description: Biological replicate 2 of 4 of timepoint T42h of sexual reproduction time course with ∆SMR1_T42h Mat- as female

value: S ∆SMR1 mat-

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name of biosource 4


title: Intestinal tumor tissues of mice gavage with feces from healthy controls, biological rep4 [FMT_AH9]

value: FMT-AH group (gavage of fecal samples from healthy controls)


title: 0h WT R1: 0 hour wildtype C57BL/6J Replicate 1

tag: treatment


title: Intestinal tumor tissues of mice gavage with feces from healthy controls, biological rep3 [FMT_AH8]


title: ∆RID_T42h_female_replicate 2 (RID-SMR1)

description: Biological replicate 2 of 4 of timepoint T42h of sexual reproduction time course with ∆RID_T42h Mat- as female

value: S ∆RID mat+

value: harvested after 138h at 28°C and 42 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

value: Wild type S mat-


title: ∆RID_T42h_female_replicate 1 (RID-SMR1)

description: Biological replicate 1 of 4 of timepoint T42h of sexual reproduction time course with ∆RID_T42h Mat- as female


title: ∆RID_T42h_female_replicate 3 (RID-SMR1)

description: Biological replicate 3 of 4 of timepoint T42h of sexual reproduction time course with ∆RID_T42h Mat- as female


title: ∆RID_T42h_female_replicate 4 (RID-SMR1)

description: Biological replicate 4 of 4 of timepoint T42h of sexual reproduction time course with ∆RID_T42h Mat- as female


title: AbetaLPS_treatment_3

city: Schlieren

first: Anna

last: Mallone

address: Wagistrasse 12

department: Institute for Regenerative Medicine

description: Sample 12

data_processing:
RNA quality control: The quality of RNA sequencing data was assessed using fastqc (v. 0.11.5) and RSeQC (v. 2.6.4 2).
Reads mapping: The reads were mapped to the reference genome using HiSat2 (v. 2.1.0).
Reads count: FeatureCounts (v. 1.6.0) was used to count the number of reads overlapping with each gene as specified in the genome annotation (Mus_musculus.GRCm38.91).
Differential gene expression between groups: the Bioconductor package DESeq2 was used to test for differential gene expression between the experimental groups. The log-fold change of each gene was adjusted to include the evidence based on which the log-fold change was estimated and to extrapolate the adjusted p-value (adjp). A false discovery rate correction was applied using DESeq2, based on the Benjamini-Hochberg procedure.
GO enrichment analysis: the gene ontology enrichment analysis was performed with TopGo and GOSeq. These tools were used to identify gene ontology terms and KEGG pathways containing unusual differentially expressed genes. Genes were ranked within a GO term using a two-fold approach including (1) the Fisher’s exact test, comparing the proportion of differentially expressed genes among all genes assigned to the GO term with all other genes, and (2) the Kolmogorov-Smirnov test, which orders all genes by p-value and tests if the genes assigned to a particular GO term are enriched at the top or the bottom of this table.
All analyses were run in R (version 3.4.4, 2018-03-15)
Genome_build: Mus_musculus.GRCm38.91
Supplementary_files_format_and_content: xlsx files describing the comparative quatitation of the different treatments. The files include the normalized abundance measurements  for each treatment (triplicate), the log2 of the Fold change, the p-value of the comparison and the adjusted p-value.

source_name: Bone marrow

growth_protocol: Bone marrow-derived progenitor cells were isolated from femurs, tibiae and hip bones of non-transgenic C57BL/6 mice according to established protocols (Dubrot, Duraes et al. 2014). After 9 days of incubation at 37°C and 5% CO2 progenitor cells completely differentiated into immature bone marrow-derived dendritic cells (BM-DCs).

extract_protocol:
Total RNA was extracted using the GenElute Mammalian TotalRNA Kit (Sigma). The RNA concentration was measured using RNA HS Assay kit (Thermo Fisher Scientific) and RNA integrity was analyzed with the Qubit RNA IQ Assay (Thermo Fisher Scientific).
The library of mRNA sense transcripts was prepared using the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Maturation of BM-DCs was achieved by an 18 h LPS-treatment at 100 ng/ml followed by an up-regulation of antigen-presentation markers such as MHC class II. During antigen presentation assays BM-DCs were treated with oligomeric Aβ1-42 (0.5 µM) on day 8 of the cultivation process prior maturation.

value: wild type

tag: age

value: post-natal week 12

tag: cell type

value: Dendritic cells

tag: cell treatment

value: Abeta1-42 oligomer treatment (4d) + LPS treatment (18h)


title: Titanium dioxide 062619AFE14

description: Titanium dioxide

tag: cell line


title: Intestinal tumor tissues of mice gavage with feces from healthy controls, biological rep2 [FMT_AH5]


title: Titanium dioxide  062619AFE15

description: Titanium dioxide


title: AbetaLPS_treatment_2

description: Sample 11


title: ChIPseq_SMC3_Rep2

city: Riverside

first: Xueqing

middle: Maggie

last: Lu

state: CA

address: 3401 Watkins Drive, Genomics, Room 2126

department: Cell Biology

institute: University of California, Riverside

data_processing:
Raw read quality was first analyzed using FastQC, and the last base was removed using Trimmomatic. Any base with a quality score below 25 was trimmed using Sickle.  Trimmed reads were then mapped to P. falciparum genome (v38) using Bowtie2 (v2.3.4.1) . Uniquely mapped reads were further filtered, and read coverage per nucleotide was determined using BEDTools. Both libraries were  normalized by numbers of million mapped reads. For each nucleotide, the signal from the negative control library was then subtracted from the SMC3 ChIP-seq library, and any negative values were replaced by zeros. Genome browser tracks were generated and viewed using the Integrative Genomic Viewer (IGV) by Broad institute.
Genome_build: P. falciparum 3D7 genome (v38)
Supplementary_files_format_and_content: tdf file generated by Integrative Genomic Viewer (IGV) by Broad institute.

organism: Plasmodium falciparum

source_name: Erythrocytic cycle

growth_protocol: P. falciparum strain 3D7 was maintained in human O+ erythrocytes in 5% haematocrit according to a previously described protocol (Trager et al., Science 1976).

extract_protocol:
Synchronized parasite cultures were collected and subsequently lysed by incubating in 0.15% saponin for 10 min on ice. Parasites were centrifuged at 3,234 x g for 10 min at 4°C, and washed three times with PBS. For each wash, parasites were resuspended in cold PBS and centrifuged for 10 min at 3,234 x g at 4°C. Subsequently, parasites were crosslinked for 10 min with 1% formaldehyde in PBS at 37°C.  Glycine was added to a final concentration of 0.125 M to quench the crosslinking reaction, and incubated for 5 min at 37°C. Parasites were centrifuged for 5 min at 2,500 x g at 4°C, washed twice with cold PBS and stored at -80°C. For chromatin immunoprecipitation, parasites were first incubated on ice in nuclear extraction buffer (10 mM HEPES, 10 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, 1 mM DTT, 0.5 mM 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), EDTA-free protease inhibitor cocktail (Roche) and phosphatase inhibitor cocktail (Roche)). After 30 min, Igepal CA-360 (Sigma-Aldrich) was added to a final concentration of 0.25% and the parasites were lysed by passing the suspension through a 26 G ½ inch needle seven times. Parasite nuclei were centrifuged at 4°C for 20 min at 2,500 x g.  Parasite nuclei were resuspended in shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris HCl pH 7.5, EDTA-free protease inhibitor cocktail, and phosphatase inhibitor cocktail). Chromatin was fragmented using the Covaris Ultra Sonicator (S220) for 10 min with the following settings; 5% duty cycle, 140 intensity peak incident power, 200 cycles per burst). To remove insoluble material, samples were centrifuged for 10 min at 17,000 x g at 4°C. Fragmented chromatin was diluted 1:1 in ChIP dilution buffer (30 mM Tris-HCl pH 8, 3 mM EDTA, 0.1% SDS, 300 mM NaCl, 1.8% Triton X-100, EDTA-free protease inhibitor cocktail and phosphatase inhibitor cocktail). Samples were precleared with Protein A Agarose beads to reduce non-specific background and incubated overnight at 4°C with 2 μg of custom anti-SMC3 antibody (Thermo Fisher Scientific). A sample with no antibody was also incubated overnight at 4°C to be used as the negative control. Antibody-protein complexes were recovered using Protein A Agarose beads, followed by extensive washes with low salt immune complex wash buffer, high salt immune complex was buffer, LiCl immune complex wash buffer and TE buffer. Chromatin was eluted from the beads by incubating twice with freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) for 15 min at RT. Samples were reverse crosslinked overnight at 45°C by adding NaCl to a final concentration of 0.5 M. RNase A (Life Technologies) was added to the samples and incubated for 30 min at 37°C followed by a 2 h incubation at 45°C with the addition of EDTA (final concentration 8 mM), Tris-HCl pH 7 (final concentration 33 mM) and proteinase K (final concentration 66 μg/mL; New England Biolabs). DNA was extracted by phenol:chloroform:isoamylalcohol and ethanol precipitation. Extracted DNA was purified using 1.8X Agencourt AMPure XP Beads (Beckman Coulter).
Libraries from the ChIP samples were prepared using the KAPA Library Preparation Kit (KAPA Biosystems).  Libraries were amplified for a total of 12 PCR cycles (12 cycles of [15 s at 98°C, 30 s at 55°C, 30 s at 62°C]) using the KAPA HiFi HotStart Ready Mix (KAPA Biosystems).  Libraries were sequenced with a NextSeq500 DNA sequencer (Illumina)

tag: Stage

value: Trophozoite

tag: chip antibody

value: Custom generated anti-SMC3 antibody (Thermo Fisher Scientific)


title: ChIPseq_SMC3_control

value: No antibody


title: ChIPseq_SMC3_Rep1


title: Rice csRNAinput r2

description: small RNA-seq in rice leaves as a control for csRNA-seq

data_processing:
Adapter sequences were first removed from the 3' end of reads for csRNA-seq and small RNA-seq libraries (AGATCGGAAGAGCACACGTCT). Reads were then aligned to the appropriate genome using HISAT2 (v2.1.0) with default settings. Normalized, single nucleotide resolution bigWig files and TSS cluster calls were generated using HOMER's makeUCSCfile and findcsRNATSS.pl tools, respectively (v4.11). findcsRNATSS.pl uses small RNA sequencing and total RNA-seq data as controls to remove non-TSS artifacts in the csRNA-seq data when identifying TSS clusters. http://homer.ucsd.edu/homer/ngs/csRNAseq/
Genome_build: hg38, mm10, ASM20922v1, NC12, IRGSP-1.0, C_owczarzaki_V2
Supplementary_files_format_and_content: BigWig files (.bigWig/.bw) were generated by constructing normalized, single-nucleotide resolution bedGraph files based on 5' read positions using HOMER and converted to bigWigs using UCSC's bedGraphToBigWig utility. TSS text files contain TSS cluster positions defined using HOMER's findcsRNATSS.pl command (tab-delimited text files).

organism: Oryza sativa

source_name: rice leaves

extract_protocol:
K562 cells were grown in RPMI1640+L‐Glutamine with heat inactivated 10% FBS (Biowest Cat No.S1620, Lot 61N16) and 1x Pen/Strep (Gibco15140-163) and 1x L-Glutamine (Gibco25030164) in T75 flasks at 37°C with 5% CO2. HCT116 CMV-osTIR1 RAD21-mAC cells were obtained from Masato T. Kanemaki (Natsume et al., 2016) and cultured in McCoy’s 5A medium supplemented with 10% FBS. Cells were washed twice in 1x cold PBS (Gibco 10010023) and RNA isolated using Trizol LS. Human H9 cell RNA was provided by Yuanyuan Li and Mark H. Tuszynski (UC San Diego). H9 cells were grown as described in (Lu et al. 2017) and RNA isolated using the Qiagen RNA kit. Murine BMDMs were isolated, cultured and RNA extracted as described (Link et al. 2018). Nematostella vectensis (planula stage) was kindly provided by Drs. James Gahan and Fabian Rentzsch (University of Bergen). Neurospora crassa was provided by Dr. Jason Stajich (University of California, Riverside) and grown in Vogels media under constant light and gentle agitation (Wang et al. 2015). Rice was grown in the SALK greenhouse with 12 h light and leaves from adult plants provided by Dr. Joanne Chory (Salk Institute for Biological Studies). All non-mammalian samples were flash frozen in liquid N2, pulverized with a mortar and pestle and RNA extracted using Trizol LS as described by the manufacturer. Capsaspora owczarzaki RNA (Sebé-Pedrós et al. 2016) was gifted by Dr. Iñaki Ruiz-Trillo (Institut de Biologia Evolutiva; CSIC-Universitat Pompeu Fabra).
Small RNAs of ~20-60 nt were size selected form 2-15 µg of total RNA by denaturing gel electrophoresis.  A 10% input sample was taken aside and the remainder enriched for 5’Caped RNAs with 3’-OH. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequent 5’dephosporylation by CIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’adapter ligation by T4 RNA ligase 1 (NEB). The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) without prior 3’ repair to select against degraded RNA fragments.  Following cDNA synthesis, libraries were amplified for 12-14 cycles and sequenced SE75 on the Illumina NextSeq500. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) and sequenced PE100 on Illumina HiSeq 2500. A comprehensive description of the csRNA-seq method and analysis software can be found in the supplement as well as under http://homer.ucsd.edu/homer/ngs/csRNAseq/.

value: rice leaves

tag: assay

value: small RNA input

tag: genome build

tag: library id

tag: assayed molecule

value: total short RNA (20-65nt)

tag: library strategy

value: small RNA-seq


title: Rice csRNAinput r1


title: Abeta_treatment_rep3

description: Sample 9

tag: strain

tag: genotype

value: Abeta1-42 oligomer treatment (4d)


title: 70S_RPF_ΔksgA

city: Guwahati

first: B

last: Anand

state: Assam

address: North guwahati

department: Biosciences and Bioengineering

country: India

institute: Indian institute of technology guwahati

data_processing:
Reads were filtered by removing reads with Phred score <20 using fastq_quality_trimmer
Trimming of 3’-end adapter sequences [5’-TGGAATTCTCGGGTGCCAAGGAACTC-3’] using Cutadapt-1.5
Alignment with E. coli reference genome NC_000913.3 using STAR 2.5.3 to remove reads mapping to genes for rRNA, tRNA, sRNA and other non-coding RNAs
Filtered reads aligned to E. coli reference genome using  STAR 2.5.3 with  spliced alignment turned off (--alignIntronMax 1), forced end to end alignment (--alignEndsType EndToEnd) and allowing 8 mismatches per 100 nt (--outFilterMismatchNoverLmax 0.08)
Sam to Bam conversion was accomplished using Samtools-1.4.1. Metagene analysis for mapping the reads to START and STOP codons was performed by employing custom written shell scripts utilizing Samtools-1.4.1.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: .txt files with  read counts in tabular format with geneIDs and counts per sample.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Wt or mutants were grown at 25 °C in 2 litres of LB medium. The culture was allowed to grow till OD600 reached 0.3.

extract_protocol:
Ribosomes bound to mRNA were relieved using MNase.The treated sample was again sepeated into 30S and 70S fractions using ultracentrifugation on a 10-40% sucrose gradient. The 30S and 70S fractions were decrosslinked and ribosome protected fragments were size selcted for 10-80 nucleotide on a denaturing Urea PAGE.
Libraries were prepared strictly according to the manufacturers recommendations using the TruSeq Small RNA Sample Preparation kit (Illumina, U.S.A)

treatment_protocol: Cells were snap chilled using ice and crosslinked with formaldehyde. Glycine was added to arrest the crosslinking after which the cells were pelleted and lysed by freeze thaw method followed by clarification of the lysate. Lysate was loaded on a 10-20 % sucrose gradient and the ribosome pellets were resuspeded in fresh lysis buffer

tag: strain background

tag: genotype/variation

value: ksgA mutant

tag: molecule subtype

value: 70S subunit ribosome protected fragment


title: Titanium dioxide and estrogen 062619AFE17

description: Titanium dioxide and estrogen

source_name: J774 macrophages exposed to titanium dioxide and estrogen


title: miRNA_WT_L_1

extract_protocol:
mouse prostate is dissected and treated with Collagenase and Trypsin to get single cells. Luminal cells are purified through FACS by antibody staining and gating of Sca-1(+), lin(-) and CD49f(low) cells.
Followed the methods described in Zhang et al. Genome Biology 2013, 14:R111

tag: tissue

value: prostate

value: luminal cells

value: 10 weeks

value: WT

tag: background strain

tag: gender

value: male


title: 70S_RPF_ΔrbfA

value: rbfA mutant


title: Rice csRNA-seq r3

city: La Jolla

first: Christopher

last: Benner

description: csRNA-seq in rice leaves to identify TSS

tag: treatment

value: csRNA-seq

value: capped short RNA (20-65nt)

value: capped short RNA-seq (csRNA-seq)


title: Rice csRNA-seq r2


title: Rice csRNA-seq r1


title: AbetaLPS_treatment_1

institute: University of Zurich

description: Sample 10

value: wild type

tag: age

value: post-natal week 12

tag: cell type

value: Dendritic cells

tag: cell treatment

value: Abeta1-42 oligomer treatment (4d) + LPS treatment (18h)


title: 30S_RPF_ΔksgA

value: 30S subunit ribosome protected fragment


title: Titanium dioxide and estrogen 062619AFE16

description: Titanium dioxide and estrogen

tag: cell line


title: Wild Type T30h_replicate C (RID-SMR1)

description: Biological replicate 2 of 3 of timepoint T30h of sexual reproduction time course

tag: female strain

value: Wild type S mat+

tag: growth condition

value: harvested after 126h at 28°C and 30 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

tag: male strain

value: Wild type S mat-

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 2

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: name of biosource 3

tag: biosource 4

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.

tag: name of biosource 4


title: 70S_RPF_Wt

tag: strain background

tag: genotype/variation

tag: molecule subtype

value: 70S subunit ribosome protected fragment


title: 30S RPF_ΔrbfA

value: rbfA mutant


title: LPS_treatment_rep2

description: Sample 5

tag: strain

tag: genotype

tag: age

tag: cell type

value: LPS treatment (18h)


title: LPS_treatment_rep1

description: Sample 4

tag: cell treatment


title: Abeta_treatment_rep2

description: Sample 8

value: Abeta1-42 oligomer treatment (4d)


title: CTX-RNA-setd5-8 cortex

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
FASTQ reads were quality checked and adaptor trimmed with FastQC (Andrews, S.. FastQC A Quality Control tool for High Throughput Sequence Data).
High quality trimmed reads were mapped to the mm10/GRCm38.p6 reference genome with Bowtie2 v2.3.4.3 (Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359).
Gene counts were calculated with featureCount using latest GENCODE main annotation file (Liao, Y., Smyth, G. K., & Shi, W. (2014). FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930).
Differential gene expression was calculated with DESeq2 (Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550).
Genome_build: mm10/GRCm38.p6

source_name: Cerebral cortex

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: tissue

value: Cerebral cortex

value: wildtype


title: Abeta_treatment_rep1

description: Sample 7

value: wild type

value: post-natal week 12


title: 2CTRL cortex


title: 3CTRL cortex


title: Intestinal tumor tissues of mice gavage with feces from healthy controls, biological rep1 [FMT_AH4]

value: Apcmin/+ mice

value: Intestinal tumor tissues

tag: sample group

value: FMT-AH group (gavage of fecal samples from healthy controls)


title: Wild Type T24h_replicate A (RID-SMR1)

description: Biological replicate 1 of 3 of timepoint T24h of sexual reproduction time course

tag: female strain

value: Wild type S mat+

tag: growth condition

value: harvested after 120h at 28°C and 24 hours after fertilization with microconidia of a wild strain S mat-, M2 media covered with a cheesecloth

tag: male strain

tag: biosource 1

tag: name of biosource 1


title: Neurospora csRNAinput r1

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description: small RNA-seq in Neurospora as a control for csRNA-seq

organism: Neurospora crassa

source_name: whole organism (mixed stages)

value: whole organism (mixed stages)

tag: treatment

tag: assay

value: small RNA input

tag: genome build

tag: library id

tag: assayed molecule

value: total short RNA (20-65nt)

tag: library strategy

value: small RNA-seq